From 06857d54025dfb710258c7e2175c1cf13c66804b Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 8 Jan 2026 16:26:58 -0500
Subject: [PATCH 001/126] Moved TestRow into its own file.

---
 tests/common/google_sheet_test_cases.py | 54 +------------------------
 tests/common/testrow.py                 | 54 +++++++++++++++++++++++++
 2 files changed, 55 insertions(+), 53 deletions(-)
 create mode 100644 tests/common/testrow.py

diff --git a/tests/common/google_sheet_test_cases.py b/tests/common/google_sheet_test_cases.py
index aecdda91..e3ed9813 100644
--- a/tests/common/google_sheet_test_cases.py
+++ b/tests/common/google_sheet_test_cases.py
@@ -4,65 +4,13 @@
 # This library contains classes and methods for accessing those test cases.
 import csv
 import io
-from dataclasses import dataclass
 from collections import Counter
 
 import pytest
 import requests
 from _pytest.mark import ParameterSet
 
-
-@dataclass(frozen=True)
-class TestRow:
-    """
-    A TestRow models a single row from a GoogleSheet.
-    """
-    Category: str
-    ExpectPassInNodeNorm: bool
-    ExpectPassInNameRes: bool
-    Flags: set[str]
-    QueryLabel: str
-    PreferredLabel: str
-    AdditionalLabels: list[str]
-    QueryID: str
-    PreferredID: str
-    AdditionalIDs: list[str]
-    Conflations: set[str]
-    BiolinkClasses: set[str]
-    Prefixes: set[str]
-    Source: str
-    SourceURL: str
-    Notes: str
-
-    # Mark as not a test despite starting with TestRow.
-    __test__ = False
-
-    # A string representation of this test row.
-    def __str__(self):
-        return f"TestRow of category {self.Category} for preferred {self.PreferredID} ({self.PreferredLabel}) with " + \
-            f"query {self.QueryID} ({self.QueryLabel}) from source {self.Source} ({self.SourceURL})"
-
-
-    @staticmethod
-    def from_data_row(row):
-        return TestRow(
-            Category=row.get('Category', ''),
-            ExpectPassInNodeNorm=row.get('Passes in NodeNorm', '') == 'y',
-            ExpectPassInNameRes=row.get('Passes in NameRes', '') == 'y',
-            Flags=set(row.get('Flags', '').split('|')),
-            QueryLabel=row.get('Query Label', ''),
-            QueryID=row.get('Query ID', ''),
-            PreferredID=row.get('Preferred ID', ''),
-            AdditionalIDs=row.get('Additional IDs', '').split('|'),
-            PreferredLabel=row.get('Preferred Label', ''),
-            AdditionalLabels=row.get('Additional Labels', '').split('|'),
-            Conflations=set(row.get('Conflations', '').split('|')),
-            BiolinkClasses=set(row.get('Biolink Classes', '').split('|')),
-            Prefixes=set(row.get('Prefixes', '').split('|')),
-            Source=row.get('Source', ''),
-            SourceURL=row.get('Source URL', ''),
-            Notes=row.get('Notes', '')
-        )
+from tests.common.testrow import TestRow
 
 
 class GoogleSheetTestCases:
diff --git a/tests/common/testrow.py b/tests/common/testrow.py
new file mode 100644
index 00000000..64a7478d
--- /dev/null
+++ b/tests/common/testrow.py
@@ -0,0 +1,54 @@
+from dataclasses import dataclass
+
+
+@dataclass(frozen=True)
+class TestRow:
+    """
+    A TestRow models a single row from a GoogleSheet.
+    """
+    Category: str
+    ExpectPassInNodeNorm: bool
+    ExpectPassInNameRes: bool
+    Flags: set[str]
+    QueryLabel: str
+    PreferredLabel: str
+    AdditionalLabels: list[str]
+    QueryID: str
+    PreferredID: str
+    AdditionalIDs: list[str]
+    Conflations: set[str]
+    BiolinkClasses: set[str]
+    Prefixes: set[str]
+    Source: str
+    SourceURL: str
+    Notes: str
+
+    # Mark as not a test despite starting with TestRow.
+    __test__ = False
+
+    # A string representation of this test row.
+    def __str__(self):
+        return f"TestRow of category {self.Category} for preferred {self.PreferredID} ({self.PreferredLabel}) with " + \
+            f"query {self.QueryID} ({self.QueryLabel}) from source {self.Source} ({self.SourceURL})"
+
+
+    @staticmethod
+    def from_data_row(row):
+        return TestRow(
+            Category=row.get('Category', ''),
+            ExpectPassInNodeNorm=row.get('Passes in NodeNorm', '') == 'y',
+            ExpectPassInNameRes=row.get('Passes in NameRes', '') == 'y',
+            Flags=set(row.get('Flags', '').split('|')),
+            QueryLabel=row.get('Query Label', ''),
+            QueryID=row.get('Query ID', ''),
+            PreferredID=row.get('Preferred ID', ''),
+            AdditionalIDs=row.get('Additional IDs', '').split('|'),
+            PreferredLabel=row.get('Preferred Label', ''),
+            AdditionalLabels=row.get('Additional Labels', '').split('|'),
+            Conflations=set(row.get('Conflations', '').split('|')),
+            BiolinkClasses=set(row.get('Biolink Classes', '').split('|')),
+            Prefixes=set(row.get('Prefixes', '').split('|')),
+            Source=row.get('Source', ''),
+            SourceURL=row.get('Source URL', ''),
+            Notes=row.get('Notes', '')
+        )

From a0325b67d8b77fc1effd8d83baef1089241d12b6 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 8 Jan 2026 17:02:48 -0500
Subject: [PATCH 002/126] Added /.env to .gitignore.

---
 .gitignore | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.gitignore b/.gitignore
index a1480ec8..4bb67d43 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,6 @@
+# Ignore the root .env file.
+/.env
+
 # Ignore all data files.
 data/
 

From 0009dc002195680b0729bc8737ab4a98a9e781bf Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 8 Jan 2026 18:58:38 -0500
Subject: [PATCH 003/126] Implemented basic GitHub issue testing (but it
 doesn't work at all).

---
 pyproject.toml                              |   3 +
 tests/__init__.py                           |   0
 tests/common/github_issues_test_cases.py    | 256 ++++++++++++++++++++
 tests/common/testrow.py                     |  15 ++
 tests/github_issues/test_github_issues.py   |  35 +++
 tests/nameres/test_nameres_from_gsheet.py   |   2 +-
 tests/nodenorm/test_nodenorm_from_gsheet.py |   2 +-
 uv.lock                                     | 244 +++++++++++++++++++
 8 files changed, 555 insertions(+), 2 deletions(-)
 create mode 100644 tests/__init__.py
 create mode 100644 tests/common/github_issues_test_cases.py
 create mode 100644 tests/github_issues/test_github_issues.py

diff --git a/pyproject.toml b/pyproject.toml
index b728bf07..6584107b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,9 +8,12 @@ requires-python = ">=3.11"
 dependencies = [
     "black>=25.9.0",
     "deepdiff>=8.6.1",
+    "dotenv>=0.9.9",
     "openapi-spec-validator>=0.7.2",
+    "pygithub>=2.8.1",
     "pytest>=8.4.2",
     "requests>=2.32.5",
+    "tqdm>=4.67.1",
 ]
 
 [project.urls]
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/common/github_issues_test_cases.py b/tests/common/github_issues_test_cases.py
new file mode 100644
index 00000000..a5f0ff46
--- /dev/null
+++ b/tests/common/github_issues_test_cases.py
@@ -0,0 +1,256 @@
+import json
+import logging
+import re
+import time
+from typing import Iterator
+
+import requests
+import yaml
+
+from tests.common.testrow import TestRow, TestResult, TestStatus
+from github import Github, Auth, Issue
+from tqdm import tqdm
+
+class CachedNodeNorm:
+    def __init__(self, nodenorm_url: str):
+        self.nodenorm_url = nodenorm_url
+        self.logger = logging.getLogger(str(self))
+        self.cache = {}
+
+    def __str__(self):
+        return f"CachedNodeNorm({self.nodenorm_url})"
+
+    def normalize_curies(self, curies: list[str], **params) -> str:
+        time_started = time.time_ns()
+        curies_set = set(curies)
+        cached_curies = curies_set & self.cache.keys()
+        curies_to_be_queried = curies_set - cached_curies
+
+        # Make query.
+        params['curies'] = list(curies_to_be_queried)
+
+        response = requests.post(self.nodenorm_url + "get_normalized_nodes", json=params)
+        response.raise_for_status()
+        result = response.json()
+
+        for curie in cached_curies:
+            result[curie] = self.cache[curie]
+
+        for curie in curies_to_be_queried:
+            self.cache[curie] = result.get(curie, None)
+
+        time_taken_sec = (time.time_ns() - time_started) / 1E9
+        self.logger.info(f"Normalizing {len(curies_to_be_queried)} CURIEs {curies_to_be_queried} (with {len(cached_curies)} CURIEs cached) with params {params} on {self} in {time_taken_sec:.3f}s")
+
+        return result
+
+    def normalize_curie(self, curie, **params):
+        if curie in self.cache:
+            return self.cache[curie]
+        return self.normalize_curies([curie], **params)[curie]
+
+
+class GitHubIssueTest:
+    def __init__(self, github_issue: Issue.Issue, assertion: str, param_sets: list[list[str]] = None):
+        self.github_issue = github_issue
+        self.assertion = assertion
+        if param_sets is None:
+            param_sets = []
+        self.param_sets = param_sets
+
+        self.logger = logging.getLogger(str(self))
+        self.logger.info(f"Creating GitHubIssueTest for {github_issue.html_url} {assertion}({param_sets})")
+
+    def __str__(self):
+        return f"{self.github_issue.repository.organization.name}/{self.github_issue.repository.name}#{self.github_issue.number}: {self.assertion}({json.dumps(self.param_sets)})"
+
+    def expect_param_count(self, params: list[str], expected_count: int):
+        if len(params) != expected_count:
+            raise ValueError(f"Expected {expected_count} parameters for assertion {self.assertion}, but got {len(params)}")
+
+    def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
+        match self.assertion.lower():
+            case "resolves":
+                curies_to_resolve = [params[0] for params in self.param_sets]
+                nodenorm.normalize_curies(curies_to_resolve)
+
+                for params in self.param_sets:
+                    self.expect_param_count(params, 1)
+                    curie = params[0]
+
+                    # Make sure we can resolve this CURIE.
+                    result = nodenorm.normalize_curie(curie)
+                    if not result:
+                        yield TestResult(status=TestStatus.Failed, message=f"Could not resolve {curie} with NodeNormalization service {nodenorm}")
+                    else:
+                        yield TestResult(status=TestStatus.Passed, message=f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\") with NodeNormalization service {nodenorm}")
+
+            case "resolveswith":
+                curies_to_test = set()
+                for params in self.param_sets:
+                    curies_to_test.add(params[0])
+                    curies_to_test.add(params[1])
+
+                nodenorm.normalize_curies(list(curies_to_test))
+                for params in self.param_sets:
+                    self.expect_param_count(params, 2)
+                    curie, expected_curie = params
+
+                    # Make sure we can resolve this CURIE.
+                    result = self.nodenorm.normalize_curie(curie)
+                    if not result:
+                        yield TestResult(status=TestStatus.Failed, message=f"Could not resolve {curie} with NodeNormalization service {nodenorm}")
+                    elif result['id']['identifier'] == expected_curie:
+                        yield TestResult(status=TestStatus.Passed, message=f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\") with NodeNormalization service {nodenorm} as expected")
+                    else:
+                        yield TestResult(status=TestStatus.Failed, message=f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\") with NodeNormalization service {nodenorm}, but expected {expected_curie}")
+
+            case _:
+                raise ValueError(f"Unknown assertion type: {self.assertion}")
+
+    def test_with_nameres(self) -> TestResult:
+        match self.assertion.lower():
+            case "resolves":
+                # Nothing we can do about this with NameRes.
+                return TestResult(status=TestStatus.Skipped, message="Cannot test Resolves assertion with Name Resolution service")
+            case "resolveswith":
+                # Nothing we can do about this with NameRes.
+                return TestResult(status=TestStatus.Skipped, message="Cannot test Resolves assertion with Name Resolution service")
+            case _:
+                raise ValueError(f"Unknown assertion type: {self.assertion}")
+
+
+class GitHubIssuesTestCases:
+    """
+    The idea here is to allow test cases to be efficiently embedded within GitHub issues, to test them
+    regularly, and to provide a list of cases where either:
+    - An open issue has test cases that are now passing (and so should be updated or maybe even closed).
+    - A closed issue has test cases that are now failing (and so should be reopened).
+    """
+
+    def __init__(self, github_token: str, github_repositories=None):
+        """
+        Create a GitHubIssuesTestCase object.
+
+        Requires a GitHub authentication token. You can generate a personal authentication token
+        at https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens#about-personal-access-tokens,
+        or you can read the GITHUB_TOKEN during a GitHub Action (https://docs.github.com/en/actions/tutorials/authenticate-with-github_token).
+
+        :param github_token: A GitHub authentication to use for making these queries.
+        :param github_repositories: A list of GitHub repositories to pull issues from, specified as 'organization/repo'.
+        """
+        self.github_token = github_token
+        self.github = Github(auth=Auth.Token(self.github_token))
+        self.logger = logging.getLogger(self.__class__.__name__)
+        self.logger.info("Set up GitHub object ({self.github})")
+
+        if github_repositories is None:
+            github_repositories = [
+                'NCATSTranslator/Babel',                # https://github.com/NCATSTranslator/Babel
+                'NCATSTranslator/NodeNormalization',    # https://github.com/NCATSTranslator/NodeNormalization
+                'NCATSTranslator/NameResolution',       # https://github.com/NCATSTranslator/NameResolution
+                'TranslatorSRI/babel-validation',       # https://github.com/TranslatorSRI/babel-validation
+            ]
+        self.github_repositories = github_repositories
+
+        # Prepare regular expressions.
+        self.babeltest_pattern = re.compile(r'{{BabelTest\|.*?}}')
+        self.babeltest_yaml_pattern = re.compile(r'```yaml\s+babel_tests:\s+.*?\s+```', re.DOTALL)
+
+    def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIssueTest]:
+        """
+        Extract test rows from a single GitHub issue.
+
+        This is where we describe our test case recording language. I think we should support two formats:
+        - Wiki syntax: {{BabelTest|AssertionType|param1|param2|...}}
+        - YAML syntax, which requires a YAML type box that looks like this:
+
+        ```yaml
+        babel_tests:
+            assertion:
+            - param1
+            - ['param1', 'param2']
+            - {'param1': 'value1', 'param2': 'value2'}
+        ```
+
+        We currently support the following assertions:
+        - Resolves: Test whether param1 (CURIE) resolves to anything.
+        - ResolvesWith: Test whether param1 (CURIE) resolves to param2 (CURIE).
+
+        :param github_issue: A single GitHub issue to extract test cases from.
+        :return: An iterator over TestRows.
+        """
+
+        self.logger.debug(f"Looking for tests in issue #{github_issue.number}: {github_issue.title} ({str(github_issue.state)}, {github_issue.html_url})")
+
+        # Is there an issue body at all?
+        if not github_issue.body or github_issue.body.strip() == '':
+            return []
+
+        # Look for BabelTest syntax.
+        testrows = []
+
+        babeltest_matches = re.findall(self.babeltest_pattern, github_issue.body)
+        if babeltest_matches:
+            for match in babeltest_matches:
+                self.logger.info(f"Found BabelTest in issue #{github_issue.number}: {match}")
+
+                # Figure out parameters.
+                test_string = match
+                if test_string.startswith("{{BabelTest|"):
+                    test_string = test_string[12:]
+                if test_string.endswith("}}"):
+                    test_string = test_string[:-2]
+                params = test_string.split("|")
+                if len(params) < 2:
+                    raise ValueError(f"Too few parameters found in BabelTest in issue #{github_issue.number}: {match}")
+                elif len(params) == 2:
+                    testrows.append(GitHubIssueTest(github_issue, params[1], [params[0]]))
+                else:
+                    testrows.append(GitHubIssueTest(github_issue, params[1], [params[0], params[2:]]))
+
+        babeltest_yaml_matches = re.findall(self.babeltest_yaml_pattern, github_issue.body)
+        if babeltest_yaml_matches:
+            for match in babeltest_yaml_matches:
+                self.logger.info(f"Found BabelTest YAML in issue #{github_issue.number}: {match}")
+
+                # Parse string as YAML.
+                if match.startswith("```yaml"):
+                    match = match[7:]
+                if match.endswith("```"):
+                    match = match[:-3]
+                yaml_dict = yaml.safe_load(match)
+
+                for assertion, param_sets in yaml_dict['babel_tests'].items():
+                    testrows.append(GitHubIssueTest(github_issue, assertion, param_sets))
+
+        return testrows
+
+    def get_test_issues(self, github_repositories = None, include_issues_without_tests = False) -> Iterator[GitHubIssueTest]:
+        """
+        Get a list of test rows from one or more repositories.
+
+        :param github_repositories: A list of GitHub repositories to search for test cases. If none is provided,
+            we default to the list specified when creating this GitHubIssuesTestCases class.
+        :param include_issues_without_tests: If true, include issues that do not contain any test cases. Default: false.
+        :return: A list of TestRows to process.
+        """
+        if github_repositories is None:
+            github_repositories = self.github_repositories
+
+        for repo_id in github_repositories:
+            self.logger.info(f"Looking up issues in GitHub repository {repo_id}")
+            repo = self.github.get_repo(repo_id)
+
+            issue_count = 0
+            for issue in tqdm(repo.get_issues(state='all', sort='updated'), desc=f"Processing issues in {repo_id}"):
+                issue_count += 1
+                test_issues = self.get_test_issues_from_issue(issue)
+
+                if not include_issues_without_tests and not test_issues:
+                    continue
+
+                for test_issue in test_issues:
+                    yield test_issue
+
+            self.logger.info(f"Found {issue_count} issues in GitHub repository {repo_id}")
\ No newline at end of file
diff --git a/tests/common/testrow.py b/tests/common/testrow.py
index 64a7478d..30528279 100644
--- a/tests/common/testrow.py
+++ b/tests/common/testrow.py
@@ -1,4 +1,5 @@
 from dataclasses import dataclass
+from enum import Enum
 
 
 @dataclass(frozen=True)
@@ -52,3 +53,17 @@ def from_data_row(row):
             SourceURL=row.get('Source URL', ''),
             Notes=row.get('Notes', '')
         )
+
+class TestStatus(Enum):
+    Passed = "pass"
+    Failed = "fail"
+    Skipped = "skip"
+
+@dataclass
+class TestResult:
+    status: TestStatus
+    message: str = ""
+    github_issue_test: 'GitHubIssueTest' = None
+
+
+
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
new file mode 100644
index 00000000..7bbfff9c
--- /dev/null
+++ b/tests/github_issues/test_github_issues.py
@@ -0,0 +1,35 @@
+import os
+
+import dotenv
+import pytest
+
+from tests.common.github_issues_test_cases import GitHubIssuesTestCases, CachedNodeNorm
+from tests.common.testrow import TestResult, TestStatus
+
+# Initialize the test.
+dotenv.load_dotenv()
+github_token = os.getenv('GITHUB_TOKEN')
+github_issues_test_cases = GitHubIssuesTestCases(github_token, [
+    'NCATSTranslator/Babel',                # https://github.com/NCATSTranslator/Babel
+    'NCATSTranslator/NodeNormalization',    # https://github.com/NCATSTranslator/NodeNormalization
+    'NCATSTranslator/NameResolution',       # https://github.com/NCATSTranslator/NameResolution
+    'TranslatorSRI/babel-validation',       # https://github.com/TranslatorSRI/babel-validation
+])
+
+@pytest.mark.parametrize("test_issue", github_issues_test_cases.get_test_issues())
+def test_github_issue_testrow(target_info, test_issue):
+    print(f"Test issue: {test_issue}")
+
+    nodenorm = CachedNodeNorm(target_info['NodeNormURL'])
+    results = test_issue.test_with_nodenorm(nodenorm)
+
+    for result in results:
+        match result:
+            case TestResult(status=TestStatus.Passed, message=message):
+                assert True, message
+            case TestResult(status=TestStatus.Failed, message=message):
+                assert False, message
+            case TestResult(status=TestStatus.Skipped, message=message):
+                pytest.skip(message)
+            case _:
+                assert False, f"Unknown result: {result}"
\ No newline at end of file
diff --git a/tests/nameres/test_nameres_from_gsheet.py b/tests/nameres/test_nameres_from_gsheet.py
index 199e074d..b03c7c0d 100644
--- a/tests/nameres/test_nameres_from_gsheet.py
+++ b/tests/nameres/test_nameres_from_gsheet.py
@@ -1,7 +1,7 @@
 import urllib.parse
 import requests
 import pytest
-from common.google_sheet_test_cases import GoogleSheetTestCases, TestRow
+from tests.common.google_sheet_test_cases import GoogleSheetTestCases
 
 # Configuration options
 NAMERES_TIMEOUT = 10 # If we don't get a response in 10 seconds, that's a fail.
diff --git a/tests/nodenorm/test_nodenorm_from_gsheet.py b/tests/nodenorm/test_nodenorm_from_gsheet.py
index 5dfe43fb..ce0ecb2c 100644
--- a/tests/nodenorm/test_nodenorm_from_gsheet.py
+++ b/tests/nodenorm/test_nodenorm_from_gsheet.py
@@ -2,7 +2,7 @@
 import urllib.parse
 import requests
 import pytest
-from common.google_sheet_test_cases import GoogleSheetTestCases, TestRow
+from tests.common.google_sheet_test_cases import GoogleSheetTestCases
 
 # We generate a set of tests from the GoogleSheetTestCases.
 gsheet = GoogleSheetTestCases()
diff --git a/uv.lock b/uv.lock
index 33690434..8c42f024 100644
--- a/uv.lock
+++ b/uv.lock
@@ -18,18 +18,24 @@ source = { virtual = "." }
 dependencies = [
     { name = "black" },
     { name = "deepdiff" },
+    { name = "dotenv" },
     { name = "openapi-spec-validator" },
+    { name = "pygithub" },
     { name = "pytest" },
     { name = "requests" },
+    { name = "tqdm" },
 ]
 
 [package.metadata]
 requires-dist = [
     { name = "black", specifier = ">=25.9.0" },
     { name = "deepdiff", specifier = ">=8.6.1" },
+    { name = "dotenv", specifier = ">=0.9.9" },
     { name = "openapi-spec-validator", specifier = ">=0.7.2" },
+    { name = "pygithub", specifier = ">=2.8.1" },
     { name = "pytest", specifier = ">=8.4.2" },
     { name = "requests", specifier = ">=2.32.5" },
+    { name = "tqdm", specifier = ">=4.67.1" },
 ]
 
 [[package]]
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+    { url = "https://files.pythonhosted.org/packages/be/7b/4845bbf88e94586ec47a432da4e9107e3fc3ce37eb412b1398630a37f7dd/pynacl-1.6.2-cp38-abi3-macosx_10_10_universal2.whl", hash = "sha256:c949ea47e4206af7c8f604b8278093b674f7c79ed0d4719cc836902bf4517465", size = 388458, upload-time = "2026-01-01T17:32:16.829Z" },
+    { url = "https://files.pythonhosted.org/packages/1e/b4/e927e0653ba63b02a4ca5b4d852a8d1d678afbf69b3dbf9c4d0785ac905c/pynacl-1.6.2-cp38-abi3-manylinux2014_aarch64.manylinux_2_17_aarch64.whl", hash = "sha256:8845c0631c0be43abdd865511c41eab235e0be69c81dc66a50911594198679b0", size = 800020, upload-time = "2026-01-01T17:32:18.34Z" },
+    { url = "https://files.pythonhosted.org/packages/7f/81/d60984052df5c97b1d24365bc1e30024379b42c4edcd79d2436b1b9806f2/pynacl-1.6.2-cp38-abi3-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:22de65bb9010a725b0dac248f353bb072969c94fa8d6b1f34b87d7953cf7bbe4", size = 1399174, upload-time = "2026-01-01T17:32:20.239Z" },
+    { url = "https://files.pythonhosted.org/packages/68/f7/322f2f9915c4ef27d140101dd0ed26b479f7e6f5f183590fd32dfc48c4d3/pynacl-1.6.2-cp38-abi3-manylinux_2_26_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:46065496ab748469cdd999246d17e301b2c24ae2fdf739132e580a0e94c94a87", size = 835085, upload-time = "2026-01-01T17:32:22.24Z" },
+    { url = "https://files.pythonhosted.org/packages/3e/d0/f301f83ac8dbe53442c5a43f6a39016f94f754d7a9815a875b65e218a307/pynacl-1.6.2-cp38-abi3-manylinux_2_26_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:8a66d6fb6ae7661c58995f9c6435bda2b1e68b54b598a6a10247bfcdadac996c", size = 1437614, upload-time = "2026-01-01T17:32:23.766Z" },
+    { url = "https://files.pythonhosted.org/packages/c4/58/fc6e649762b029315325ace1a8c6be66125e42f67416d3dbd47b69563d61/pynacl-1.6.2-cp38-abi3-manylinux_2_34_aarch64.whl", hash = "sha256:26bfcd00dcf2cf160f122186af731ae30ab120c18e8375684ec2670dccd28130", size = 818251, upload-time = "2026-01-01T17:32:25.69Z" },
+    { url = "https://files.pythonhosted.org/packages/c9/a8/b917096b1accc9acd878819a49d3d84875731a41eb665f6ebc826b1af99e/pynacl-1.6.2-cp38-abi3-manylinux_2_34_x86_64.whl", hash = "sha256:c8a231e36ec2cab018c4ad4358c386e36eede0319a0c41fed24f840b1dac59f6", size = 1402859, upload-time = "2026-01-01T17:32:27.215Z" },
+    { url = "https://files.pythonhosted.org/packages/85/42/fe60b5f4473e12c72f977548e4028156f4d340b884c635ec6b063fe7e9a5/pynacl-1.6.2-cp38-abi3-musllinux_1_2_aarch64.whl", hash = "sha256:68be3a09455743ff9505491220b64440ced8973fe930f270c8e07ccfa25b1f9e", size = 791926, upload-time = "2026-01-01T17:32:29.314Z" },
+    { url = "https://files.pythonhosted.org/packages/fa/f9/e40e318c604259301cc091a2a63f237d9e7b424c4851cafaea4ea7c4834e/pynacl-1.6.2-cp38-abi3-musllinux_1_2_x86_64.whl", hash = "sha256:8b097553b380236d51ed11356c953bf8ce36a29a3e596e934ecabe76c985a577", size = 1363101, upload-time = "2026-01-01T17:32:31.263Z" },
+    { url = "https://files.pythonhosted.org/packages/48/47/e761c254f410c023a469284a9bc210933e18588ca87706ae93002c05114c/pynacl-1.6.2-cp38-abi3-win32.whl", hash = "sha256:5811c72b473b2f38f7e2a3dc4f8642e3a3e9b5e7317266e4ced1fba85cae41aa", size = 227421, upload-time = "2026-01-01T17:32:33.076Z" },
+    { url = "https://files.pythonhosted.org/packages/41/ad/334600e8cacc7d86587fe5f565480fde569dfb487389c8e1be56ac21d8ac/pynacl-1.6.2-cp38-abi3-win_amd64.whl", hash = "sha256:62985f233210dee6548c223301b6c25440852e13d59a8b81490203c3227c5ba0", size = 239754, upload-time = "2026-01-01T17:32:34.557Z" },
+    { url = "https://files.pythonhosted.org/packages/29/7d/5945b5af29534641820d3bd7b00962abbbdfee84ec7e19f0d5b3175f9a31/pynacl-1.6.2-cp38-abi3-win_arm64.whl", hash = "sha256:834a43af110f743a754448463e8fd61259cd4ab5bbedcf70f9dabad1d28a394c", size = 184801, upload-time = "2026-01-01T17:32:36.309Z" },
+]
+
 [[package]]
 name = "pytest"
 version = "8.4.2"
@@ -392,6 +615,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/a8/a4/20da314d277121d6534b3a980b29035dcd51e6744bd79075a6ce8fa4eb8d/pytest-8.4.2-py3-none-any.whl", hash = "sha256:872f880de3fc3a5bdc88a11b39c9710c3497a547cfa9320bc3c5e62fbf272e79", size = 365750, upload-time = "2025-09-04T14:34:20.226Z" },
 ]
 
+[[package]]
+name = "python-dotenv"
+version = "1.2.1"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/f0/26/19cadc79a718c5edbec86fd4919a6b6d3f681039a2f6d66d14be94e75fb9/python_dotenv-1.2.1.tar.gz", hash = "sha256:42667e897e16ab0d66954af0e60a9caa94f0fd4ecf3aaf6d2d260eec1aa36ad6", size = 44221, upload-time = "2025-10-26T15:12:10.434Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/14/1b/a298b06749107c305e1fe0f814c6c74aea7b2f1e10989cb30f544a1b3253/python_dotenv-1.2.1-py3-none-any.whl", hash = "sha256:b81ee9561e9ca4004139c6cbba3a238c32b03e4894671e181b671e8cb8425d61", size = 21230, upload-time = "2025-10-26T15:12:09.109Z" },
+]
+
 [[package]]
 name = "pytokens"
 version = "0.2.0"
@@ -614,6 +846,18 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/b7/ce/149a00dd41f10bc29e5921b496af8b574d8413afcd5e30dfa0ed46c2cc5e/six-1.17.0-py2.py3-none-any.whl", hash = "sha256:4721f391ed90541fddacab5acf947aa0d3dc7d27b2e1e8eda2be8970586c3274", size = 11050, upload-time = "2024-12-04T17:35:26.475Z" },
 ]
 
+[[package]]
+name = "tqdm"
+version = "4.67.1"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "colorama", marker = "sys_platform == 'win32'" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/a8/4b/29b4ef32e036bb34e4ab51796dd745cdba7ed47ad142a9f4a1eb8e0c744d/tqdm-4.67.1.tar.gz", hash = "sha256:f8aef9c52c08c13a65f30ea34f4e5aac3fd1a34959879d7e59e63027286627f2", size = 169737, upload-time = "2024-11-24T20:12:22.481Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/d0/30/dc54f88dd4a2b5dc8a0279bdd7270e735851848b762aeb1c1184ed1f6b14/tqdm-4.67.1-py3-none-any.whl", hash = "sha256:26445eca388f82e72884e0d580d5464cd801a3ea01e63e5601bdff9ba6a48de2", size = 78540, upload-time = "2024-11-24T20:12:19.698Z" },
+]
+
 [[package]]
 name = "typing-extensions"
 version = "4.15.0"

From f2977359489e02b4deb859631231bcd0f740c623 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 11 Jan 2026 23:47:05 -0500
Subject: [PATCH 004/126] Check for a GitHub Authentication Token.

---
 tests/common/github_issues_test_cases.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/common/github_issues_test_cases.py b/tests/common/github_issues_test_cases.py
index a5f0ff46..65646eac 100644
--- a/tests/common/github_issues_test_cases.py
+++ b/tests/common/github_issues_test_cases.py
@@ -140,6 +140,9 @@ def __init__(self, github_token: str, github_repositories=None):
         :param github_repositories: A list of GitHub repositories to pull issues from, specified as 'organization/repo'.
         """
         self.github_token = github_token
+        if not self.github_token or self.github_token.strip() == '':
+            raise ValueError("No GitHub authentication token provided.")
+
         self.github = Github(auth=Auth.Token(self.github_token))
         self.logger = logging.getLogger(self.__class__.__name__)
         self.logger.info("Set up GitHub object ({self.github})")

From 9b96675cdb86bdeb432a871d480f8ddc9da8fa99 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 11 Jan 2026 23:47:50 -0500
Subject: [PATCH 005/126] Add support for `--issue` to specify one or more
 GitHub issues to check.

---
 tests/conftest.py                         | 15 ++++++++++++++-
 tests/github_issues/test_github_issues.py | 22 +++++++++++++++++++---
 2 files changed, 33 insertions(+), 4 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 2515e227..63a069da 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -47,6 +47,14 @@ def pytest_addoption(parser):
         help="The categories of tests to exclude."
     )
 
+    # The issue option is only used by
+    parser.addoption(
+        '--issue',
+        default=[],
+        action='append',
+        help="One or more GitHub issues to test. Should be specified as either 'organization/repo#110', 'repo#110' or '110'"
+    )
+
 
 def read_targets(config_path):
     cp = configparser.ConfigParser()
@@ -119,4 +127,9 @@ def category_test(cat):
                 return False
             return True
 
-    return category_test
\ No newline at end of file
+    return category_test
+
+# Issue is only used by the GitHub issue tests (tests/github_issues/*)
+@pytest.fixture
+def github_issues(pytestconfig):
+    return pytestconfig.getoption('issue')
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 7bbfff9c..0c7e9088 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -17,9 +17,25 @@
 ])
 
 @pytest.mark.parametrize("test_issue", github_issues_test_cases.get_test_issues())
-def test_github_issue_testrow(target_info, test_issue):
-    print(f"Test issue: {test_issue}")
+def test_github_issue(target_info, test_issue, github_issues):
+    # If github_issues is provided, we can skip all others.
+    if github_issues:
+        # Come up with the three possible ways in which this issue might be specified.
+        github_issue = test_issue.github_issue
+        possible_issue_strings = set([
+            str(github_issue.number),
+            f"{test_issue.github_issue.repository.name}#{github_issue.number}",
+            f"{test_issue.github_issue.repository.organization.name}/{test_issue.github_issue.repository.name}#{github_issue.number}"
+        ])
 
+        if possible_issue_strings & set(github_issues):
+            # This issue is one of those that should be tested.
+            pass
+        else:
+            pytest.skip(f"GitHub Issue {str(test_issue)} not included in list of GitHub issues to be tested: {github_issues}.")
+            return
+
+    # Test this issue.
     nodenorm = CachedNodeNorm(target_info['NodeNormURL'])
     results = test_issue.test_with_nodenorm(nodenorm)
 
@@ -32,4 +48,4 @@ def test_github_issue_testrow(target_info, test_issue):
             case TestResult(status=TestStatus.Skipped, message=message):
                 pytest.skip(message)
             case _:
-                assert False, f"Unknown result: {result}"
\ No newline at end of file
+                assert False, f"Unknown result: {result}"

From 97bb7a67747b07bd81f1988641990c46a08aac7c Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 11 Jan 2026 23:48:36 -0500
Subject: [PATCH 006/126] Cleaned up some code.

---
 tests/common/github_issues_test_cases.py | 20 +++++++++++---------
 tests/common/testrow.py                  |  8 ++++++--
 2 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/tests/common/github_issues_test_cases.py b/tests/common/github_issues_test_cases.py
index 65646eac..4b53c1d8 100644
--- a/tests/common/github_issues_test_cases.py
+++ b/tests/common/github_issues_test_cases.py
@@ -177,14 +177,16 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
         ```
 
         We currently support the following assertions:
-        - Resolves: Test whether param1 (CURIE) resolves to anything.
-        - ResolvesWith: Test whether param1 (CURIE) resolves to param2 (CURIE).
+        - Resolves: Test whether any of the parameters can be resolved.
+        - DoesNotResolve: Ensure that the parameters do not resolve.
+        - ResolvesWith: Test whether all the parameters resolve together.
 
         :param github_issue: A single GitHub issue to extract test cases from.
         :return: An iterator over TestRows.
         """
 
-        self.logger.debug(f"Looking for tests in issue #{github_issue.number}: {github_issue.title} ({str(github_issue.state)}, {github_issue.html_url})")
+        github_issue_id = f"{github_issue.repository.organization.name}/{github_issue.repository.name}#{github_issue.number}"
+        self.logger.debug(f"Looking for tests in issue {github_issue_id}: {github_issue.title} ({str(github_issue.state)}, {github_issue.html_url})")
 
         # Is there an issue body at all?
         if not github_issue.body or github_issue.body.strip() == '':
@@ -196,7 +198,7 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
         babeltest_matches = re.findall(self.babeltest_pattern, github_issue.body)
         if babeltest_matches:
             for match in babeltest_matches:
-                self.logger.info(f"Found BabelTest in issue #{github_issue.number}: {match}")
+                self.logger.info(f"Found BabelTest in issue {github_issue_id}: {match}")
 
                 # Figure out parameters.
                 test_string = match
@@ -206,16 +208,16 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
                     test_string = test_string[:-2]
                 params = test_string.split("|")
                 if len(params) < 2:
-                    raise ValueError(f"Too few parameters found in BabelTest in issue #{github_issue.number}: {match}")
+                    raise ValueError(f"Too few parameters found in BabelTest in issue {github_issue_id}: {match}")
                 elif len(params) == 2:
-                    testrows.append(GitHubIssueTest(github_issue, params[1], [params[0]]))
+                    testrows.append(GitHubIssueTest(github_issue, params[0], [params]))
                 else:
-                    testrows.append(GitHubIssueTest(github_issue, params[1], [params[0], params[2:]]))
+                    testrows.append(GitHubIssueTest(github_issue, params[0], [params]))
 
         babeltest_yaml_matches = re.findall(self.babeltest_yaml_pattern, github_issue.body)
         if babeltest_yaml_matches:
             for match in babeltest_yaml_matches:
-                self.logger.info(f"Found BabelTest YAML in issue #{github_issue.number}: {match}")
+                self.logger.info(f"Found BabelTest YAML in issue {github_issue_id}: {match}")
 
                 # Parse string as YAML.
                 if match.startswith("```yaml"):
@@ -256,4 +258,4 @@ def get_test_issues(self, github_repositories = None, include_issues_without_tes
                 for test_issue in test_issues:
                     yield test_issue
 
-            self.logger.info(f"Found {issue_count} issues in GitHub repository {repo_id}")
\ No newline at end of file
+            self.logger.info(f"Found {issue_count} issues in GitHub repository {repo_id}")
diff --git a/tests/common/testrow.py b/tests/common/testrow.py
index 30528279..88ae3828 100644
--- a/tests/common/testrow.py
+++ b/tests/common/testrow.py
@@ -24,7 +24,7 @@ class TestRow:
     SourceURL: str
     Notes: str
 
-    # Mark as not a test despite starting with TestRow.
+    # Mark as not a test despite starting with Test*.
     __test__ = False
 
     # A string representation of this test row.
@@ -59,11 +59,15 @@ class TestStatus(Enum):
     Failed = "fail"
     Skipped = "skip"
 
+    # Mark as not a test despite starting with Test*.
+    __test__ = False
+
 @dataclass
 class TestResult:
     status: TestStatus
     message: str = ""
     github_issue_test: 'GitHubIssueTest' = None
 
-
+    # Mark as not a test despite starting with Test*.
+    __test__ = False
 

From ed8f1dbbce9132478d41bc885bd813d86ddeb86f Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Mon, 12 Jan 2026 00:41:26 -0500
Subject: [PATCH 007/126] Sped up tests, made things work better.

---
 tests/common/github_issues_test_cases.py  | 139 +++++++++++++++-------
 tests/conftest.py                         |   2 +-
 tests/github_issues/test_github_issues.py |  54 +++++----
 3 files changed, 130 insertions(+), 65 deletions(-)

diff --git a/tests/common/github_issues_test_cases.py b/tests/common/github_issues_test_cases.py
index 4b53c1d8..dfb91021 100644
--- a/tests/common/github_issues_test_cases.py
+++ b/tests/common/github_issues_test_cases.py
@@ -11,6 +11,8 @@
 from github import Github, Auth, Issue
 from tqdm import tqdm
 
+cached_node_norms_by_url = {}
+
 class CachedNodeNorm:
     def __init__(self, nodenorm_url: str):
         self.nodenorm_url = nodenorm_url
@@ -20,7 +22,13 @@ def __init__(self, nodenorm_url: str):
     def __str__(self):
         return f"CachedNodeNorm({self.nodenorm_url})"
 
-    def normalize_curies(self, curies: list[str], **params) -> str:
+    @staticmethod
+    def from_url(nodenorm_url: str) -> 'CachedNodeNorm':
+        if nodenorm_url not in cached_node_norms_by_url:
+            cached_node_norms_by_url[nodenorm_url] = CachedNodeNorm(nodenorm_url)
+        return cached_node_norms_by_url[nodenorm_url]
+
+    def normalize_curies(self, curies: list[str], **params) -> dict[str, dict]:
         time_started = time.time_ns()
         curies_set = set(curies)
         cached_curies = curies_set & self.cache.keys()
@@ -62,48 +70,105 @@ def __init__(self, github_issue: Issue.Issue, assertion: str, param_sets: list[l
         self.logger.info(f"Creating GitHubIssueTest for {github_issue.html_url} {assertion}({param_sets})")
 
     def __str__(self):
-        return f"{self.github_issue.repository.organization.name}/{self.github_issue.repository.name}#{self.github_issue.number}: {self.assertion}({json.dumps(self.param_sets)})"
-
-    def expect_param_count(self, params: list[str], expected_count: int):
-        if len(params) != expected_count:
-            raise ValueError(f"Expected {expected_count} parameters for assertion {self.assertion}, but got {len(params)}")
+        return f"{self.github_issue.repository.organization.name}/{self.github_issue.repository.name}#{self.github_issue.number}: {self.assertion}({len(self.param_sets)} param sets: {json.dumps(self.param_sets)})"
 
     def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
         match self.assertion.lower():
             case "resolves":
+                if not self.param_sets:
+                    return TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")
+
                 curies_to_resolve = [params[0] for params in self.param_sets]
                 nodenorm.normalize_curies(curies_to_resolve)
 
-                for params in self.param_sets:
-                    self.expect_param_count(params, 1)
-                    curie = params[0]
+                # Enumerate params.
+                yielded_values = False
+                for index, params in enumerate(self.param_sets):
+                    if not params:
+                        return TestResult(status=TestStatus.Failed, message=f"No parameters provided in paramset {index} in {self}")
+
+                    for curie in params:
+                        result = nodenorm.normalize_curie(curie)
+                        if not result:
+                            yield TestResult(status=TestStatus.Failed, message=f"Could not resolve {curie} with NodeNormalization service {nodenorm}")
+                            yielded_values = True
+                        else:
+                            yield TestResult(status=TestStatus.Passed, message=f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\") with NodeNormalization service {nodenorm}")
+                            yielded_values = True
+
+                if not yielded_values:
+                    return TestResult(status=TestStatus.Failed, message=f"No test results returned in {self}")
 
-                    # Make sure we can resolve this CURIE.
-                    result = nodenorm.normalize_curie(curie)
-                    if not result:
-                        yield TestResult(status=TestStatus.Failed, message=f"Could not resolve {curie} with NodeNormalization service {nodenorm}")
-                    else:
-                        yield TestResult(status=TestStatus.Passed, message=f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\") with NodeNormalization service {nodenorm}")
+            case "doesnotresolve":
+                if not self.param_sets:
+                    return TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")
+
+                curies_to_resolve = [params[0] for params in self.param_sets]
+                nodenorm.normalize_curies(curies_to_resolve)
+
+                # Enumerate params.
+                yielded_values = False
+                for index, params in enumerate(self.param_sets):
+                    if not params:
+                        return TestResult(status=TestStatus.Failed, message=f"No parameters provided in paramset {index} in {self}")
+
+                    for curie in params:
+                        result = nodenorm.normalize_curie(curie)
+                        if not result:
+                            yield TestResult(status=TestStatus.Passed, message=f"Could not resolve {curie} with NodeNormalization service {nodenorm} as expected")
+                            yielded_values = True
+                        else:
+                            yield TestResult(status=TestStatus.Failed, message=f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\") with NodeNormalization service {nodenorm}, but expected not to resolve")
+                            yielded_values = True
+
+                if not yielded_values:
+                    return TestResult(status=TestStatus.Failed, message=f"No test results returned in {self}")
 
             case "resolveswith":
-                curies_to_test = set()
-                for params in self.param_sets:
-                    curies_to_test.add(params[0])
-                    curies_to_test.add(params[1])
+                if not self.param_sets:
+                    return TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")
 
-                nodenorm.normalize_curies(list(curies_to_test))
+                curies_to_resolve = [params[0] for params in self.param_sets]
+                nodenorm.normalize_curies(curies_to_resolve)
+
+                nodenorm.normalize_curies(list(curies_to_resolve))
+
+                yielded_values = False
                 for params in self.param_sets:
-                    self.expect_param_count(params, 2)
-                    curie, expected_curie = params
-
-                    # Make sure we can resolve this CURIE.
-                    result = self.nodenorm.normalize_curie(curie)
-                    if not result:
-                        yield TestResult(status=TestStatus.Failed, message=f"Could not resolve {curie} with NodeNormalization service {nodenorm}")
-                    elif result['id']['identifier'] == expected_curie:
-                        yield TestResult(status=TestStatus.Passed, message=f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\") with NodeNormalization service {nodenorm} as expected")
-                    else:
-                        yield TestResult(status=TestStatus.Failed, message=f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\") with NodeNormalization service {nodenorm}, but expected {expected_curie}")
+                    results = nodenorm.normalize_curies(params)
+
+                    # We expect there to be a single unique value here.
+                    unique_results = set([json.dumps(value, sort_keys=True) for value in results.values()])
+
+                    if len(unique_results) == 1 and len(results.values()) == len(params) and results.values()[0] is not None:
+                        return TestResult(status=TestStatus.Passed, message=f"All the CURIEs {params} resolved to the same result on {nodenorm}: {json.dumps(unique_results[0], indent=2, sort_keys=True)}")
+
+                    # Find the first good result.
+                    first_good_result = None
+                    for curie, result in results.items():
+                        if result is not None and first_good_result is None:
+                            first_good_result = curie
+                            break
+
+                    if first_good_result is None:
+                        return TestResult(status=TestStatus.Failed, message=f"None of the CURIEs {params} could be resolved on {nodenorm}")
+
+                    # Check all the results.
+                    for curie, result in results.items():
+                        if result is None:
+                            yield TestResult(status=TestStatus.Failed, message=f"CURIE {curie} could not be resolved, and so is not euqal to the expected result {json.dumps(first_good_result, indent=2, sort_keys=True)} on {nodenorm}")
+                            yielded_values = True
+                            continue
+
+                        if json.dumps(first_good_result, sort_keys=True) == json.dumps(result, sort_keys=True):
+                            yield TestResult(status=TestStatus.Passed, message=f"Resolved {curie} to the expected result {json.dumps(first_good_result, indent=2, sort_keys=True)}")
+                            yielded_values = True
+                        else:
+                            yield TestResult(status=TestStatus.Failed, message=f"Resolved {curie} to {json.dumps(result, indent=2, sort_keys=True)}, which is different from the expected result {json.dumps(first_good_result, indent=2, sort_keys=True)} on {nodenorm}")
+                            yielded_values = True
+
+                if not yielded_values:
+                    return TestResult(status=TestStatus.Failed, message=f"No test results returned in {self}")
 
             case _:
                 raise ValueError(f"Unknown assertion type: {self.assertion}")
@@ -231,7 +296,7 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
 
         return testrows
 
-    def get_test_issues(self, github_repositories = None, include_issues_without_tests = False) -> Iterator[GitHubIssueTest]:
+    def get_all_issues(self, github_repositories = None) -> Iterator[Issue.Issue]:
         """
         Get a list of test rows from one or more repositories.
 
@@ -245,17 +310,11 @@ def get_test_issues(self, github_repositories = None, include_issues_without_tes
 
         for repo_id in github_repositories:
             self.logger.info(f"Looking up issues in GitHub repository {repo_id}")
-            repo = self.github.get_repo(repo_id)
+            repo = self.github.get_repo(repo_id, lazy=True)
 
             issue_count = 0
             for issue in tqdm(repo.get_issues(state='all', sort='updated'), desc=f"Processing issues in {repo_id}"):
                 issue_count += 1
-                test_issues = self.get_test_issues_from_issue(issue)
-
-                if not include_issues_without_tests and not test_issues:
-                    continue
-
-                for test_issue in test_issues:
-                    yield test_issue
+                yield issue
 
             self.logger.info(f"Found {issue_count} issues in GitHub repository {repo_id}")
diff --git a/tests/conftest.py b/tests/conftest.py
index 63a069da..bf5d233c 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -131,5 +131,5 @@ def category_test(cat):
 
 # Issue is only used by the GitHub issue tests (tests/github_issues/*)
 @pytest.fixture
-def github_issues(pytestconfig):
+def selected_github_issues(pytestconfig):
     return pytestconfig.getoption('issue')
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 0c7e9088..b83783a2 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -16,36 +16,42 @@
     'TranslatorSRI/babel-validation',       # https://github.com/TranslatorSRI/babel-validation
 ])
 
-@pytest.mark.parametrize("test_issue", github_issues_test_cases.get_test_issues())
-def test_github_issue(target_info, test_issue, github_issues):
+@pytest.mark.parametrize("github_issue", github_issues_test_cases.get_all_issues())
+def test_github_issue(target_info, github_issue, selected_github_issues):
     # If github_issues is provided, we can skip all others.
-    if github_issues:
-        # Come up with the three possible ways in which this issue might be specified.
-        github_issue = test_issue.github_issue
-        possible_issue_strings = set([
-            str(github_issue.number),
-            f"{test_issue.github_issue.repository.name}#{github_issue.number}",
-            f"{test_issue.github_issue.repository.organization.name}/{test_issue.github_issue.repository.name}#{github_issue.number}"
-        ])
+    if selected_github_issues:
+        # Check all three possible ways in which this issue might be specified.
+        github_issue_matched = False
+        for selected_github_issue in selected_github_issues:
+            if '/' in selected_github_issue:
+                github_issue_matched = (f"{github_issue.repository.organization.name}/{github_issue.repository.name}#{github_issue.number}" == selected_github_issue)
+            elif '#' in selected_github_issue:
+                github_issue_matched = (f"{github_issue.repository.name}#{github_issue.number}" == selected_github_issue)
+            else:
+                github_issue_matched = int(selected_github_issue) == github_issue.number
+            if github_issue_matched:
+                break
 
-        if possible_issue_strings & set(github_issues):
+        if github_issue_matched:
             # This issue is one of those that should be tested.
             pass
         else:
-            pytest.skip(f"GitHub Issue {str(test_issue)} not included in list of GitHub issues to be tested: {github_issues}.")
+            pytest.skip(f"GitHub Issue {str(github_issue)} not included in list of GitHub issues to be tested: {selected_github_issues}.")
             return
 
     # Test this issue.
-    nodenorm = CachedNodeNorm(target_info['NodeNormURL'])
-    results = test_issue.test_with_nodenorm(nodenorm)
+    nodenorm = CachedNodeNorm.from_url(target_info['NodeNormURL'])
+    tests = github_issues_test_cases.get_test_issues_from_issue(github_issue)
+    for test_issue in tests:
+        results = test_issue.test_with_nodenorm(nodenorm)
 
-    for result in results:
-        match result:
-            case TestResult(status=TestStatus.Passed, message=message):
-                assert True, message
-            case TestResult(status=TestStatus.Failed, message=message):
-                assert False, message
-            case TestResult(status=TestStatus.Skipped, message=message):
-                pytest.skip(message)
-            case _:
-                assert False, f"Unknown result: {result}"
+        for result in results:
+            match result:
+                case TestResult(status=TestStatus.Passed, message=message):
+                    assert True, message
+                case TestResult(status=TestStatus.Failed, message=message):
+                    assert False, message
+                case TestResult(status=TestStatus.Skipped, message=message):
+                    pytest.skip(message)
+                case _:
+                    assert False, f"Unknown result: {result}"

From f0342ce751cb0bf5e175816b3a6ea99114a70280 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Mon, 12 Jan 2026 00:50:27 -0500
Subject: [PATCH 008/126] Fixed some issues.

---
 tests/common/github_issues_test_cases.py  | 17 +++++++++++++----
 tests/github_issues/test_github_issues.py |  5 +++++
 2 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/tests/common/github_issues_test_cases.py b/tests/common/github_issues_test_cases.py
index dfb91021..56a30f3c 100644
--- a/tests/common/github_issues_test_cases.py
+++ b/tests/common/github_issues_test_cases.py
@@ -78,7 +78,7 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
                 if not self.param_sets:
                     return TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")
 
-                curies_to_resolve = [params[0] for params in self.param_sets]
+                curies_to_resolve = [param for params in self.param_sets for param in params]
                 nodenorm.normalize_curies(curies_to_resolve)
 
                 # Enumerate params.
@@ -103,7 +103,7 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
                 if not self.param_sets:
                     return TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")
 
-                curies_to_resolve = [params[0] for params in self.param_sets]
+                curies_to_resolve = [param for params in self.param_sets for param in params]
                 nodenorm.normalize_curies(curies_to_resolve)
 
                 # Enumerate params.
@@ -170,8 +170,12 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
                 if not yielded_values:
                     return TestResult(status=TestStatus.Failed, message=f"No test results returned in {self}")
 
+            # These are NameRes tests, not NodeNorm tests.
+            case "searchbyname":
+                return
+
             case _:
-                raise ValueError(f"Unknown assertion type: {self.assertion}")
+                raise ValueError(f"Unknown assertion type for {self}: {self.assertion}")
 
     def test_with_nameres(self) -> TestResult:
         match self.assertion.lower():
@@ -250,7 +254,12 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
         :return: An iterator over TestRows.
         """
 
-        github_issue_id = f"{github_issue.repository.organization.name}/{github_issue.repository.name}#{github_issue.number}"
+        github_issue_id = f"{github_issue.number}"
+            # Ideally, we would use:
+            #   f"{github_issue.repository.organization.name}/{github_issue.repository.name}#{github_issue.number}"
+            # But that is very slow.
+            # TODO: Wrap Issue.Issue so that we can store orgName and repoName locally so we don't need to call out
+            # to figure it out.
         self.logger.debug(f"Looking for tests in issue {github_issue_id}: {github_issue.title} ({str(github_issue.state)}, {github_issue.html_url})")
 
         # Is there an issue body at all?
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index b83783a2..bc3b707a 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -40,8 +40,13 @@ def test_github_issue(target_info, github_issue, selected_github_issues):
             return
 
     # Test this issue.
+    print(f"Testing issue {str(github_issue)}")
     nodenorm = CachedNodeNorm.from_url(target_info['NodeNormURL'])
     tests = github_issues_test_cases.get_test_issues_from_issue(github_issue)
+    if not tests:
+        pytest.skip(f"No tests found in issue {github_issue}")
+        return
+
     for test_issue in tests:
         results = test_issue.test_with_nodenorm(nodenorm)
 

From ebac7abf7d9273e92507fd0bc12737b426054bfe Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Mon, 12 Jan 2026 01:12:14 -0500
Subject: [PATCH 009/126] It works! But it shouldn't. Cross that bridge later
 etc.

---
 tests/common/github_issues_test_cases.py | 69 ++++++++++++++----------
 1 file changed, 40 insertions(+), 29 deletions(-)

diff --git a/tests/common/github_issues_test_cases.py b/tests/common/github_issues_test_cases.py
index 56a30f3c..5997bc27 100644
--- a/tests/common/github_issues_test_cases.py
+++ b/tests/common/github_issues_test_cases.py
@@ -29,24 +29,32 @@ def from_url(nodenorm_url: str) -> 'CachedNodeNorm':
         return cached_node_norms_by_url[nodenorm_url]
 
     def normalize_curies(self, curies: list[str], **params) -> dict[str, dict]:
+        if not curies:
+            raise ValueError(f"curies must not be empty when calling normalize_curies({curies}, {params}) on {self}")
+        if not isinstance(curies, list):
+            raise ValueError(f"curies must be a list when calling normalize_curies({curies}, {params}) on {self}")
+
         time_started = time.time_ns()
         curies_set = set(curies)
         cached_curies = curies_set & self.cache.keys()
         curies_to_be_queried = curies_set - cached_curies
 
         # Make query.
-        params['curies'] = list(curies_to_be_queried)
+        result = {}
+        if curies_to_be_queried:
+            params['curies'] = list(curies_to_be_queried)
+
+            print(f"Called NodeNorm {self} with params {params}")
+            response = requests.post(self.nodenorm_url + "get_normalized_nodes", json=params)
+            response.raise_for_status()
+            result = response.json()
 
-        response = requests.post(self.nodenorm_url + "get_normalized_nodes", json=params)
-        response.raise_for_status()
-        result = response.json()
+            for curie in curies_to_be_queried:
+                self.cache[curie] = result.get(curie, None)
 
         for curie in cached_curies:
             result[curie] = self.cache[curie]
 
-        for curie in curies_to_be_queried:
-            self.cache[curie] = result.get(curie, None)
-
         time_taken_sec = (time.time_ns() - time_started) / 1E9
         self.logger.info(f"Normalizing {len(curies_to_be_queried)} CURIEs {curies_to_be_queried} (with {len(cached_curies)} CURIEs cached) with params {params} on {self} in {time_taken_sec:.3f}s")
 
@@ -65,6 +73,8 @@ def __init__(self, github_issue: Issue.Issue, assertion: str, param_sets: list[l
         if param_sets is None:
             param_sets = []
         self.param_sets = param_sets
+        if not isinstance(self.param_sets, list):
+            raise ValueError(f"param_sets must be a list when creating a GitHubIssueTest({self.github_issue}, {self.assertion}, {self.param_sets})")
 
         self.logger = logging.getLogger(str(self))
         self.logger.info(f"Creating GitHubIssueTest for {github_issue.html_url} {assertion}({param_sets})")
@@ -81,13 +91,13 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
                 curies_to_resolve = [param for params in self.param_sets for param in params]
                 nodenorm.normalize_curies(curies_to_resolve)
 
-                # Enumerate params.
+                # Enumerate curies.
                 yielded_values = False
-                for index, params in enumerate(self.param_sets):
-                    if not params:
+                for index, curies in enumerate(self.param_sets):
+                    if not curies:
                         return TestResult(status=TestStatus.Failed, message=f"No parameters provided in paramset {index} in {self}")
 
-                    for curie in params:
+                    for curie in curies:
                         result = nodenorm.normalize_curie(curie)
                         if not result:
                             yield TestResult(status=TestStatus.Failed, message=f"Could not resolve {curie} with NodeNormalization service {nodenorm}")
@@ -106,13 +116,13 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
                 curies_to_resolve = [param for params in self.param_sets for param in params]
                 nodenorm.normalize_curies(curies_to_resolve)
 
-                # Enumerate params.
+                # Enumerate curies.
                 yielded_values = False
-                for index, params in enumerate(self.param_sets):
-                    if not params:
+                for index, curies in enumerate(self.param_sets):
+                    if not curies:
                         return TestResult(status=TestStatus.Failed, message=f"No parameters provided in paramset {index} in {self}")
 
-                    for curie in params:
+                    for curie in curies:
                         result = nodenorm.normalize_curie(curie)
                         if not result:
                             yield TestResult(status=TestStatus.Passed, message=f"Could not resolve {curie} with NodeNormalization service {nodenorm} as expected")
@@ -128,30 +138,22 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
                 if not self.param_sets:
                     return TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")
 
-                curies_to_resolve = [params[0] for params in self.param_sets]
+                curies_to_resolve = [param for params in self.param_sets for param in params]
                 nodenorm.normalize_curies(curies_to_resolve)
 
-                nodenorm.normalize_curies(list(curies_to_resolve))
-
                 yielded_values = False
-                for params in self.param_sets:
-                    results = nodenorm.normalize_curies(params)
-
-                    # We expect there to be a single unique value here.
-                    unique_results = set([json.dumps(value, sort_keys=True) for value in results.values()])
-
-                    if len(unique_results) == 1 and len(results.values()) == len(params) and results.values()[0] is not None:
-                        return TestResult(status=TestStatus.Passed, message=f"All the CURIEs {params} resolved to the same result on {nodenorm}: {json.dumps(unique_results[0], indent=2, sort_keys=True)}")
+                for curies in self.param_sets:
+                    results = nodenorm.normalize_curies(curies)
 
                     # Find the first good result.
                     first_good_result = None
                     for curie, result in results.items():
                         if result is not None and first_good_result is None:
-                            first_good_result = curie
+                            first_good_result = result
                             break
 
                     if first_good_result is None:
-                        return TestResult(status=TestStatus.Failed, message=f"None of the CURIEs {params} could be resolved on {nodenorm}")
+                        return TestResult(status=TestStatus.Failed, message=f"None of the CURIEs {curies} could be resolved on {nodenorm}")
 
                     # Check all the results.
                     for curie, result in results.items():
@@ -163,6 +165,7 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
                         if json.dumps(first_good_result, sort_keys=True) == json.dumps(result, sort_keys=True):
                             yield TestResult(status=TestStatus.Passed, message=f"Resolved {curie} to the expected result {json.dumps(first_good_result, indent=2, sort_keys=True)}")
                             yielded_values = True
+
                         else:
                             yield TestResult(status=TestStatus.Failed, message=f"Resolved {curie} to {json.dumps(result, indent=2, sort_keys=True)}, which is different from the expected result {json.dumps(first_good_result, indent=2, sort_keys=True)} on {nodenorm}")
                             yielded_values = True
@@ -300,7 +303,15 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
                     match = match[:-3]
                 yaml_dict = yaml.safe_load(match)
 
-                for assertion, param_sets in yaml_dict['babel_tests'].items():
+                for assertion, original_param_sets in yaml_dict['babel_tests'].items():
+                    param_sets = []
+                    for param_set in original_param_sets:
+                        if isinstance(param_set, str):
+                            param_sets.append([param_set])
+                        elif isinstance(param_set, list):
+                            param_sets.append(param_set)
+                        else:
+                            raise RuntimeError(f"Unknown parameter set type {param_set} in issue {github_issue_id}")
                     testrows.append(GitHubIssueTest(github_issue, assertion, param_sets))
 
         return testrows

From 05b767e9178c2109c88cb28c5bc8163a98527d0b Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Mon, 12 Jan 2026 01:50:25 -0500
Subject: [PATCH 010/126] Various improvements.

---
 tests/common/github_issues_test_cases.py  |  8 +++-----
 tests/github_issues/test_github_issues.py | 11 ++++++++---
 2 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/tests/common/github_issues_test_cases.py b/tests/common/github_issues_test_cases.py
index 5997bc27..9444bafe 100644
--- a/tests/common/github_issues_test_cases.py
+++ b/tests/common/github_issues_test_cases.py
@@ -44,7 +44,7 @@ def normalize_curies(self, curies: list[str], **params) -> dict[str, dict]:
         if curies_to_be_queried:
             params['curies'] = list(curies_to_be_queried)
 
-            print(f"Called NodeNorm {self} with params {params}")
+            self.logger.debug(f"Called NodeNorm {self} with params {params}")
             response = requests.post(self.nodenorm_url + "get_normalized_nodes", json=params)
             response.raise_for_status()
             result = response.json()
@@ -158,7 +158,7 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
                     # Check all the results.
                     for curie, result in results.items():
                         if result is None:
-                            yield TestResult(status=TestStatus.Failed, message=f"CURIE {curie} could not be resolved, and so is not euqal to the expected result {json.dumps(first_good_result, indent=2, sort_keys=True)} on {nodenorm}")
+                            yield TestResult(status=TestStatus.Failed, message=f"CURIE {curie} could not be resolved, and so is not equal to the expected result {json.dumps(first_good_result, indent=2, sort_keys=True)} on {nodenorm}")
                             yielded_values = True
                             continue
 
@@ -286,10 +286,8 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
                 params = test_string.split("|")
                 if len(params) < 2:
                     raise ValueError(f"Too few parameters found in BabelTest in issue {github_issue_id}: {match}")
-                elif len(params) == 2:
-                    testrows.append(GitHubIssueTest(github_issue, params[0], [params]))
                 else:
-                    testrows.append(GitHubIssueTest(github_issue, params[0], [params]))
+                    testrows.append(GitHubIssueTest(github_issue, params[0], [params[1:]]))
 
         babeltest_yaml_matches = re.findall(self.babeltest_yaml_pattern, github_issue.body)
         if babeltest_yaml_matches:
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index bc3b707a..6df36252 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -2,10 +2,15 @@
 
 import dotenv
 import pytest
+from github import Issue
 
 from tests.common.github_issues_test_cases import GitHubIssuesTestCases, CachedNodeNorm
 from tests.common.testrow import TestResult, TestStatus
 
+# Helper functions
+def get_github_issue_id(github_issue: Issue.Issue):
+    return f"{github_issue.repository.organization.name}/{github_issue.repository.name}#{github_issue.number}"
+
 # Initialize the test.
 dotenv.load_dotenv()
 github_token = os.getenv('GITHUB_TOKEN')
@@ -55,8 +60,8 @@ def test_github_issue(target_info, github_issue, selected_github_issues):
                 case TestResult(status=TestStatus.Passed, message=message):
                     assert True, message
                 case TestResult(status=TestStatus.Failed, message=message):
-                    assert False, message
+                    assert False, f"{get_github_issue_id(github_issue)}: {message}"
                 case TestResult(status=TestStatus.Skipped, message=message):
-                    pytest.skip(message)
+                    pytest.skip(f"{get_github_issue_id(github_issue)}: {message}")
                 case _:
-                    assert False, f"Unknown result: {result}"
+                    assert False, f"Unknown result from {get_github_issue_id(github_issue)}: {result}"

From 15b28d198c7b99ecd5c356a60787caa8da63caed Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Mon, 12 Jan 2026 01:58:29 -0500
Subject: [PATCH 011/126] Various improvements.

---
 tests/common/github_issues_test_cases.py  |  4 ++++
 tests/github_issues/test_github_issues.py | 17 ++++++++++++++---
 2 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/tests/common/github_issues_test_cases.py b/tests/common/github_issues_test_cases.py
index 9444bafe..e6a2868d 100644
--- a/tests/common/github_issues_test_cases.py
+++ b/tests/common/github_issues_test_cases.py
@@ -177,6 +177,10 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
             case "searchbyname":
                 return
 
+            # This is a special assertion to remind ourselves that we need to add tests here.
+            case "needed":
+                return TestResult(status=TestStatus.Failed, message=f"Test needed for issue")
+
             case _:
                 raise ValueError(f"Unknown assertion type for {self}: {self.assertion}")
 
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 6df36252..fa1ee567 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -45,23 +45,34 @@ def test_github_issue(target_info, github_issue, selected_github_issues):
             return
 
     # Test this issue.
-    print(f"Testing issue {str(github_issue)}")
     nodenorm = CachedNodeNorm.from_url(target_info['NodeNormURL'])
     tests = github_issues_test_cases.get_test_issues_from_issue(github_issue)
     if not tests:
         pytest.skip(f"No tests found in issue {github_issue}")
         return
 
+    # Is this test open or closed?
+    github_issue_open = (github_issue.state == 'open')
+
     for test_issue in tests:
         results = test_issue.test_with_nodenorm(nodenorm)
 
         for result in results:
             match result:
                 case TestResult(status=TestStatus.Passed, message=message):
-                    assert True, message
+                    if github_issue_open:
+                        pytest.xfail(f"{get_github_issue_id(github_issue)} CAN BE CLOSED: {message}")
+                    else:
+                        assert True, message
+
                 case TestResult(status=TestStatus.Failed, message=message):
-                    assert False, f"{get_github_issue_id(github_issue)}: {message}"
+                    if github_issue_open:
+                        pytest.xfail(f"{get_github_issue_id(github_issue)} NOT YET PASSING: {message}")
+                    else:
+                        assert False, f"{get_github_issue_id(github_issue)}: {message}"
+
                 case TestResult(status=TestStatus.Skipped, message=message):
                     pytest.skip(f"{get_github_issue_id(github_issue)}: {message}")
+
                 case _:
                     assert False, f"Unknown result from {get_github_issue_id(github_issue)}: {result}"

From a6845a323e00daa4048fabec012a25312c9a6651 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Mon, 12 Jan 2026 02:32:57 -0500
Subject: [PATCH 012/126] Got rid of xfail system (too much bother).

---
 tests/common/github_issues_test_cases.py  | 30 ++++++++++++++++++-----
 tests/github_issues/test_github_issues.py | 13 ++--------
 2 files changed, 26 insertions(+), 17 deletions(-)

diff --git a/tests/common/github_issues_test_cases.py b/tests/common/github_issues_test_cases.py
index e6a2868d..c3c24648 100644
--- a/tests/common/github_issues_test_cases.py
+++ b/tests/common/github_issues_test_cases.py
@@ -83,6 +83,7 @@ def __str__(self):
         return f"{self.github_issue.repository.organization.name}/{self.github_issue.repository.name}#{self.github_issue.number}: {self.assertion}({len(self.param_sets)} param sets: {json.dumps(self.param_sets)})"
 
     def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
+        yielded_values = False
         match self.assertion.lower():
             case "resolves":
                 if not self.param_sets:
@@ -92,7 +93,6 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
                 nodenorm.normalize_curies(curies_to_resolve)
 
                 # Enumerate curies.
-                yielded_values = False
                 for index, curies in enumerate(self.param_sets):
                     if not curies:
                         return TestResult(status=TestStatus.Failed, message=f"No parameters provided in paramset {index} in {self}")
@@ -106,9 +106,6 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
                             yield TestResult(status=TestStatus.Passed, message=f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\") with NodeNormalization service {nodenorm}")
                             yielded_values = True
 
-                if not yielded_values:
-                    return TestResult(status=TestStatus.Failed, message=f"No test results returned in {self}")
-
             case "doesnotresolve":
                 if not self.param_sets:
                     return TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")
@@ -117,7 +114,6 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
                 nodenorm.normalize_curies(curies_to_resolve)
 
                 # Enumerate curies.
-                yielded_values = False
                 for index, curies in enumerate(self.param_sets):
                     if not curies:
                         return TestResult(status=TestStatus.Failed, message=f"No parameters provided in paramset {index} in {self}")
@@ -141,7 +137,6 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
                 curies_to_resolve = [param for params in self.param_sets for param in params]
                 nodenorm.normalize_curies(curies_to_resolve)
 
-                yielded_values = False
                 for curies in self.param_sets:
                     results = nodenorm.normalize_curies(curies)
 
@@ -173,6 +168,26 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
                 if not yielded_values:
                     return TestResult(status=TestStatus.Failed, message=f"No test results returned in {self}")
 
+            case "resolveswithtype":
+                if not self.param_sets:
+                    return TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")
+
+                for index, params in enumerate(self.param_sets):
+                    if len(params) < 2:
+                        return TestResult(status=TestStatus.Failed, message=f"Too few parameters provided in param set {index} in {self}: {params}")
+                    expected_biolink_type = params[0]
+                    curies = params[1:]
+
+                    results = nodenorm.normalize_curies(curies)
+                    for curie in curies:
+                        biolink_types = results[curie]['type']
+                        if expected_biolink_type in biolink_types:
+                            yield TestResult(status=TestStatus.Passed, message=f"Biolink types {biolink_types} for CURIE {curie} includes expected Biolink type {expected_biolink_type}")
+                            yielded_values = True
+                        else:
+                            yield TestResult(status=TestStatus.Failed, message=f"Biolink types {biolink_types} for CURIE {curie} does not include expected Biolink type {expected_biolink_type}")
+                            yielded_values = True
+
             # These are NameRes tests, not NodeNorm tests.
             case "searchbyname":
                 return
@@ -184,6 +199,9 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
             case _:
                 raise ValueError(f"Unknown assertion type for {self}: {self.assertion}")
 
+        if not yielded_values:
+            return TestResult(status=TestStatus.Failed, message=f"No test results returned in {self}")
+
     def test_with_nameres(self) -> TestResult:
         match self.assertion.lower():
             case "resolves":
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index fa1ee567..7c8fa87e 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -51,25 +51,16 @@ def test_github_issue(target_info, github_issue, selected_github_issues):
         pytest.skip(f"No tests found in issue {github_issue}")
         return
 
-    # Is this test open or closed?
-    github_issue_open = (github_issue.state == 'open')
-
     for test_issue in tests:
         results = test_issue.test_with_nodenorm(nodenorm)
 
         for result in results:
             match result:
                 case TestResult(status=TestStatus.Passed, message=message):
-                    if github_issue_open:
-                        pytest.xfail(f"{get_github_issue_id(github_issue)} CAN BE CLOSED: {message}")
-                    else:
-                        assert True, message
+                    assert True, message
 
                 case TestResult(status=TestStatus.Failed, message=message):
-                    if github_issue_open:
-                        pytest.xfail(f"{get_github_issue_id(github_issue)} NOT YET PASSING: {message}")
-                    else:
-                        assert False, f"{get_github_issue_id(github_issue)}: {message}"
+                    assert False, f"{get_github_issue_id(github_issue)}: {message}"
 
                 case TestResult(status=TestStatus.Skipped, message=message):
                     pytest.skip(f"{get_github_issue_id(github_issue)}: {message}")

From 54001bb631e1f29e591f9ea7cbb4d6b52bba27bd Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Mon, 12 Jan 2026 02:35:35 -0500
Subject: [PATCH 013/126] Incorporated issue state into outputs.

---
 tests/github_issues/test_github_issues.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 7c8fa87e..1df8623a 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -50,20 +50,20 @@ def test_github_issue(target_info, github_issue, selected_github_issues):
     if not tests:
         pytest.skip(f"No tests found in issue {github_issue}")
         return
-
+    
     for test_issue in tests:
         results = test_issue.test_with_nodenorm(nodenorm)
 
         for result in results:
             match result:
                 case TestResult(status=TestStatus.Passed, message=message):
-                    assert True, message
+                    assert True, f"{get_github_issue_id(github_issue)} ({github_issue.state}): {message}"
 
                 case TestResult(status=TestStatus.Failed, message=message):
-                    assert False, f"{get_github_issue_id(github_issue)}: {message}"
+                    assert False, f"{get_github_issue_id(github_issue)} ({github_issue.state}): {message}"
 
                 case TestResult(status=TestStatus.Skipped, message=message):
-                    pytest.skip(f"{get_github_issue_id(github_issue)}: {message}")
+                    pytest.skip(f"{get_github_issue_id(github_issue)} ({github_issue.state}): {message}")
 
                 case _:
                     assert False, f"Unknown result from {get_github_issue_id(github_issue)}: {result}"

From 150f4a611ba0ca010704b1696f5dd8808a7135b7 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Mon, 12 Jan 2026 02:38:17 -0500
Subject: [PATCH 014/126] Better?

---
 tests/github_issues/test_github_issues.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 1df8623a..960854af 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -50,14 +50,20 @@ def test_github_issue(target_info, github_issue, selected_github_issues):
     if not tests:
         pytest.skip(f"No tests found in issue {github_issue}")
         return
-    
+
+    # Is this test open or closed?
+    github_issue_open = (github_issue.state == 'open')
+
     for test_issue in tests:
         results = test_issue.test_with_nodenorm(nodenorm)
 
         for result in results:
             match result:
                 case TestResult(status=TestStatus.Passed, message=message):
-                    assert True, f"{get_github_issue_id(github_issue)} ({github_issue.state}): {message}"
+                    if github_issue_open:
+                        assert False, f"{get_github_issue_id(github_issue)} ({github_issue.state}) CAN BE CLOSED: {message}"
+                    else:
+                        assert True, f"{get_github_issue_id(github_issue)} ({github_issue.state}): {message}"
 
                 case TestResult(status=TestStatus.Failed, message=message):
                     assert False, f"{get_github_issue_id(github_issue)} ({github_issue.state}): {message}"

From 92821bfafd80812b3405274789f1f0cf7c423fc5 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Mon, 12 Jan 2026 02:40:35 -0500
Subject: [PATCH 015/126] Nope, still too messy.

---
 tests/github_issues/test_github_issues.py | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 960854af..c8fc409d 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -51,19 +51,13 @@ def test_github_issue(target_info, github_issue, selected_github_issues):
         pytest.skip(f"No tests found in issue {github_issue}")
         return
 
-    # Is this test open or closed?
-    github_issue_open = (github_issue.state == 'open')
-
     for test_issue in tests:
         results = test_issue.test_with_nodenorm(nodenorm)
 
         for result in results:
             match result:
                 case TestResult(status=TestStatus.Passed, message=message):
-                    if github_issue_open:
-                        assert False, f"{get_github_issue_id(github_issue)} ({github_issue.state}) CAN BE CLOSED: {message}"
-                    else:
-                        assert True, f"{get_github_issue_id(github_issue)} ({github_issue.state}): {message}"
+                    assert True, f"{get_github_issue_id(github_issue)} ({github_issue.state}): {message}"
 
                 case TestResult(status=TestStatus.Failed, message=message):
                     assert False, f"{get_github_issue_id(github_issue)} ({github_issue.state}): {message}"

From 9a4a22ca5a95c82f8f8e3f48b87621867ad4de99 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Thu, 15 Jan 2026 00:38:08 -0500
Subject: [PATCH 016/126] Added some NameRes tests.

---
 tests/common/github_issues_test_cases.py  | 171 +++++++++++++++++++---
 tests/github_issues/test_github_issues.py |  11 +-
 2 files changed, 159 insertions(+), 23 deletions(-)

diff --git a/tests/common/github_issues_test_cases.py b/tests/common/github_issues_test_cases.py
index c3c24648..8a8701b2 100644
--- a/tests/common/github_issues_test_cases.py
+++ b/tests/common/github_issues_test_cases.py
@@ -29,6 +29,7 @@ def from_url(nodenorm_url: str) -> 'CachedNodeNorm':
         return cached_node_norms_by_url[nodenorm_url]
 
     def normalize_curies(self, curies: list[str], **params) -> dict[str, dict]:
+        # TODO: eventually we'll need some way to cache the parameters along with the curie.
         if not curies:
             raise ValueError(f"curies must not be empty when calling normalize_curies({curies}, {params}) on {self}")
         if not isinstance(curies, list):
@@ -65,6 +66,80 @@ def normalize_curie(self, curie, **params):
             return self.cache[curie]
         return self.normalize_curies([curie], **params)[curie]
 
+    def clear_curie(self, curie):
+        # This will be needed if you need to call a CURIE with different parameters.
+        if curie in self.cache:
+            del self.cache[curie]
+
+
+cached_nameres_by_url = {}
+
+class CachedNameRes:
+    # TODO: actually cache once we've implemented a param-based cache.
+    def __init__(self, nameres_url: str):
+        self.nameres_url = nameres_url
+        self.logger = logging.getLogger(str(self))
+        self.cache = {}
+
+    def __str__(self):
+        return f"CachedNameRes({self.nameres_url})"
+
+    @staticmethod
+    def from_url(nameres_url: str) -> 'CachedNameRes':
+        if nameres_url not in cached_nameres_by_url:
+            cached_nameres_by_url[nameres_url] = CachedNameRes(nameres_url)
+        return cached_nameres_by_url[nameres_url]
+
+    def bulk_lookup(self, queries: list[str], **params) -> dict[str, dict]:
+        if not queries:
+            raise ValueError(f"queries must not be empty when calling bulk_lookup({queries}, {params}) on {self}")
+        if not isinstance(queries, list):
+            raise ValueError(f"queries must be a list when calling normalize_curies({queries}, {params}) on {self}")
+
+        time_started = time.time_ns()
+        queries_set = set(queries)
+        cached_queries = queries_set & self.cache.keys()
+        queries_to_be_queried = queries_set - cached_queries
+
+        # Make query.
+        result = {}
+        if queries_to_be_queried:
+            params['strings'] = list(queries_to_be_queried)
+
+            self.logger.debug(f"Called NameRes {self} with params {params}")
+            response = requests.post(self.nameres_url + "bulk-lookup", json=params)
+            response.raise_for_status()
+            result = response.json()
+
+            for query in queries_to_be_queried:
+                self.cache[query] = result.get(query, None)
+
+        for query in cached_queries:
+            result[query] = self.cache[query]
+
+        time_taken_sec = (time.time_ns() - time_started) / 1E9
+        self.logger.info(f"Looked up {len(queries_to_be_queried)} queries {queries_to_be_queried} (with {len(cached_queries)} queries cached) with params {params} on {self} in {time_taken_sec:.3f}s")
+
+        return result
+
+    def lookup(self, query, **params):
+        if query in self.cache:
+            return self.cache[query]
+
+        params['string'] = query
+        self.logger.debug(f"Querying NameRes with params {params}")
+
+        response = requests.post(self.nameres_url + "lookup", params=params)
+        response.raise_for_status()
+        result = response.json()
+
+        self.cache[query] = result
+        return result
+
+    def delete_query(self, query):
+        if query in self.cache:
+            del self.cache[query]
+
 
 class GitHubIssueTest:
     def __init__(self, github_issue: Issue.Issue, assertion: str, param_sets: list[list[str]] = None):
@@ -87,7 +162,7 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
         match self.assertion.lower():
             case "resolves":
                 if not self.param_sets:
-                    return TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")
+                    return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")]
 
                 curies_to_resolve = [param for params in self.param_sets for param in params]
                 nodenorm.normalize_curies(curies_to_resolve)
@@ -108,7 +183,7 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
 
             case "doesnotresolve":
                 if not self.param_sets:
-                    return TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")
+                    return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")]
 
                 curies_to_resolve = [param for params in self.param_sets for param in params]
                 nodenorm.normalize_curies(curies_to_resolve)
@@ -116,7 +191,8 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
                 # Enumerate curies.
                 for index, curies in enumerate(self.param_sets):
                     if not curies:
-                        return TestResult(status=TestStatus.Failed, message=f"No parameters provided in paramset {index} in {self}")
+                        yield TestResult(status=TestStatus.Failed, message=f"No parameters provided in paramset {index} in {self}")
+                        continue
 
                     for curie in curies:
                         result = nodenorm.normalize_curie(curie)
@@ -128,11 +204,11 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
                             yielded_values = True
 
                 if not yielded_values:
-                    return TestResult(status=TestStatus.Failed, message=f"No test results returned in {self}")
+                    return [TestResult(status=TestStatus.Failed, message=f"No test results returned in {self}")]
 
             case "resolveswith":
                 if not self.param_sets:
-                    return TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")
+                    return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")]
 
                 curies_to_resolve = [param for params in self.param_sets for param in params]
                 nodenorm.normalize_curies(curies_to_resolve)
@@ -148,7 +224,7 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
                             break
 
                     if first_good_result is None:
-                        return TestResult(status=TestStatus.Failed, message=f"None of the CURIEs {curies} could be resolved on {nodenorm}")
+                        return [TestResult(status=TestStatus.Failed, message=f"None of the CURIEs {curies} could be resolved on {nodenorm}")]
 
                     # Check all the results.
                     for curie, result in results.items():
@@ -162,19 +238,20 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
                             yielded_values = True
 
                         else:
-                            yield TestResult(status=TestStatus.Failed, message=f"Resolved {curie} to {json.dumps(result, indent=2, sort_keys=True)}, which is different from the expected result {json.dumps(first_good_result, indent=2, sort_keys=True)} on {nodenorm}")
+                            yield TestResult(status=TestStatus.Failed, message=f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\"), but expected {first_good_result['id']['identifier']} ({first_good_result['type'][0]}, \"{first_good_result['id']['label']}\") on {nodenorm}")
                             yielded_values = True
 
                 if not yielded_values:
-                    return TestResult(status=TestStatus.Failed, message=f"No test results returned in {self}")
+                    return [TestResult(status=TestStatus.Failed, message=f"No test results returned in {self}")]
 
             case "resolveswithtype":
                 if not self.param_sets:
-                    return TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")
+                    return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")]
 
                 for index, params in enumerate(self.param_sets):
                     if len(params) < 2:
-                        return TestResult(status=TestStatus.Failed, message=f"Too few parameters provided in param set {index} in {self}: {params}")
+                        yield TestResult(status=TestStatus.Failed, message=f"Too few parameters provided in param set {index} in {self}: {params}")
+                        continue
                     expected_biolink_type = params[0]
                     curies = params[1:]
 
@@ -190,29 +267,85 @@ def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
 
             # These are NameRes tests, not NodeNorm tests.
             case "searchbyname":
-                return
+                return []
 
             # This is a special assertion to remind ourselves that we need to add tests here.
             case "needed":
-                return TestResult(status=TestStatus.Failed, message=f"Test needed for issue")
+                return [TestResult(status=TestStatus.Failed, message=f"Test needed for issue")]
 
             case _:
                 raise ValueError(f"Unknown assertion type for {self}: {self.assertion}")
 
         if not yielded_values:
-            return TestResult(status=TestStatus.Failed, message=f"No test results returned in {self}")
+            return [TestResult(status=TestStatus.Failed, message=f"No test results returned in {self}")]
 
-    def test_with_nameres(self) -> TestResult:
+        return [
+            TestResult(status=TestStatus.Failed, message=f"Code malfunctioned in {self} -- code reached")
+        ]
+
+    def test_with_nameres(self, nodenorm: CachedNodeNorm, nameres: CachedNameRes, pass_if_found_in_top=5) -> Iterator[TestResult]:
+        yielded_values = False
         match self.assertion.lower():
-            case "resolves":
-                # Nothing we can do about this with NameRes.
-                return TestResult(status=TestStatus.Skipped, message="Cannot test Resolves assertion with Name Resolution service")
-            case "resolveswith":
+            case "searchbyname":
+                if not self.param_sets:
+                    return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")]
+
+                for params in self.param_sets:
+                    if len(params) < 2:
+                        yield TestResult(status=TestStatus.Failed, message=f"Two parameters expected for SearchByName in {self}, but params = {params}")
+                        yielded_values = True
+                        continue
+
+                    [search_query, expected_curie_from_test, *args] = params
+                    expected_curie_result = nodenorm.normalize_curie(expected_curie_from_test, drug_chemical_conflate='true')
+                    if not expected_curie_result:
+                        yield TestResult(status=TestStatus.Failed, message=f"Unable to normalize CURIE {expected_curie_from_test} in {self}")
+                        yielded_values = True
+                        continue
+                    expected_curie = expected_curie_result['id']['identifier']
+                    expected_curie_label = expected_curie_result['id']['label']
+                    expected_curie_string = f"Expected CURIE {expected_curie_from_test}, normalized to {expected_curie} '{expected_curie_label}'"
+
+                    # We're going to search for the search name and see if we can find the expected CURIE
+                    # in the first {pass_if_found_in_top} results.
+                    results = nameres.lookup(search_query, autocomplete='false', limit=(2*pass_if_found_in_top))
+                    if not results:
+                        yield TestResult(status=TestStatus.Failed, message=f"No results found for '{search_query}' on NameRes {nameres} ({expected_curie_string}")
+                        yielded_values = True
+                        continue
+
+                    curies = [result['curie'] for result in results]
+                    try:
+                        found_index = curies.index(expected_curie)
+                    except ValueError:
+                        yield TestResult(status=TestStatus.Failed, message=f"{expected_curie_string} not found when searching for '{search_query}' in NameRes {nameres}: {json.dumps(results, indent=2, sort_keys=True)}")
+                        yielded_values = True
+                        continue
+
+                    if found_index <= pass_if_found_in_top:
+                        yield TestResult(status=TestStatus.Passed, message=f"{expected_curie_string} found at index {found_index + 1} on NameRes {nameres}")
+                    else:
+                        yield TestResult(status=TestStatus.Failed, message=f"{expected_curie_string} found at index {found_index + 1} which is greater than {pass_if_found_in_top} on NameRes {nameres}")
+                    yielded_values = True
+
+            # These are NodeNorm tests, not NameRes tests.
+            case "resolves" | "doesnotresolve" | "resolveswith" | "resolveswithtype":
                 # Nothing we can do about this with NameRes.
-                return TestResult(status=TestStatus.Skipped, message="Cannot test Resolves assertion with Name Resolution service")
+                return []
+
+            # This is a special assertion to remind ourselves that we need to add tests here.
+            case "needed":
+                return [TestResult(status=TestStatus.Failed, message=f"Test needed for issue")]
+
             case _:
                 raise ValueError(f"Unknown assertion type: {self.assertion}")
 
+        if not yielded_values:
+            return [TestResult(status=TestStatus.Failed, message=f"No test results returned in {self}")]
+
+        return [
+            TestResult(status=TestStatus.Failed, message=f"Code malfunctioned in {self} -- code reached")
+        ]
 
 class GitHubIssuesTestCases:
     """
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index c8fc409d..6ef81a24 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -1,10 +1,11 @@
+import itertools
 import os
 
 import dotenv
 import pytest
 from github import Issue
 
-from tests.common.github_issues_test_cases import GitHubIssuesTestCases, CachedNodeNorm
+from tests.common.github_issues_test_cases import GitHubIssuesTestCases, CachedNodeNorm, CachedNameRes
 from tests.common.testrow import TestResult, TestStatus
 
 # Helper functions
@@ -44,17 +45,19 @@ def test_github_issue(target_info, github_issue, selected_github_issues):
             pytest.skip(f"GitHub Issue {str(github_issue)} not included in list of GitHub issues to be tested: {selected_github_issues}.")
             return
 
-    # Test this issue.
+    # Test this issue with NodeNorm.
     nodenorm = CachedNodeNorm.from_url(target_info['NodeNormURL'])
+    nameres = CachedNameRes.from_url(target_info['NameResURL'])
     tests = github_issues_test_cases.get_test_issues_from_issue(github_issue)
     if not tests:
         pytest.skip(f"No tests found in issue {github_issue}")
         return
 
     for test_issue in tests:
-        results = test_issue.test_with_nodenorm(nodenorm)
+        results_nodenorm = test_issue.test_with_nodenorm(nodenorm)
+        results_nameres = test_issue.test_with_nameres(nodenorm, nameres)
 
-        for result in results:
+        for result in itertools.chain(results_nodenorm, results_nameres):
             match result:
                 case TestResult(status=TestStatus.Passed, message=message):
                     assert True, f"{get_github_issue_id(github_issue)} ({github_issue.state}): {message}"

From 0848de460820f625e21c92a85f6bc3561866e92f Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 15 Feb 2026 21:23:54 -0500
Subject: [PATCH 017/126] Reorganized test files.

---
 {tests/common => src}/__init__.py                             | 0
 src/babel_validation/__init__.py                              | 0
 src/babel_validation/core/__init__.py                         | 0
 {tests/common => src/babel_validation/core}/testrow.py        | 0
 src/babel_validation/sources/__init__.py                      | 0
 .../babel_validation/sources}/github_issues_test_cases.py     | 2 +-
 .../babel_validation/sources}/google_sheet_test_cases.py      | 4 ++--
 tests/github_issues/test_github_issues.py                     | 4 ++--
 tests/nameres/test_nameres_from_gsheet.py                     | 2 +-
 tests/nodenorm/test_nodenorm_from_gsheet.py                   | 4 ++--
 tests/{ => test_environment}/test_env.py                      | 4 ++--
 11 files changed, 10 insertions(+), 10 deletions(-)
 rename {tests/common => src}/__init__.py (100%)
 create mode 100644 src/babel_validation/__init__.py
 create mode 100644 src/babel_validation/core/__init__.py
 rename {tests/common => src/babel_validation/core}/testrow.py (100%)
 create mode 100644 src/babel_validation/sources/__init__.py
 rename {tests/common => src/babel_validation/sources}/github_issues_test_cases.py (99%)
 rename {tests/common => src/babel_validation/sources}/google_sheet_test_cases.py (98%)
 rename tests/{ => test_environment}/test_env.py (81%)

diff --git a/tests/common/__init__.py b/src/__init__.py
similarity index 100%
rename from tests/common/__init__.py
rename to src/__init__.py
diff --git a/src/babel_validation/__init__.py b/src/babel_validation/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/babel_validation/core/__init__.py b/src/babel_validation/core/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/common/testrow.py b/src/babel_validation/core/testrow.py
similarity index 100%
rename from tests/common/testrow.py
rename to src/babel_validation/core/testrow.py
diff --git a/src/babel_validation/sources/__init__.py b/src/babel_validation/sources/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/common/github_issues_test_cases.py b/src/babel_validation/sources/github_issues_test_cases.py
similarity index 99%
rename from tests/common/github_issues_test_cases.py
rename to src/babel_validation/sources/github_issues_test_cases.py
index 8a8701b2..581b36fe 100644
--- a/tests/common/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github_issues_test_cases.py
@@ -7,7 +7,7 @@
 import requests
 import yaml
 
-from tests.common.testrow import TestRow, TestResult, TestStatus
+from src.babel_validation.core.testrow import TestResult, TestStatus
 from github import Github, Auth, Issue
 from tqdm import tqdm
 
diff --git a/tests/common/google_sheet_test_cases.py b/src/babel_validation/sources/google_sheet_test_cases.py
similarity index 98%
rename from tests/common/google_sheet_test_cases.py
rename to src/babel_validation/sources/google_sheet_test_cases.py
index e3ed9813..152af4bb 100644
--- a/tests/common/google_sheet_test_cases.py
+++ b/src/babel_validation/sources/google_sheet_test_cases.py
@@ -10,7 +10,7 @@
 import requests
 from _pytest.mark import ParameterSet
 
-from tests.common.testrow import TestRow
+from src.babel_validation.core.testrow import TestRow
 
 
 class GoogleSheetTestCases:
@@ -89,4 +89,4 @@ def has_nonempty_value(d: dict):
 
     def categories(self):
         """ Return a dict of all the categories of tests available with their counts. """
-        return Counter(map(lambda t: t.get('Category', ''), self.rows))
\ No newline at end of file
+        return Counter(map(lambda t: t.get('Category', ''), self.rows))
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 6ef81a24..01d4acd2 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -5,8 +5,8 @@
 import pytest
 from github import Issue
 
-from tests.common.github_issues_test_cases import GitHubIssuesTestCases, CachedNodeNorm, CachedNameRes
-from tests.common.testrow import TestResult, TestStatus
+from src.babel_validation.sources.github_issues_test_cases import GitHubIssuesTestCases, CachedNodeNorm, CachedNameRes
+from src.babel_validation.core.testrow import TestResult, TestStatus
 
 # Helper functions
 def get_github_issue_id(github_issue: Issue.Issue):
diff --git a/tests/nameres/test_nameres_from_gsheet.py b/tests/nameres/test_nameres_from_gsheet.py
index b03c7c0d..8914aa5b 100644
--- a/tests/nameres/test_nameres_from_gsheet.py
+++ b/tests/nameres/test_nameres_from_gsheet.py
@@ -1,7 +1,7 @@
 import urllib.parse
 import requests
 import pytest
-from tests.common.google_sheet_test_cases import GoogleSheetTestCases
+from src.babel_validation.sources.google_sheet_test_cases import GoogleSheetTestCases
 
 # Configuration options
 NAMERES_TIMEOUT = 10 # If we don't get a response in 10 seconds, that's a fail.
diff --git a/tests/nodenorm/test_nodenorm_from_gsheet.py b/tests/nodenorm/test_nodenorm_from_gsheet.py
index ce0ecb2c..535d8e01 100644
--- a/tests/nodenorm/test_nodenorm_from_gsheet.py
+++ b/tests/nodenorm/test_nodenorm_from_gsheet.py
@@ -2,7 +2,7 @@
 import urllib.parse
 import requests
 import pytest
-from tests.common.google_sheet_test_cases import GoogleSheetTestCases
+from src.babel_validation.sources.google_sheet_test_cases import GoogleSheetTestCases
 
 # We generate a set of tests from the GoogleSheetTestCases.
 gsheet = GoogleSheetTestCases()
@@ -89,4 +89,4 @@ def test_normalization(target_info, test_row, test_category):
                                                                 f"found in types: {biolink_types}")
             else:
                 assert biolink_type in set(biolink_types), (f"{test_summary} biolink type {biolink_type} not found in "
-                                                            f"types: {biolink_types}")
\ No newline at end of file
+                                                            f"types: {biolink_types}")
diff --git a/tests/test_env.py b/tests/test_environment/test_env.py
similarity index 81%
rename from tests/test_env.py
rename to tests/test_environment/test_env.py
index 87a4f6af..9f572b5a 100644
--- a/tests/test_env.py
+++ b/tests/test_environment/test_env.py
@@ -1,7 +1,7 @@
 # Test whether the test environment is functional.
 import json
 
-from common.google_sheet_test_cases import GoogleSheetTestCases
+from src.babel_validation.sources.google_sheet_test_cases import GoogleSheetTestCases
 
 
 def test_google_sheet_has_test_cases():
@@ -13,4 +13,4 @@ def test_google_sheet_has_test_cases():
     print(f"Found {len(gsheet.rows)} test cases in {gsheet}: {json.dumps(gsheet.rows[:10], indent=2)}")
 
     categories = gsheet.categories()
-    assert 'Unit Tests' in categories
\ No newline at end of file
+    assert 'Unit Tests' in categories

From 127cca1cbbdc3a47c8922abe248d6c98130431ea Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 15 Feb 2026 21:24:20 -0500
Subject: [PATCH 018/126] Don't need __init__.py in top-level src directory.

---
 src/__init__.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 src/__init__.py

diff --git a/src/__init__.py b/src/__init__.py
deleted file mode 100644
index e69de29b..00000000

From b91609f76743e2198733d336ecda472788b0d157 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 19 Feb 2026 16:09:38 -0500
Subject: [PATCH 019/126] Moved NodeNorm/NameRes into own files.

---
 src/__init__.py                               |   0
 src/babel_validation/services/__init__.py     |   0
 src/babel_validation/services/nameres.py      |  72 ++++++++++
 src/babel_validation/services/nodenorm.py     |  64 +++++++++
 .../sources/github_issues_test_cases.py       | 132 +-----------------
 tests/github_issues/test_github_issues.py     |   4 +-
 6 files changed, 141 insertions(+), 131 deletions(-)
 create mode 100644 src/__init__.py
 create mode 100644 src/babel_validation/services/__init__.py
 create mode 100644 src/babel_validation/services/nameres.py
 create mode 100644 src/babel_validation/services/nodenorm.py

diff --git a/src/__init__.py b/src/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/babel_validation/services/__init__.py b/src/babel_validation/services/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/babel_validation/services/nameres.py b/src/babel_validation/services/nameres.py
new file mode 100644
index 00000000..5dcee5c1
--- /dev/null
+++ b/src/babel_validation/services/nameres.py
@@ -0,0 +1,72 @@
+import logging
+import time
+
+import requests
+
+cached_nameres_by_url = {}
+
+class CachedNameRes:
+    # TODO: actually cache once we've implemented a param-based cache.
+    def __init__(self, nameres_url: str):
+        self.nameres_url = nameres_url
+        self.logger = logging.getLogger(str(self))
+        self.cache = {}
+
+    def __str__(self):
+        return f"CachedNameRes({self.nameres_url})"
+
+    @staticmethod
+    def from_url(nameres_url: str) -> 'CachedNameRes':
+        if nameres_url not in cached_nameres_by_url:
+            cached_nameres_by_url[nameres_url] = CachedNameRes(nameres_url)
+        return cached_nameres_by_url[nameres_url]
+
+    def bulk_lookup(self, queries: list[str], **params) -> dict[str, dict]:
+        if not queries:
+            raise ValueError(f"queries must not be empty when calling bulk_lookup({queries}, {params}) on {self}")
+        if not isinstance(queries, list):
+            raise ValueError(f"queries must be a list when calling normalize_curies({queries}, {params}) on {self}")
+
+        time_started = time.time_ns()
+        queries_set = set(queries)
+        cached_queries = queries_set & self.cache.keys()
+        queries_to_be_queried = queries_set - cached_queries
+
+        # Make query.
+        result = {}
+        if queries_to_be_queried:
+            params['strings'] = list(queries_to_be_queried)
+
+            self.logger.debug(f"Called NameRes {self} with params {params}")
+            response = requests.post(self.nameres_url + "bulk-lookup", json=params)
+            response.raise_for_status()
+            result = response.json()
+
+            for query in queries_to_be_queried:
+                self.cache[query] = result.get(query, None)
+
+        for query in cached_queries:
+            result[query] = self.cache[query]
+
+        time_taken_sec = (time.time_ns() - time_started) / 1E9
+        self.logger.info(f"Looked up {len(queries_to_be_queried)} queries {queries_to_be_queried} (with {len(cached_queries)} queries cached) with params {params} on {self} in {time_taken_sec:.3f}s")
+
+        return result
+
+    def lookup(self, query, **params):
+        if query in self.cache:
+            return self.cache[query]
+
+        params['string'] = query
+        self.logger.debug(f"Querying NameRes with params {params}")
+
+        response = requests.post(self.nameres_url + "lookup", params=params)
+        response.raise_for_status()
+        result = response.json()
+
+        self.cache[query] = result
+        return result
+
+    def delete_query(self, query):
+        if query in self.cache:
+            del self.cache[query]
diff --git a/src/babel_validation/services/nodenorm.py b/src/babel_validation/services/nodenorm.py
new file mode 100644
index 00000000..88a3353d
--- /dev/null
+++ b/src/babel_validation/services/nodenorm.py
@@ -0,0 +1,64 @@
+import logging
+import time
+
+import requests
+
+cached_node_norms_by_url = {}
+
+class CachedNodeNorm:
+    def __init__(self, nodenorm_url: str):
+        self.nodenorm_url = nodenorm_url
+        self.logger = logging.getLogger(str(self))
+        self.cache = {}
+
+    def __str__(self):
+        return f"CachedNodeNorm({self.nodenorm_url})"
+
+    @staticmethod
+    def from_url(nodenorm_url: str) -> 'CachedNodeNorm':
+        if nodenorm_url not in cached_node_norms_by_url:
+            cached_node_norms_by_url[nodenorm_url] = CachedNodeNorm(nodenorm_url)
+        return cached_node_norms_by_url[nodenorm_url]
+
+    def normalize_curies(self, curies: list[str], **params) -> dict[str, dict]:
+        # TODO: eventually we'll need some way to cache the parameters along with the curie.
+        if not curies:
+            raise ValueError(f"curies must not be empty when calling normalize_curies({curies}, {params}) on {self}")
+        if not isinstance(curies, list):
+            raise ValueError(f"curies must be a list when calling normalize_curies({curies}, {params}) on {self}")
+
+        time_started = time.time_ns()
+        curies_set = set(curies)
+        cached_curies = curies_set & self.cache.keys()
+        curies_to_be_queried = curies_set - cached_curies
+
+        # Make query.
+        result = {}
+        if curies_to_be_queried:
+            params['curies'] = list(curies_to_be_queried)
+
+            self.logger.debug(f"Called NodeNorm {self} with params {params}")
+            response = requests.post(self.nodenorm_url + "get_normalized_nodes", json=params)
+            response.raise_for_status()
+            result = response.json()
+
+            for curie in curies_to_be_queried:
+                self.cache[curie] = result.get(curie, None)
+
+        for curie in cached_curies:
+            result[curie] = self.cache[curie]
+
+        time_taken_sec = (time.time_ns() - time_started) / 1E9
+        self.logger.info(f"Normalizing {len(curies_to_be_queried)} CURIEs {curies_to_be_queried} (with {len(cached_curies)} CURIEs cached) with params {params} on {self} in {time_taken_sec:.3f}s")
+
+        return result
+
+    def normalize_curie(self, curie, **params):
+        if curie in self.cache:
+            return self.cache[curie]
+        return self.normalize_curies([curie], **params)[curie]
+
+    def clear_curie(self, curie):
+        # This will be needed if you need to call a CURIE with different parameters.
+        if curie in self.cache:
+            del self.cache[curie]
diff --git a/src/babel_validation/sources/github_issues_test_cases.py b/src/babel_validation/sources/github_issues_test_cases.py
index 581b36fe..bc26ece4 100644
--- a/src/babel_validation/sources/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github_issues_test_cases.py
@@ -1,144 +1,16 @@
 import json
 import logging
 import re
-import time
 from typing import Iterator
 
-import requests
 import yaml
 
 from src.babel_validation.core.testrow import TestResult, TestStatus
 from github import Github, Auth, Issue
 from tqdm import tqdm
 
-cached_node_norms_by_url = {}
-
-class CachedNodeNorm:
-    def __init__(self, nodenorm_url: str):
-        self.nodenorm_url = nodenorm_url
-        self.logger = logging.getLogger(str(self))
-        self.cache = {}
-
-    def __str__(self):
-        return f"CachedNodeNorm({self.nodenorm_url})"
-
-    @staticmethod
-    def from_url(nodenorm_url: str) -> 'CachedNodeNorm':
-        if nodenorm_url not in cached_node_norms_by_url:
-            cached_node_norms_by_url[nodenorm_url] = CachedNodeNorm(nodenorm_url)
-        return cached_node_norms_by_url[nodenorm_url]
-
-    def normalize_curies(self, curies: list[str], **params) -> dict[str, dict]:
-        # TODO: eventually we'll need some way to cache the parameters along with the curie.
-        if not curies:
-            raise ValueError(f"curies must not be empty when calling normalize_curies({curies}, {params}) on {self}")
-        if not isinstance(curies, list):
-            raise ValueError(f"curies must be a list when calling normalize_curies({curies}, {params}) on {self}")
-
-        time_started = time.time_ns()
-        curies_set = set(curies)
-        cached_curies = curies_set & self.cache.keys()
-        curies_to_be_queried = curies_set - cached_curies
-
-        # Make query.
-        result = {}
-        if curies_to_be_queried:
-            params['curies'] = list(curies_to_be_queried)
-
-            self.logger.debug(f"Called NodeNorm {self} with params {params}")
-            response = requests.post(self.nodenorm_url + "get_normalized_nodes", json=params)
-            response.raise_for_status()
-            result = response.json()
-
-            for curie in curies_to_be_queried:
-                self.cache[curie] = result.get(curie, None)
-
-        for curie in cached_curies:
-            result[curie] = self.cache[curie]
-
-        time_taken_sec = (time.time_ns() - time_started) / 1E9
-        self.logger.info(f"Normalizing {len(curies_to_be_queried)} CURIEs {curies_to_be_queried} (with {len(cached_curies)} CURIEs cached) with params {params} on {self} in {time_taken_sec:.3f}s")
-
-        return result
-
-    def normalize_curie(self, curie, **params):
-        if curie in self.cache:
-            return self.cache[curie]
-        return self.normalize_curies([curie], **params)[curie]
-
-    def clear_curie(self, curie):
-        # This will be needed if you need to call a CURIE with different parameters.
-        if curie in self.cache:
-            del self.cache[curie]
-
-
-cached_nameres_by_url = {}
-
-class CachedNameRes:
-    # TODO: actually cache once we've implemented a param-based cache.
-    def __init__(self, nameres_url: str):
-        self.nameres_url = nameres_url
-        self.logger = logging.getLogger(str(self))
-        self.cache = {}
-
-    def __str__(self):
-        return f"CachedNameRes({self.nameres_url})"
-
-    @staticmethod
-    def from_url(nameres_url: str) -> 'CachedNameRes':
-        if nameres_url not in cached_nameres_by_url:
-            cached_nameres_by_url[nameres_url] = CachedNameRes(nameres_url)
-        return cached_nameres_by_url[nameres_url]
-
-    def bulk_lookup(self, queries: list[str], **params) -> dict[str, dict]:
-        if not queries:
-            raise ValueError(f"queries must not be empty when calling bulk_lookup({queries}, {params}) on {self}")
-        if not isinstance(queries, list):
-            raise ValueError(f"queries must be a list when calling normalize_curies({queries}, {params}) on {self}")
-
-        time_started = time.time_ns()
-        queries_set = set(queries)
-        cached_queries = queries_set & self.cache.keys()
-        queries_to_be_queried = queries_set - cached_queries
-
-        # Make query.
-        result = {}
-        if queries_to_be_queried:
-            params['strings'] = list(queries_to_be_queried)
-
-            self.logger.debug(f"Called NameRes {self} with params {params}")
-            response = requests.post(self.nameres_url + "bulk-lookup", json=params)
-            response.raise_for_status()
-            result = response.json()
-
-            for query in queries_to_be_queried:
-                self.cache[query] = result.get(query, None)
-
-        for query in cached_queries:
-            result[query] = self.cache[query]
-
-        time_taken_sec = (time.time_ns() - time_started) / 1E9
-        self.logger.info(f"Looked up {len(queries_to_be_queried)} queries {queries_to_be_queried} (with {len(cached_queries)} queries cached) with params {params} on {self} in {time_taken_sec:.3f}s")
-
-        return result
-
-    def lookup(self, query, **params):
-        if query in self.cache:
-            return self.cache[query]
-
-        params['string'] = query
-        self.logger.debug(f"Querying NameRes with params {params}")
-
-        response = requests.post(self.nameres_url + "lookup", params=params)
-        response.raise_for_status()
-        result = response.json()
-
-        self.cache[query] = result
-        return result
-
-    def delete_query(self, query):
-        if query in self.cache:
-            del self.cache[query]
+from src.babel_validation.services.nameres import CachedNameRes
+from src.babel_validation.services.nodenorm import CachedNodeNorm
 
 
 class GitHubIssueTest:
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 01d4acd2..479c82e1 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -5,7 +5,9 @@
 import pytest
 from github import Issue
 
-from src.babel_validation.sources.github_issues_test_cases import GitHubIssuesTestCases, CachedNodeNorm, CachedNameRes
+from src.babel_validation.sources.github_issues_test_cases import GitHubIssuesTestCases
+from src.babel_validation.services.nameres import CachedNameRes
+from src.babel_validation.services.nodenorm import CachedNodeNorm
 from src.babel_validation.core.testrow import TestResult, TestStatus
 
 # Helper functions

From 8a08e9a163c78bd671985f9f8592b89964fb527f Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 19 Feb 2026 16:13:29 -0500
Subject: [PATCH 020/126] Moved sources into separate directories.

---
 src/babel_validation/sources/github/__init__.py                | 0
 .../sources/{ => github}/github_issues_test_cases.py           | 0
 src/babel_validation/sources/google_sheets/__init__.py         | 0
 .../sources/{ => google_sheets}/google_sheet_test_cases.py     | 0
 tests/github_issues/test_github_issues.py                      | 2 +-
 tests/nameres/test_nameres_from_gsheet.py                      | 2 +-
 tests/nodenorm/test_nodenorm_from_gsheet.py                    | 3 +--
 tests/test_environment/test_env.py                             | 2 +-
 8 files changed, 4 insertions(+), 5 deletions(-)
 create mode 100644 src/babel_validation/sources/github/__init__.py
 rename src/babel_validation/sources/{ => github}/github_issues_test_cases.py (100%)
 create mode 100644 src/babel_validation/sources/google_sheets/__init__.py
 rename src/babel_validation/sources/{ => google_sheets}/google_sheet_test_cases.py (100%)

diff --git a/src/babel_validation/sources/github/__init__.py b/src/babel_validation/sources/github/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/babel_validation/sources/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
similarity index 100%
rename from src/babel_validation/sources/github_issues_test_cases.py
rename to src/babel_validation/sources/github/github_issues_test_cases.py
diff --git a/src/babel_validation/sources/google_sheets/__init__.py b/src/babel_validation/sources/google_sheets/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/babel_validation/sources/google_sheet_test_cases.py b/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py
similarity index 100%
rename from src/babel_validation/sources/google_sheet_test_cases.py
rename to src/babel_validation/sources/google_sheets/google_sheet_test_cases.py
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 479c82e1..94252f22 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -5,7 +5,7 @@
 import pytest
 from github import Issue
 
-from src.babel_validation.sources.github_issues_test_cases import GitHubIssuesTestCases
+from src.babel_validation.sources.github.github_issues_test_cases import GitHubIssuesTestCases
 from src.babel_validation.services.nameres import CachedNameRes
 from src.babel_validation.services.nodenorm import CachedNodeNorm
 from src.babel_validation.core.testrow import TestResult, TestStatus
diff --git a/tests/nameres/test_nameres_from_gsheet.py b/tests/nameres/test_nameres_from_gsheet.py
index 8914aa5b..5c5993d5 100644
--- a/tests/nameres/test_nameres_from_gsheet.py
+++ b/tests/nameres/test_nameres_from_gsheet.py
@@ -1,7 +1,7 @@
 import urllib.parse
 import requests
 import pytest
-from src.babel_validation.sources.google_sheet_test_cases import GoogleSheetTestCases
+from src.babel_validation.sources.google_sheets.google_sheet_test_cases import GoogleSheetTestCases
 
 # Configuration options
 NAMERES_TIMEOUT = 10 # If we don't get a response in 10 seconds, that's a fail.
diff --git a/tests/nodenorm/test_nodenorm_from_gsheet.py b/tests/nodenorm/test_nodenorm_from_gsheet.py
index 535d8e01..ebf4dfee 100644
--- a/tests/nodenorm/test_nodenorm_from_gsheet.py
+++ b/tests/nodenorm/test_nodenorm_from_gsheet.py
@@ -1,8 +1,7 @@
-import itertools
 import urllib.parse
 import requests
 import pytest
-from src.babel_validation.sources.google_sheet_test_cases import GoogleSheetTestCases
+from src.babel_validation.sources.google_sheets.google_sheet_test_cases import GoogleSheetTestCases
 
 # We generate a set of tests from the GoogleSheetTestCases.
 gsheet = GoogleSheetTestCases()
diff --git a/tests/test_environment/test_env.py b/tests/test_environment/test_env.py
index 9f572b5a..5302198d 100644
--- a/tests/test_environment/test_env.py
+++ b/tests/test_environment/test_env.py
@@ -1,7 +1,7 @@
 # Test whether the test environment is functional.
 import json
 
-from src.babel_validation.sources.google_sheet_test_cases import GoogleSheetTestCases
+from src.babel_validation.sources.google_sheets.google_sheet_test_cases import GoogleSheetTestCases
 
 
 def test_google_sheet_has_test_cases():

From 1f84aea3e9159f46c1f605bfff56d1f4941c2332 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 19 Feb 2026 16:23:35 -0500
Subject: [PATCH 021/126] Updated CLAUDE.md in line with updated code.

---
 CLAUDE.md | 20 ++++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/CLAUDE.md b/CLAUDE.md
index 5b8c06a4..c911bbbb 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -46,21 +46,31 @@ cd website && npm install && npm run dev   # Dev server at localhost:4321
 
 ## Architecture
 
+### Library (`src/babel_validation/`)
+
+Shared library code used by the tests and potentially other consumers.
+
+- `core/testrow.py` — `TestRow` dataclass (models a single Google Sheet test row), `TestStatus` enum, `TestResult` dataclass
+- `services/nodenorm.py` — `CachedNodeNorm`: wraps the NodeNorm `get_normalized_nodes` API with per-instance caching
+- `services/nameres.py` — `CachedNameRes`: wraps the NameRes `lookup`/`bulk-lookup` APIs with per-instance caching
+- `sources/google_sheets/google_sheet_test_cases.py` — `GoogleSheetTestCases`: downloads and parses the shared Google Sheet into `TestRow` instances and pytest `ParameterSet` lists
+- `sources/github/github_issues_test_cases.py` — `GitHubIssueTest` and `GitHubIssuesTestCases`: pull test cases embedded in GitHub issues (wiki or YAML syntax) and evaluate them against NodeNorm/NameRes
+
 ### Test Framework (`tests/`)
 
 The core of this project. Tests validate NodeNorm and NameRes services across multiple deployment environments.
 
 **Target system:** `tests/targets.ini` defines endpoints for each environment (dev, prod, test, ci, exp, localhost). Tests use `target_info` fixture to get URLs. The `conftest.py` parametrizes tests across targets via `--target` CLI option; default is `dev`.
 
-**Google Sheet integration:** ~2000+ test cases are pulled from a [shared Google Sheet](https://docs.google.com/spreadsheets/d/11zebx8Qs1Tc3ShQR9nh4HRW8QSoo8k65w_xIaftN0no/). `tests/common/google_sheet_test_cases.py` fetches and parses these into `TestRow` dataclasses. Rows marked as not expected to pass are wrapped with `pytest.mark.xfail(strict=True)`. Tests are parametrized by row, with IDs like `gsheet:row=42`.
+**Google Sheet integration:** ~2000+ test cases are pulled from a [shared Google Sheet](https://docs.google.com/spreadsheets/d/11zebx8Qs1Tc3ShQR9nh4HRW8QSoo8k65w_xIaftN0no/). `src/babel_validation/sources/google_sheets/google_sheet_test_cases.py` fetches and parses these into `TestRow` dataclasses. Rows marked as not expected to pass are wrapped with `pytest.mark.xfail(strict=True)`. Tests are parametrized by row, with IDs like `gsheet:row=42`.
 
 **Category filtering:** Google Sheet rows have a Category column. The `test_category` fixture (from conftest.py) returns a callable that tests use to `pytest.skip()` rows not matching `--category`/`--category-exclude` filters.
 
 **Test modules:**
 - `tests/nodenorm/` — NodeNorm tests (normalization accuracy, preferred IDs/labels, Biolink types, conflation, descriptions, OpenAPI spec, setid endpoint)
 - `tests/nameres/` — NameRes tests (label lookup, autocomplete, Biolink type filtering, blocklist, taxon_specific flag)
-- `tests/nodenorm/by_issue/` — Tests tied to specific GitHub issues
-- `tests/common/` — Shared utilities (`GoogleSheetTestCases`, `TestRow`)
+- `tests/nodenorm/by_issue/` — Per-issue regression tests for NodeNorm (hand-written)
+- `tests/github_issues/` — Dynamically-generated tests pulled from GitHub issue bodies via `GitHubIssuesTestCases`
 
 ### Web Applications
 
@@ -79,4 +89,6 @@ When writing new tests:
 - Use the `target_info` fixture to get NodeNorm/NameRes URLs from targets.ini
 - For Google Sheet-based tests, parametrize with `gsheet.test_rows()` and use the `test_category` fixture for category filtering
 - Use `pytest.mark.xfail(strict=True)` for known failures (strict=True means unexpected passes also fail)
-- Issue-specific tests go in `tests/nodenorm/by_issue/` or `tests/github_issues/`
+- Hand-written per-issue regression tests go in `tests/nodenorm/by_issue/`
+- GitHub-issue-driven tests are picked up automatically by `tests/github_issues/test_github_issues.py` via `GitHubIssuesTestCases`
+- Import shared classes from `src.babel_validation.*` (e.g. `from src.babel_validation.services.nodenorm import CachedNodeNorm`)

From 31b4436f20cefbe4b35b33082d644dd04ecfcf83 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 19 Feb 2026 16:23:56 -0500
Subject: [PATCH 022/126] Claude suggested moving blocklist code into src/ so
 we did.

---
 tests/nameres/test_blocklist.py | 72 +--------------------------------
 1 file changed, 1 insertion(+), 71 deletions(-)

diff --git a/tests/nameres/test_blocklist.py b/tests/nameres/test_blocklist.py
index 3e7c2c4e..3f3eb2e5 100644
--- a/tests/nameres/test_blocklist.py
+++ b/tests/nameres/test_blocklist.py
@@ -1,79 +1,9 @@
-import csv
-import io
 import logging
-import urllib.parse
-from dataclasses import dataclass
-from typing import Optional
 
 import requests
 import pytest
 
-
-# The Translator Blocklist is stored in a private GitHub repository; however,
-# we are currently using a spreadsheet to manage "Red Team" exercises where
-# multiple Translator members try out different offensive terms and log them
-# into a single spreadsheet. Eventually this test will support both, but since
-# my immediate need is to check the spreadsheet, I'll start with that.
-@dataclass(frozen=True)
-class BlocklistEntry:
-    """
-    A single Blocklist entry.
-    """
-    Query: Optional[str] = None
-    CURIE: Optional[str] = None
-    Blocked: str = None
-    Status: str = None
-    Issue: str = None
-    TreatsOnly: str = None
-    Submitter: str = None
-    Comment: str = None
-
-    def is_blocked(self):
-        """ Is this term supposed to be blocked? """
-        if self.Blocked is not None and self.Blocked == 'y':
-            return True
-        return False
-
-    @staticmethod
-    def from_gsheet_dict(row):
-        """
-        Given a dictionary from a row in Google Sheets, fill in the necessary fields.
-
-        :return: A BlocklistEntry with the filled in fields.
-        """
-
-        return BlocklistEntry(
-            Query=row.get('String (optional)', None),
-            CURIE=row.get('CURIE (optional)', None),
-            Blocked=row['Blocked?'],
-            Status=row['Status (Feb 21, 2024)'],
-            Issue=row['Blocklist issue'],
-            TreatsOnly=row['Block for "treats" only?'],
-            Submitter=row['Submitter'],
-            Comment=row['Comment (optional)'],
-        )
-
-
-def load_blocklist_from_gsheet():
-    """
-    Load the Blocklist from a Google Sheet.
-
-    :param google_sheet_id: The Google Sheet ID containing the blocklist.
-    :return: A list of BlocklistEntry.
-    """
-    google_sheet_id = '1UR2eplHBvFRwaSIVOhlB44wpfNPY1z7AVzUkqzDqIWA'
-    csv_url = f"https://docs.google.com/spreadsheets/d/{google_sheet_id}/gviz/tq?tqx=out:csv&sheet=Tests"
-
-    response = requests.get(csv_url)
-    csv_content = response.text
-
-    rows = []
-    with io.StringIO(csv_content) as f:
-        reader = csv.DictReader(f)
-        for row in reader:
-            rows.append(BlocklistEntry.from_gsheet_dict(row))
-
-    return rows
+from src.babel_validation.sources.google_sheets.blocklist import BlocklistEntry, load_blocklist_from_gsheet
 
 # Parameterize blocklist entries.
 blocklist_entries = load_blocklist_from_gsheet()

From 6b6032503e00fc069782737696216ca7caddea49 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 19 Feb 2026 16:25:56 -0500
Subject: [PATCH 023/126] Added blocklist.py where a lot of the blocklist code
 has moved.

---
 .../sources/google_sheets/blocklist.py        | 66 +++++++++++++++++++
 1 file changed, 66 insertions(+)
 create mode 100644 src/babel_validation/sources/google_sheets/blocklist.py

diff --git a/src/babel_validation/sources/google_sheets/blocklist.py b/src/babel_validation/sources/google_sheets/blocklist.py
new file mode 100644
index 00000000..6e349d46
--- /dev/null
+++ b/src/babel_validation/sources/google_sheets/blocklist.py
@@ -0,0 +1,66 @@
+import csv
+import io
+from dataclasses import dataclass
+from typing import Optional
+
+import requests
+
+
+@dataclass(frozen=True)
+class BlocklistEntry:
+    """
+    A single Blocklist entry.
+    """
+    Query: Optional[str] = None
+    CURIE: Optional[str] = None
+    Blocked: str = None
+    Status: str = None
+    Issue: str = None
+    TreatsOnly: str = None
+    Submitter: str = None
+    Comment: str = None
+
+    def is_blocked(self):
+        """ Is this term supposed to be blocked? """
+        if self.Blocked is not None and self.Blocked == 'y':
+            return True
+        return False
+
+    @staticmethod
+    def from_gsheet_dict(row):
+        """
+        Given a dictionary from a row in Google Sheets, fill in the necessary fields.
+
+        :return: A BlocklistEntry with the filled in fields.
+        """
+        return BlocklistEntry(
+            Query=row.get('String (optional)', None),
+            CURIE=row.get('CURIE (optional)', None),
+            Blocked=row['Blocked?'],
+            Status=row['Status (Feb 21, 2024)'],
+            Issue=row['Blocklist issue'],
+            TreatsOnly=row['Block for "treats" only?'],
+            Submitter=row['Submitter'],
+            Comment=row['Comment (optional)'],
+        )
+
+
+def load_blocklist_from_gsheet():
+    """
+    Load the Blocklist from a Google Sheet.
+
+    :return: A list of BlocklistEntry.
+    """
+    google_sheet_id = '1UR2eplHBvFRwaSIVOhlB44wpfNPY1z7AVzUkqzDqIWA'
+    csv_url = f"https://docs.google.com/spreadsheets/d/{google_sheet_id}/gviz/tq?tqx=out:csv&sheet=Tests"
+
+    response = requests.get(csv_url)
+    csv_content = response.text
+
+    rows = []
+    with io.StringIO(csv_content) as f:
+        reader = csv.DictReader(f)
+        for row in reader:
+            rows.append(BlocklistEntry.from_gsheet_dict(row))
+
+    return rows

From ac41e08ac56f6814dba2d776f6df86e3249009d5 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 19 Feb 2026 17:06:31 -0500
Subject: [PATCH 024/126] Refactor GitHub issue assertions into a dedicated
 package.

Each assertion type (Resolves, DoesNotResolve, ResolvesWith, ResolvesWithType,
SearchByName, Needed) is now a self-contained class in
src/babel_validation/assertions/, grouped by which service it targets
(nodenorm.py, nameres.py, common.py). A central ASSERTION_HANDLERS registry
in __init__.py maps lowercase assertion names to handler instances, and
NodeNormAssertion / NameResAssertion marker base classes allow isinstance()
checks for applicability. GitHubIssueTest.test_with_nodenorm() and
test_with_nameres() are now 3-line dispatchers. A README.md documents all
supported assertion types with examples in both wiki and YAML syntax.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 src/babel_validation/assertions/README.md     | 185 +++++++++++++++
 src/babel_validation/assertions/__init__.py   |  78 +++++++
 src/babel_validation/assertions/common.py     |  14 ++
 src/babel_validation/assertions/nameres.py    |  65 ++++++
 src/babel_validation/assertions/nodenorm.py   | 153 +++++++++++++
 .../github/github_issues_test_cases.py        | 212 ++----------------
 6 files changed, 511 insertions(+), 196 deletions(-)
 create mode 100644 src/babel_validation/assertions/README.md
 create mode 100644 src/babel_validation/assertions/__init__.py
 create mode 100644 src/babel_validation/assertions/common.py
 create mode 100644 src/babel_validation/assertions/nameres.py
 create mode 100644 src/babel_validation/assertions/nodenorm.py

diff --git a/src/babel_validation/assertions/README.md b/src/babel_validation/assertions/README.md
new file mode 100644
index 00000000..fc7a12cf
--- /dev/null
+++ b/src/babel_validation/assertions/README.md
@@ -0,0 +1,185 @@
+# BabelTest Assertion Types
+
+This package defines the assertion types that can be embedded in GitHub issue bodies and evaluated against the NodeNorm and NameRes services.
+
+## Embedding Tests in Issues
+
+Two syntaxes are supported:
+
+**Wiki syntax** (one assertion per line):
+```
+{{BabelTest|AssertionType|param1|param2|...}}
+```
+
+**YAML syntax** (multiple assertions, multiple param sets):
+````
+```yaml
+babel_tests:
+  AssertionType:
+    - param1
+    - [param1, param2]
+```
+````
+
+Assertion names are case-insensitive.
+
+---
+
+## NodeNorm Assertions
+
+These assertions test the [NodeNorm](https://nodenorm.transltr.io/docs) service.
+
+### Resolves
+
+**Applies to:** NodeNorm
+
+Verifies that every CURIE in every param_set can be resolved to a non-null result.
+
+**Parameters:** One or more CURIEs per param_set.
+
+**Wiki syntax:**
+```
+{{BabelTest|Resolves|CHEBI:15365}}
+{{BabelTest|Resolves|MONDO:0005015|DOID:9351}}
+```
+
+**YAML syntax:**
+```yaml
+babel_tests:
+  Resolves:
+    - CHEBI:15365
+    - [MONDO:0005015, DOID:9351]
+```
+
+---
+
+### DoesNotResolve
+
+**Applies to:** NodeNorm
+
+Verifies that every CURIE in every param_set fails to resolve (returns null). Use this to confirm that an identifier is intentionally not normalizable.
+
+**Parameters:** One or more CURIEs per param_set.
+
+**Wiki syntax:**
+```
+{{BabelTest|DoesNotResolve|FAKENS:99999}}
+```
+
+**YAML syntax:**
+```yaml
+babel_tests:
+  DoesNotResolve:
+    - FAKENS:99999
+```
+
+---
+
+### ResolvesWith
+
+**Applies to:** NodeNorm
+
+Verifies that all CURIEs in a param_set resolve to the **identical** normalized result. Use this to assert that two or more identifiers are equivalent (same clique in NodeNorm).
+
+**Parameters:** Two or more CURIEs per param_set. All must resolve and produce the same result.
+
+**Wiki syntax:**
+```
+{{BabelTest|ResolvesWith|CHEBI:15365|PUBCHEM.COMPOUND:1}}
+```
+
+**YAML syntax:**
+```yaml
+babel_tests:
+  ResolvesWith:
+    - [CHEBI:15365, PUBCHEM.COMPOUND:1]
+    - [MONDO:0005015, DOID:9351]
+```
+
+---
+
+### ResolvesWithType
+
+**Applies to:** NodeNorm
+
+Verifies that one or more CURIEs resolve with a specific Biolink type in their `type` list.
+
+**Parameters:** Each param_set must have at least two elements. The **first** element is the expected Biolink type (e.g. `biolink:Gene`); the remaining elements are CURIEs to check.
+
+**Wiki syntax:**
+```
+{{BabelTest|ResolvesWithType|biolink:Gene|NCBIGene:1}}
+```
+
+**YAML syntax:**
+```yaml
+babel_tests:
+  ResolvesWithType:
+    - [biolink:Gene, NCBIGene:1, HGNC:5]
+```
+
+---
+
+## NameRes Assertions
+
+These assertions test the [NameRes](https://name-lookup.transltr.io/docs) service.
+
+### SearchByName
+
+**Applies to:** NameRes
+
+Verifies that a name search returns an expected CURIE within the top-N results (default N=5).
+
+The expected CURIE is first normalized via NodeNorm (with drug/chemical conflation enabled) to find its preferred identifier; that identifier must appear in the top results.
+
+**Parameters:** Each param_set must have at least two elements: the **search query string** and the **expected CURIE**.
+
+**Wiki syntax:**
+```
+{{BabelTest|SearchByName|water|CHEBI:15377}}
+```
+
+**YAML syntax:**
+```yaml
+babel_tests:
+  SearchByName:
+    - [water, CHEBI:15377]
+    - [diabetes, MONDO:0005015]
+```
+
+---
+
+## Special Assertions
+
+### Needed
+
+**Applies to:** NodeNorm and NameRes
+
+A placeholder that always fails. Use this on issues where you know a test is required but haven't written it yet.
+
+**Wiki syntax:**
+```
+{{BabelTest|Needed}}
+```
+
+**YAML syntax:**
+```yaml
+babel_tests:
+  Needed:
+    - placeholder
+```
+
+---
+
+## Adding a New Assertion Type
+
+1. Choose the right module:
+   - `nodenorm.py` — for NodeNorm-only assertions (subclass `NodeNormAssertion`)
+   - `nameres.py` — for NameRes-only assertions (subclass `NameResAssertion`)
+   - `common.py` — for assertions that apply to both services (subclass `AssertionHandler`)
+
+2. Define the class with `NAME`, `DESCRIPTION`, and the relevant `test_with_nodenorm()` / `test_with_nameres()` method(s).
+
+3. Import it in `__init__.py` and add an instance to `ASSERTION_HANDLERS`.
+
+4. Document it in this README.
diff --git a/src/babel_validation/assertions/__init__.py b/src/babel_validation/assertions/__init__.py
new file mode 100644
index 00000000..bc6cecff
--- /dev/null
+++ b/src/babel_validation/assertions/__init__.py
@@ -0,0 +1,78 @@
+"""
+babel_validation.assertions
+===========================
+
+This package defines the assertion types that can be embedded in GitHub issue bodies
+and evaluated against the NodeNorm and NameRes services.
+
+Supported assertion types are registered in ASSERTION_HANDLERS. To see everything
+that is currently supported, scan that dict or read assertions/README.md.
+
+Adding a new assertion type
+---------------------------
+1. Create a subclass of AssertionHandler (or NodeNormAssertion / NameResAssertion)
+   in the appropriate module (nodenorm.py, nameres.py, or common.py).
+2. Set NAME and DESCRIPTION class attributes.
+3. Override test_with_nodenorm() and/or test_with_nameres().
+4. Import it here and add an instance to ASSERTION_HANDLERS.
+"""
+
+from typing import Iterator
+
+from src.babel_validation.core.testrow import TestResult
+
+
+class AssertionHandler:
+    """Base class for all BabelTest assertion handlers."""
+    NAME: str           # lowercase assertion name as used in issue bodies
+    DESCRIPTION: str    # one-line human-readable description
+
+    def test_with_nodenorm(self, param_sets: list[list[str]], nodenorm,
+                           label: str = "") -> Iterator[TestResult]:
+        """Evaluate this assertion against NodeNorm. Returns [] if not applicable."""
+        return []
+
+    def test_with_nameres(self, param_sets: list[list[str]], nodenorm, nameres,
+                          pass_if_found_in_top: int = 5,
+                          label: str = "") -> Iterator[TestResult]:
+        """Evaluate this assertion against NameRes. Returns [] if not applicable."""
+        return []
+
+
+class NodeNormAssertion(AssertionHandler):
+    """Marker base class for assertions that test NodeNorm.
+
+    Subclasses must override test_with_nodenorm().
+    test_with_nameres() returns [] and need not be overridden.
+    Use isinstance(handler, NodeNormAssertion) to check applicability.
+    """
+    pass
+
+
+class NameResAssertion(AssertionHandler):
+    """Marker base class for assertions that test NameRes.
+
+    Subclasses must override test_with_nameres().
+    test_with_nodenorm() returns [] and need not be overridden.
+    Use isinstance(handler, NameResAssertion) to check applicability.
+    """
+    pass
+
+
+# Registry — import submodules after base classes are defined to avoid circular imports.
+from src.babel_validation.assertions.nodenorm import (  # noqa: E402
+    ResolvesHandler, DoesNotResolveHandler, ResolvesWithHandler, ResolvesWithTypeHandler,
+)
+from src.babel_validation.assertions.nameres import SearchByNameHandler  # noqa: E402
+from src.babel_validation.assertions.common import NeededHandler  # noqa: E402
+
+ASSERTION_HANDLERS: dict[str, AssertionHandler] = {
+    h.NAME: h for h in [
+        ResolvesHandler(),
+        DoesNotResolveHandler(),
+        ResolvesWithHandler(),
+        ResolvesWithTypeHandler(),
+        SearchByNameHandler(),
+        NeededHandler(),
+    ]
+}
diff --git a/src/babel_validation/assertions/common.py b/src/babel_validation/assertions/common.py
new file mode 100644
index 00000000..f9f1aabf
--- /dev/null
+++ b/src/babel_validation/assertions/common.py
@@ -0,0 +1,14 @@
+from src.babel_validation.assertions import AssertionHandler
+from src.babel_validation.core.testrow import TestResult, TestStatus
+
+
+class NeededHandler(AssertionHandler):
+    """Placeholder assertion indicating that a test still needs to be written for this issue."""
+    NAME = "needed"
+    DESCRIPTION = "Marks an issue as needing a test — always fails as a reminder to add real assertions."
+
+    def test_with_nodenorm(self, param_sets, nodenorm, label=""):
+        return [TestResult(status=TestStatus.Failed, message=f"Test needed for issue")]
+
+    def test_with_nameres(self, param_sets, nodenorm, nameres, pass_if_found_in_top=5, label=""):
+        return [TestResult(status=TestStatus.Failed, message=f"Test needed for issue")]
diff --git a/src/babel_validation/assertions/nameres.py b/src/babel_validation/assertions/nameres.py
new file mode 100644
index 00000000..cec0ec17
--- /dev/null
+++ b/src/babel_validation/assertions/nameres.py
@@ -0,0 +1,65 @@
+import json
+from typing import Iterator
+
+from src.babel_validation.assertions import NameResAssertion
+from src.babel_validation.core.testrow import TestResult, TestStatus
+from src.babel_validation.services.nameres import CachedNameRes
+from src.babel_validation.services.nodenorm import CachedNodeNorm
+
+
+class SearchByNameHandler(NameResAssertion):
+    """Test that a name search returns an expected CURIE in the top-N results in NameRes."""
+    NAME = "searchbyname"
+    DESCRIPTION = (
+        "Each param_set must have at least two elements: a search query string and an expected CURIE. "
+        "The test passes if the CURIE's normalized identifier appears within the top N results "
+        "(default N=5) when NameRes looks up the search query."
+    )
+
+    def test_with_nameres(self, param_sets: list[list[str]], nodenorm: CachedNodeNorm,
+                          nameres: CachedNameRes, pass_if_found_in_top: int = 5,
+                          label: str = "") -> Iterator[TestResult]:
+        if not param_sets:
+            return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {label}")]
+
+        yielded_values = False
+        for params in param_sets:
+            if len(params) < 2:
+                yield TestResult(status=TestStatus.Failed, message=f"Two parameters expected for SearchByName in {label}, but params = {params}")
+                yielded_values = True
+                continue
+
+            [search_query, expected_curie_from_test, *args] = params
+            expected_curie_result = nodenorm.normalize_curie(expected_curie_from_test, drug_chemical_conflate='true')
+            if not expected_curie_result:
+                yield TestResult(status=TestStatus.Failed, message=f"Unable to normalize CURIE {expected_curie_from_test} in {label}")
+                yielded_values = True
+                continue
+
+            expected_curie = expected_curie_result['id']['identifier']
+            expected_curie_label = expected_curie_result['id']['label']
+            expected_curie_string = f"Expected CURIE {expected_curie_from_test}, normalized to {expected_curie} '{expected_curie_label}'"
+
+            # Search for the expected CURIE in the first {pass_if_found_in_top} results.
+            results = nameres.lookup(search_query, autocomplete='false', limit=(2 * pass_if_found_in_top))
+            if not results:
+                yield TestResult(status=TestStatus.Failed, message=f"No results found for '{search_query}' on NameRes {nameres} ({expected_curie_string}")
+                yielded_values = True
+                continue
+
+            curies = [result['curie'] for result in results]
+            try:
+                found_index = curies.index(expected_curie)
+            except ValueError:
+                yield TestResult(status=TestStatus.Failed, message=f"{expected_curie_string} not found when searching for '{search_query}' in NameRes {nameres}: {json.dumps(results, indent=2, sort_keys=True)}")
+                yielded_values = True
+                continue
+
+            if found_index <= pass_if_found_in_top:
+                yield TestResult(status=TestStatus.Passed, message=f"{expected_curie_string} found at index {found_index + 1} on NameRes {nameres}")
+            else:
+                yield TestResult(status=TestStatus.Failed, message=f"{expected_curie_string} found at index {found_index + 1} which is greater than {pass_if_found_in_top} on NameRes {nameres}")
+            yielded_values = True
+
+        if not yielded_values:
+            return [TestResult(status=TestStatus.Failed, message=f"No test results returned in {label}")]
diff --git a/src/babel_validation/assertions/nodenorm.py b/src/babel_validation/assertions/nodenorm.py
new file mode 100644
index 00000000..e00a9dd0
--- /dev/null
+++ b/src/babel_validation/assertions/nodenorm.py
@@ -0,0 +1,153 @@
+import json
+from typing import Iterator
+
+from src.babel_validation.assertions import NodeNormAssertion
+from src.babel_validation.core.testrow import TestResult, TestStatus
+from src.babel_validation.services.nodenorm import CachedNodeNorm
+
+
+class ResolvesHandler(NodeNormAssertion):
+    """Test that every CURIE in every param_set resolves in NodeNorm."""
+    NAME = "resolves"
+    DESCRIPTION = "Each CURIE in each param_set must resolve to a non-null result in NodeNorm."
+
+    def test_with_nodenorm(self, param_sets: list[list[str]], nodenorm: CachedNodeNorm,
+                           label: str = "") -> Iterator[TestResult]:
+        if not param_sets:
+            return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {label}")]
+
+        curies_to_resolve = [param for params in param_sets for param in params]
+        nodenorm.normalize_curies(curies_to_resolve)
+
+        yielded_values = False
+        for index, curies in enumerate(param_sets):
+            if not curies:
+                return TestResult(status=TestStatus.Failed, message=f"No parameters provided in paramset {index} in {label}")
+
+            for curie in curies:
+                result = nodenorm.normalize_curie(curie)
+                if not result:
+                    yield TestResult(status=TestStatus.Failed, message=f"Could not resolve {curie} with NodeNormalization service {nodenorm}")
+                    yielded_values = True
+                else:
+                    yield TestResult(status=TestStatus.Passed, message=f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\") with NodeNormalization service {nodenorm}")
+                    yielded_values = True
+
+        if not yielded_values:
+            return [TestResult(status=TestStatus.Failed, message=f"No test results returned in {label}")]
+
+
+class DoesNotResolveHandler(NodeNormAssertion):
+    """Test that every CURIE in every param_set does NOT resolve in NodeNorm."""
+    NAME = "doesnotresolve"
+    DESCRIPTION = "Each CURIE in each param_set must fail to resolve (return null) in NodeNorm."
+
+    def test_with_nodenorm(self, param_sets: list[list[str]], nodenorm: CachedNodeNorm,
+                           label: str = "") -> Iterator[TestResult]:
+        if not param_sets:
+            return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {label}")]
+
+        curies_to_resolve = [param for params in param_sets for param in params]
+        nodenorm.normalize_curies(curies_to_resolve)
+
+        yielded_values = False
+        for index, curies in enumerate(param_sets):
+            if not curies:
+                yield TestResult(status=TestStatus.Failed, message=f"No parameters provided in paramset {index} in {label}")
+                continue
+
+            for curie in curies:
+                result = nodenorm.normalize_curie(curie)
+                if not result:
+                    yield TestResult(status=TestStatus.Passed, message=f"Could not resolve {curie} with NodeNormalization service {nodenorm} as expected")
+                    yielded_values = True
+                else:
+                    yield TestResult(status=TestStatus.Failed, message=f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\") with NodeNormalization service {nodenorm}, but expected not to resolve")
+                    yielded_values = True
+
+        if not yielded_values:
+            return [TestResult(status=TestStatus.Failed, message=f"No test results returned in {label}")]
+
+
+class ResolvesWithHandler(NodeNormAssertion):
+    """Test that all CURIEs in a param_set resolve to the same normalized result in NodeNorm."""
+    NAME = "resolveswith"
+    DESCRIPTION = (
+        "All CURIEs within each param_set must resolve to the identical normalized result. "
+        "Use this to assert that two identifiers are equivalent."
+    )
+
+    def test_with_nodenorm(self, param_sets: list[list[str]], nodenorm: CachedNodeNorm,
+                           label: str = "") -> Iterator[TestResult]:
+        if not param_sets:
+            return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {label}")]
+
+        curies_to_resolve = [param for params in param_sets for param in params]
+        nodenorm.normalize_curies(curies_to_resolve)
+
+        yielded_values = False
+        for curies in param_sets:
+            results = nodenorm.normalize_curies(curies)
+
+            # Find the first good result.
+            first_good_result = None
+            for curie, result in results.items():
+                if result is not None and first_good_result is None:
+                    first_good_result = result
+                    break
+
+            if first_good_result is None:
+                return [TestResult(status=TestStatus.Failed, message=f"None of the CURIEs {curies} could be resolved on {nodenorm}")]
+
+            # Check all the results.
+            for curie, result in results.items():
+                if result is None:
+                    yield TestResult(status=TestStatus.Failed, message=f"CURIE {curie} could not be resolved, and so is not equal to the expected result {json.dumps(first_good_result, indent=2, sort_keys=True)} on {nodenorm}")
+                    yielded_values = True
+                    continue
+
+                if json.dumps(first_good_result, sort_keys=True) == json.dumps(result, sort_keys=True):
+                    yield TestResult(status=TestStatus.Passed, message=f"Resolved {curie} to the expected result {json.dumps(first_good_result, indent=2, sort_keys=True)}")
+                    yielded_values = True
+                else:
+                    yield TestResult(status=TestStatus.Failed, message=f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\"), but expected {first_good_result['id']['identifier']} ({first_good_result['type'][0]}, \"{first_good_result['id']['label']}\") on {nodenorm}")
+                    yielded_values = True
+
+        if not yielded_values:
+            return [TestResult(status=TestStatus.Failed, message=f"No test results returned in {label}")]
+
+
+class ResolvesWithTypeHandler(NodeNormAssertion):
+    """Test that CURIEs resolve with a specific Biolink type in NodeNorm."""
+    NAME = "resolveswithtype"
+    DESCRIPTION = (
+        "Each param_set must have at least two elements: the first is the expected Biolink type "
+        "(e.g. 'biolink:Gene'), and the remainder are CURIEs that must resolve with that type."
+    )
+
+    def test_with_nodenorm(self, param_sets: list[list[str]], nodenorm: CachedNodeNorm,
+                           label: str = "") -> Iterator[TestResult]:
+        if not param_sets:
+            return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {label}")]
+
+        yielded_values = False
+        for index, params in enumerate(param_sets):
+            if len(params) < 2:
+                yield TestResult(status=TestStatus.Failed, message=f"Too few parameters provided in param set {index} in {label}: {params}")
+                continue
+
+            expected_biolink_type = params[0]
+            curies = params[1:]
+
+            results = nodenorm.normalize_curies(curies)
+            for curie in curies:
+                biolink_types = results[curie]['type']
+                if expected_biolink_type in biolink_types:
+                    yield TestResult(status=TestStatus.Passed, message=f"Biolink types {biolink_types} for CURIE {curie} includes expected Biolink type {expected_biolink_type}")
+                    yielded_values = True
+                else:
+                    yield TestResult(status=TestStatus.Failed, message=f"Biolink types {biolink_types} for CURIE {curie} does not include expected Biolink type {expected_biolink_type}")
+                    yielded_values = True
+
+        if not yielded_values:
+            return [TestResult(status=TestStatus.Failed, message=f"No test results returned in {label}")]
diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index bc26ece4..f7c7b821 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -5,10 +5,11 @@
 
 import yaml
 
-from src.babel_validation.core.testrow import TestResult, TestStatus
 from github import Github, Auth, Issue
 from tqdm import tqdm
 
+from src.babel_validation.assertions import ASSERTION_HANDLERS
+from src.babel_validation.core.testrow import TestResult
 from src.babel_validation.services.nameres import CachedNameRes
 from src.babel_validation.services.nodenorm import CachedNodeNorm
 
@@ -30,194 +31,17 @@ def __str__(self):
         return f"{self.github_issue.repository.organization.name}/{self.github_issue.repository.name}#{self.github_issue.number}: {self.assertion}({len(self.param_sets)} param sets: {json.dumps(self.param_sets)})"
 
     def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
-        yielded_values = False
-        match self.assertion.lower():
-            case "resolves":
-                if not self.param_sets:
-                    return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")]
-
-                curies_to_resolve = [param for params in self.param_sets for param in params]
-                nodenorm.normalize_curies(curies_to_resolve)
-
-                # Enumerate curies.
-                for index, curies in enumerate(self.param_sets):
-                    if not curies:
-                        return TestResult(status=TestStatus.Failed, message=f"No parameters provided in paramset {index} in {self}")
-
-                    for curie in curies:
-                        result = nodenorm.normalize_curie(curie)
-                        if not result:
-                            yield TestResult(status=TestStatus.Failed, message=f"Could not resolve {curie} with NodeNormalization service {nodenorm}")
-                            yielded_values = True
-                        else:
-                            yield TestResult(status=TestStatus.Passed, message=f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\") with NodeNormalization service {nodenorm}")
-                            yielded_values = True
-
-            case "doesnotresolve":
-                if not self.param_sets:
-                    return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")]
-
-                curies_to_resolve = [param for params in self.param_sets for param in params]
-                nodenorm.normalize_curies(curies_to_resolve)
-
-                # Enumerate curies.
-                for index, curies in enumerate(self.param_sets):
-                    if not curies:
-                        yield TestResult(status=TestStatus.Failed, message=f"No parameters provided in paramset {index} in {self}")
-                        continue
-
-                    for curie in curies:
-                        result = nodenorm.normalize_curie(curie)
-                        if not result:
-                            yield TestResult(status=TestStatus.Passed, message=f"Could not resolve {curie} with NodeNormalization service {nodenorm} as expected")
-                            yielded_values = True
-                        else:
-                            yield TestResult(status=TestStatus.Failed, message=f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\") with NodeNormalization service {nodenorm}, but expected not to resolve")
-                            yielded_values = True
-
-                if not yielded_values:
-                    return [TestResult(status=TestStatus.Failed, message=f"No test results returned in {self}")]
-
-            case "resolveswith":
-                if not self.param_sets:
-                    return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")]
-
-                curies_to_resolve = [param for params in self.param_sets for param in params]
-                nodenorm.normalize_curies(curies_to_resolve)
-
-                for curies in self.param_sets:
-                    results = nodenorm.normalize_curies(curies)
-
-                    # Find the first good result.
-                    first_good_result = None
-                    for curie, result in results.items():
-                        if result is not None and first_good_result is None:
-                            first_good_result = result
-                            break
-
-                    if first_good_result is None:
-                        return [TestResult(status=TestStatus.Failed, message=f"None of the CURIEs {curies} could be resolved on {nodenorm}")]
-
-                    # Check all the results.
-                    for curie, result in results.items():
-                        if result is None:
-                            yield TestResult(status=TestStatus.Failed, message=f"CURIE {curie} could not be resolved, and so is not equal to the expected result {json.dumps(first_good_result, indent=2, sort_keys=True)} on {nodenorm}")
-                            yielded_values = True
-                            continue
-
-                        if json.dumps(first_good_result, sort_keys=True) == json.dumps(result, sort_keys=True):
-                            yield TestResult(status=TestStatus.Passed, message=f"Resolved {curie} to the expected result {json.dumps(first_good_result, indent=2, sort_keys=True)}")
-                            yielded_values = True
-
-                        else:
-                            yield TestResult(status=TestStatus.Failed, message=f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\"), but expected {first_good_result['id']['identifier']} ({first_good_result['type'][0]}, \"{first_good_result['id']['label']}\") on {nodenorm}")
-                            yielded_values = True
-
-                if not yielded_values:
-                    return [TestResult(status=TestStatus.Failed, message=f"No test results returned in {self}")]
-
-            case "resolveswithtype":
-                if not self.param_sets:
-                    return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")]
-
-                for index, params in enumerate(self.param_sets):
-                    if len(params) < 2:
-                        yield TestResult(status=TestStatus.Failed, message=f"Too few parameters provided in param set {index} in {self}: {params}")
-                        continue
-                    expected_biolink_type = params[0]
-                    curies = params[1:]
-
-                    results = nodenorm.normalize_curies(curies)
-                    for curie in curies:
-                        biolink_types = results[curie]['type']
-                        if expected_biolink_type in biolink_types:
-                            yield TestResult(status=TestStatus.Passed, message=f"Biolink types {biolink_types} for CURIE {curie} includes expected Biolink type {expected_biolink_type}")
-                            yielded_values = True
-                        else:
-                            yield TestResult(status=TestStatus.Failed, message=f"Biolink types {biolink_types} for CURIE {curie} does not include expected Biolink type {expected_biolink_type}")
-                            yielded_values = True
-
-            # These are NameRes tests, not NodeNorm tests.
-            case "searchbyname":
-                return []
-
-            # This is a special assertion to remind ourselves that we need to add tests here.
-            case "needed":
-                return [TestResult(status=TestStatus.Failed, message=f"Test needed for issue")]
-
-            case _:
-                raise ValueError(f"Unknown assertion type for {self}: {self.assertion}")
-
-        if not yielded_values:
-            return [TestResult(status=TestStatus.Failed, message=f"No test results returned in {self}")]
-
-        return [
-            TestResult(status=TestStatus.Failed, message=f"Code malfunctioned in {self} -- code reached")
-        ]
+        handler = ASSERTION_HANDLERS.get(self.assertion.lower())
+        if handler is None:
+            raise ValueError(f"Unknown assertion type for {self}: {self.assertion}")
+        return handler.test_with_nodenorm(self.param_sets, nodenorm, label=str(self))
 
     def test_with_nameres(self, nodenorm: CachedNodeNorm, nameres: CachedNameRes, pass_if_found_in_top=5) -> Iterator[TestResult]:
-        yielded_values = False
-        match self.assertion.lower():
-            case "searchbyname":
-                if not self.param_sets:
-                    return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {self}")]
-
-                for params in self.param_sets:
-                    if len(params) < 2:
-                        yield TestResult(status=TestStatus.Failed, message=f"Two parameters expected for SearchByName in {self}, but params = {params}")
-                        yielded_values = True
-                        continue
-
-                    [search_query, expected_curie_from_test, *args] = params
-                    expected_curie_result = nodenorm.normalize_curie(expected_curie_from_test, drug_chemical_conflate='true')
-                    if not expected_curie_result:
-                        yield TestResult(status=TestStatus.Failed, message=f"Unable to normalize CURIE {expected_curie_from_test} in {self}")
-                        yielded_values = True
-                        continue
-                    expected_curie = expected_curie_result['id']['identifier']
-                    expected_curie_label = expected_curie_result['id']['label']
-                    expected_curie_string = f"Expected CURIE {expected_curie_from_test}, normalized to {expected_curie} '{expected_curie_label}'"
-
-                    # We're going to search for the search name and see if we can find the expected CURIE
-                    # in the first {pass_if_found_in_top} results.
-                    results = nameres.lookup(search_query, autocomplete='false', limit=(2*pass_if_found_in_top))
-                    if not results:
-                        yield TestResult(status=TestStatus.Failed, message=f"No results found for '{search_query}' on NameRes {nameres} ({expected_curie_string}")
-                        yielded_values = True
-                        continue
-
-                    curies = [result['curie'] for result in results]
-                    try:
-                        found_index = curies.index(expected_curie)
-                    except ValueError:
-                        yield TestResult(status=TestStatus.Failed, message=f"{expected_curie_string} not found when searching for '{search_query}' in NameRes {nameres}: {json.dumps(results, indent=2, sort_keys=True)}")
-                        yielded_values = True
-                        continue
-
-                    if found_index <= pass_if_found_in_top:
-                        yield TestResult(status=TestStatus.Passed, message=f"{expected_curie_string} found at index {found_index + 1} on NameRes {nameres}")
-                    else:
-                        yield TestResult(status=TestStatus.Failed, message=f"{expected_curie_string} found at index {found_index + 1} which is greater than {pass_if_found_in_top} on NameRes {nameres}")
-                    yielded_values = True
-
-            # These are NodeNorm tests, not NameRes tests.
-            case "resolves" | "doesnotresolve" | "resolveswith" | "resolveswithtype":
-                # Nothing we can do about this with NameRes.
-                return []
-
-            # This is a special assertion to remind ourselves that we need to add tests here.
-            case "needed":
-                return [TestResult(status=TestStatus.Failed, message=f"Test needed for issue")]
-
-            case _:
-                raise ValueError(f"Unknown assertion type: {self.assertion}")
-
-        if not yielded_values:
-            return [TestResult(status=TestStatus.Failed, message=f"No test results returned in {self}")]
-
-        return [
-            TestResult(status=TestStatus.Failed, message=f"Code malfunctioned in {self} -- code reached")
-        ]
+        handler = ASSERTION_HANDLERS.get(self.assertion.lower())
+        if handler is None:
+            raise ValueError(f"Unknown assertion type: {self.assertion}")
+        return handler.test_with_nameres(self.param_sets, nodenorm, nameres, pass_if_found_in_top, label=str(self))
+
 
 class GitHubIssuesTestCases:
     """
@@ -263,25 +87,22 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
         """
         Extract test rows from a single GitHub issue.
 
-        This is where we describe our test case recording language. I think we should support two formats:
+        Two syntaxes are supported:
         - Wiki syntax: {{BabelTest|AssertionType|param1|param2|...}}
-        - YAML syntax, which requires a YAML type box that looks like this:
+        - YAML syntax:
 
         ```yaml
         babel_tests:
             assertion:
             - param1
             - ['param1', 'param2']
-            - {'param1': 'value1', 'param2': 'value2'}
         ```
 
-        We currently support the following assertions:
-        - Resolves: Test whether any of the parameters can be resolved.
-        - DoesNotResolve: Ensure that the parameters do not resolve.
-        - ResolvesWith: Test whether all the parameters resolve together.
+        For the full list of supported assertion types and their parameters, see
+        src/babel_validation/assertions/README.md or inspect ASSERTION_HANDLERS.keys().
 
         :param github_issue: A single GitHub issue to extract test cases from.
-        :return: An iterator over TestRows.
+        :return: A list of GitHubIssueTest objects found in the issue body.
         """
 
         github_issue_id = f"{github_issue.number}"
@@ -347,7 +168,6 @@ def get_all_issues(self, github_repositories = None) -> Iterator[Issue.Issue]:
 
         :param github_repositories: A list of GitHub repositories to search for test cases. If none is provided,
             we default to the list specified when creating this GitHubIssuesTestCases class.
-        :param include_issues_without_tests: If true, include issues that do not contain any test cases. Default: false.
         :return: A list of TestRows to process.
         """
         if github_repositories is None:

From ffbc70fe3f59ad912ed1e1291b91c8ddb444cf5e Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 19 Feb 2026 19:03:21 -0500
Subject: [PATCH 025/126] Use pytest subtests for GitHub issue tests so all
 assertions run independently.

Bumps pytest to >=9.0 (which includes built-in subtests support). Each
TestResult is now evaluated in its own subtest block, so a failure no longer
short-circuits the rest. Adds post-loop state-consistency subtests: a closed
issue with failing tests fails with a "consider reopening" message, and an open
issue where all tests pass emits an xfail "consider closing" hint.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 pyproject.toml                            |  2 +-
 tests/github_issues/test_github_issues.py | 43 +++++++++++++++++------
 uv.lock                                   |  8 ++---
 3 files changed, 38 insertions(+), 15 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6584107b..2dca9751 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,7 +11,7 @@ dependencies = [
     "dotenv>=0.9.9",
     "openapi-spec-validator>=0.7.2",
     "pygithub>=2.8.1",
-    "pytest>=8.4.2",
+    "pytest>=9.0",
     "requests>=2.32.5",
     "tqdm>=4.67.1",
 ]
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 94252f22..4d19867d 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -25,7 +25,7 @@ def get_github_issue_id(github_issue: Issue.Issue):
 ])
 
 @pytest.mark.parametrize("github_issue", github_issues_test_cases.get_all_issues())
-def test_github_issue(target_info, github_issue, selected_github_issues):
+def test_github_issue(target_info, github_issue, selected_github_issues, subtests):
     # If github_issues is provided, we can skip all others.
     if selected_github_issues:
         # Check all three possible ways in which this issue might be specified.
@@ -55,20 +55,43 @@ def test_github_issue(target_info, github_issue, selected_github_issues):
         pytest.skip(f"No tests found in issue {github_issue}")
         return
 
+    issue_id = get_github_issue_id(github_issue)
+    subtests_passed = 0
+    subtests_failed = 0
+
     for test_issue in tests:
         results_nodenorm = test_issue.test_with_nodenorm(nodenorm)
         results_nameres = test_issue.test_with_nameres(nodenorm, nameres)
 
         for result in itertools.chain(results_nodenorm, results_nameres):
-            match result:
-                case TestResult(status=TestStatus.Passed, message=message):
-                    assert True, f"{get_github_issue_id(github_issue)} ({github_issue.state}): {message}"
+            with subtests.test(msg=f"{issue_id} ({github_issue.state}): {result.message}"):
+                match result:
+                    case TestResult(status=TestStatus.Passed, message=message):
+                        subtests_passed += 1
+                        assert True, f"{issue_id} ({github_issue.state}): {message}"
+
+                    case TestResult(status=TestStatus.Failed, message=message):
+                        subtests_failed += 1
+                        assert False, f"{issue_id} ({github_issue.state}): {message}"
+
+                    case TestResult(status=TestStatus.Skipped, message=message):
+                        pytest.skip(f"{issue_id} ({github_issue.state}): {message}")
 
-                case TestResult(status=TestStatus.Failed, message=message):
-                    assert False, f"{get_github_issue_id(github_issue)} ({github_issue.state}): {message}"
+                    case _:
+                        subtests_failed += 1
+                        assert False, f"Unknown result from {issue_id}: {result}"
 
-                case TestResult(status=TestStatus.Skipped, message=message):
-                    pytest.skip(f"{get_github_issue_id(github_issue)} ({github_issue.state}): {message}")
+    # Issue state vs. test results consistency checks
+    if github_issue.state == "closed" and subtests_failed > 0:
+        with subtests.test(msg=f"Issue state: {issue_id} is closed but has failing tests"):
+            assert False, (
+                f"Issue {issue_id} is closed but {subtests_failed} subtest(s) failed. "
+                f"Consider reopening: {github_issue.html_url}"
+            )
 
-                case _:
-                    assert False, f"Unknown result from {get_github_issue_id(github_issue)}: {result}"
+    if github_issue.state == "open" and subtests_passed > 0 and subtests_failed == 0:
+        with subtests.test(msg=f"Issue state: {issue_id} is open but all tests pass"):
+            pytest.xfail(
+                f"Issue {issue_id} is open but all {subtests_passed} subtest(s) passed. "
+                f"Consider closing: {github_issue.html_url}"
+            )
diff --git a/uv.lock b/uv.lock
index 8c42f024..07752575 100644
--- a/uv.lock
+++ b/uv.lock
@@ -33,7 +33,7 @@ requires-dist = [
     { name = "dotenv", specifier = ">=0.9.9" },
     { name = "openapi-spec-validator", specifier = ">=0.7.2" },
     { name = "pygithub", specifier = ">=2.8.1" },
-    { name = "pytest", specifier = ">=8.4.2" },
+    { name = "pytest", specifier = ">=9.0" },
     { name = "requests", specifier = ">=2.32.5" },
     { name = "tqdm", specifier = ">=4.67.1" },
 ]
@@ -601,7 +601,7 @@ wheels = [
 
 [[package]]
 name = "pytest"
-version = "8.4.2"
+version = "9.0.2"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "colorama", marker = "sys_platform == 'win32'" },
@@ -610,9 +610,9 @@ dependencies = [
     { name = "pluggy" },
     { name = "pygments" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/a3/5c/00a0e072241553e1a7496d638deababa67c5058571567b92a7eaa258397c/pytest-8.4.2.tar.gz", hash = "sha256:86c0d0b93306b961d58d62a4db4879f27fe25513d4b969df351abdddb3c30e01", size = 1519618, upload-time = "2025-09-04T14:34:22.711Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/d1/db/7ef3487e0fb0049ddb5ce41d3a49c235bf9ad299b6a25d5780a89f19230f/pytest-9.0.2.tar.gz", hash = "sha256:75186651a92bd89611d1d9fc20f0b4345fd827c41ccd5c299a868a05d70edf11", size = 1568901, upload-time = "2025-12-06T21:30:51.014Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/a8/a4/20da314d277121d6534b3a980b29035dcd51e6744bd79075a6ce8fa4eb8d/pytest-8.4.2-py3-none-any.whl", hash = "sha256:872f880de3fc3a5bdc88a11b39c9710c3497a547cfa9320bc3c5e62fbf272e79", size = 365750, upload-time = "2025-09-04T14:34:20.226Z" },
+    { url = "https://files.pythonhosted.org/packages/3b/ab/b3226f0bd7cdcf710fbede2b3548584366da3b19b5021e74f5bde2a8fa3f/pytest-9.0.2-py3-none-any.whl", hash = "sha256:711ffd45bf766d5264d487b917733b453d917afd2b0ad65223959f59089f875b", size = 374801, upload-time = "2025-12-06T21:30:49.154Z" },
 ]
 
 [[package]]

From 1524b2794a316b635335f485be89a6b1cf9970e2 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 19 Feb 2026 19:05:23 -0500
Subject: [PATCH 026/126] Avoid slow GitHub API calls when building issue IDs.

Previously, get_github_issue_id() and GitHubIssueTest.__str__() both resolved
the org/repo name via github_issue.repository.organization.name, which triggers
lazy PyGitHub API calls. Parse org/repo from html_url instead (always present
in the issue JSON, no extra round-trip needed). Also resolves the TODO comment
in get_test_issues_from_issue().

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .../sources/github/github_issues_test_cases.py    | 15 ++++++++-------
 tests/github_issues/test_github_issues.py         |  3 ++-
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index f7c7b821..269001e2 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -24,11 +24,16 @@ def __init__(self, github_issue: Issue.Issue, assertion: str, param_sets: list[l
         if not isinstance(self.param_sets, list):
             raise ValueError(f"param_sets must be a list when creating a GitHubIssueTest({self.github_issue}, {self.assertion}, {self.param_sets})")
 
+        # Derive repo_id from html_url (e.g. https://github.com/org/repo/issues/1 → "org/repo")
+        # to avoid slow lazy API calls via github_issue.repository.organization.name.
+        parts = github_issue.html_url.split('/')
+        self.repo_id = f"{parts[3]}/{parts[4]}"
+
         self.logger = logging.getLogger(str(self))
         self.logger.info(f"Creating GitHubIssueTest for {github_issue.html_url} {assertion}({param_sets})")
 
     def __str__(self):
-        return f"{self.github_issue.repository.organization.name}/{self.github_issue.repository.name}#{self.github_issue.number}: {self.assertion}({len(self.param_sets)} param sets: {json.dumps(self.param_sets)})"
+        return f"{self.repo_id}#{self.github_issue.number}: {self.assertion}({len(self.param_sets)} param sets: {json.dumps(self.param_sets)})"
 
     def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
         handler = ASSERTION_HANDLERS.get(self.assertion.lower())
@@ -105,12 +110,8 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
         :return: A list of GitHubIssueTest objects found in the issue body.
         """
 
-        github_issue_id = f"{github_issue.number}"
-            # Ideally, we would use:
-            #   f"{github_issue.repository.organization.name}/{github_issue.repository.name}#{github_issue.number}"
-            # But that is very slow.
-            # TODO: Wrap Issue.Issue so that we can store orgName and repoName locally so we don't need to call out
-            # to figure it out.
+        parts = github_issue.html_url.split('/')
+        github_issue_id = f"{parts[3]}/{parts[4]}#{github_issue.number}"
         self.logger.debug(f"Looking for tests in issue {github_issue_id}: {github_issue.title} ({str(github_issue.state)}, {github_issue.html_url})")
 
         # Is there an issue body at all?
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 4d19867d..497afd71 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -12,7 +12,8 @@
 
 # Helper functions
 def get_github_issue_id(github_issue: Issue.Issue):
-    return f"{github_issue.repository.organization.name}/{github_issue.repository.name}#{github_issue.number}"
+    parts = github_issue.html_url.split('/')
+    return f"{parts[3]}/{parts[4]}#{github_issue.number}"
 
 # Initialize the test.
 dotenv.load_dotenv()

From 9a19e450ae7725936eacc47f8334f437b912f1c3 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 19 Feb 2026 19:10:48 -0500
Subject: [PATCH 027/126] Cleaned up some Claude code.

---
 .../github/github_issues_test_cases.py        | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index 269001e2..c3422e88 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -15,7 +15,7 @@
 
 
 class GitHubIssueTest:
-    def __init__(self, github_issue: Issue.Issue, assertion: str, param_sets: list[list[str]] = None):
+    def __init__(self, github_issue_id: str, github_issue: Issue.Issue, assertion: str, param_sets: list[list[str]] = None):
         self.github_issue = github_issue
         self.assertion = assertion
         if param_sets is None:
@@ -24,16 +24,13 @@ def __init__(self, github_issue: Issue.Issue, assertion: str, param_sets: list[l
         if not isinstance(self.param_sets, list):
             raise ValueError(f"param_sets must be a list when creating a GitHubIssueTest({self.github_issue}, {self.assertion}, {self.param_sets})")
 
-        # Derive repo_id from html_url (e.g. https://github.com/org/repo/issues/1 → "org/repo")
-        # to avoid slow lazy API calls via github_issue.repository.organization.name.
-        parts = github_issue.html_url.split('/')
-        self.repo_id = f"{parts[3]}/{parts[4]}"
+        self.github_issue_id = github_issue_id
 
         self.logger = logging.getLogger(str(self))
         self.logger.info(f"Creating GitHubIssueTest for {github_issue.html_url} {assertion}({param_sets})")
 
     def __str__(self):
-        return f"{self.repo_id}#{self.github_issue.number}: {self.assertion}({len(self.param_sets)} param sets: {json.dumps(self.param_sets)})"
+        return f"{self.github_issue_id}: {self.assertion}({len(self.param_sets)} param sets: {json.dumps(self.param_sets)})"
 
     def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
         handler = ASSERTION_HANDLERS.get(self.assertion.lower())
@@ -110,8 +107,10 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
         :return: A list of GitHubIssueTest objects found in the issue body.
         """
 
-        parts = github_issue.html_url.split('/')
-        github_issue_id = f"{parts[3]}/{parts[4]}#{github_issue.number}"
+        github_org = github_issue.repository.organization.name
+        github_repo = github_issue.repository.name
+
+        github_issue_id = f"{github_org}/{github_repo}#{github_issue.number}"
         self.logger.debug(f"Looking for tests in issue {github_issue_id}: {github_issue.title} ({str(github_issue.state)}, {github_issue.html_url})")
 
         # Is there an issue body at all?
@@ -136,7 +135,7 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
                 if len(params) < 2:
                     raise ValueError(f"Too few parameters found in BabelTest in issue {github_issue_id}: {match}")
                 else:
-                    testrows.append(GitHubIssueTest(github_issue, params[0], [params[1:]]))
+                    testrows.append(GitHubIssueTest(github_issue_id, github_issue, params[0], [params[1:]]))
 
         babeltest_yaml_matches = re.findall(self.babeltest_yaml_pattern, github_issue.body)
         if babeltest_yaml_matches:
@@ -159,7 +158,7 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
                             param_sets.append(param_set)
                         else:
                             raise RuntimeError(f"Unknown parameter set type {param_set} in issue {github_issue_id}")
-                    testrows.append(GitHubIssueTest(github_issue, assertion, param_sets))
+                    testrows.append(GitHubIssueTest(github_issue_id, github_issue, assertion, param_sets))
 
         return testrows
 

From 0ec9e20f45c18c613bbb265f463e4aab684d147e Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Fri, 20 Feb 2026 16:59:22 -0500
Subject: [PATCH 028/126] Refactor assertions into a proper framework for easy
 authoring
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Promote NodeNormAssertion and NameResAssertion from empty marker classes
to full framework base classes (renamed NodeNormTest / NameResTest).
All boilerplate (empty-param guards, CURIE pre-warming, yielded-values
tracking) now lives in the base class test_with_nodenorm / test_with_nameres
methods, which dispatch to a new test_param_set() hook.

Handler authors now only override test_param_set() and call self.passed()
/ self.failed() — no TestResult/TestStatus construction, no loop
scaffolding, no return-inside-generator bugs.

Also fixes a latent bug where `return [TestResult(...)]` inside a generator
body silently discarded the result (the list went to StopIteration.value
instead of being yielded to the caller).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 src/babel_validation/assertions/README.md   |   8 +-
 src/babel_validation/assertions/__init__.py |  86 ++++++++--
 src/babel_validation/assertions/common.py   |   5 +-
 src/babel_validation/assertions/nameres.py  |  87 +++++-----
 src/babel_validation/assertions/nodenorm.py | 174 +++++++-------------
 5 files changed, 170 insertions(+), 190 deletions(-)

diff --git a/src/babel_validation/assertions/README.md b/src/babel_validation/assertions/README.md
index fc7a12cf..751e9efb 100644
--- a/src/babel_validation/assertions/README.md
+++ b/src/babel_validation/assertions/README.md
@@ -174,11 +174,11 @@ babel_tests:
 ## Adding a New Assertion Type
 
 1. Choose the right module:
-   - `nodenorm.py` — for NodeNorm-only assertions (subclass `NodeNormAssertion`)
-   - `nameres.py` — for NameRes-only assertions (subclass `NameResAssertion`)
-   - `common.py` — for assertions that apply to both services (subclass `AssertionHandler`)
+   - `nodenorm.py` — for NodeNorm-only assertions (subclass `NodeNormTest`, override `test_param_set`)
+   - `nameres.py` — for NameRes-only assertions (subclass `NameResTest`, override `test_param_set`)
+   - `common.py` — for assertions that apply to both services (subclass `AssertionHandler`, override `test_with_nodenorm` and/or `test_with_nameres`)
 
-2. Define the class with `NAME`, `DESCRIPTION`, and the relevant `test_with_nodenorm()` / `test_with_nameres()` method(s).
+2. Define the class with `NAME`, `DESCRIPTION`, and `test_param_set()` (or both `test_with_*` methods for `AssertionHandler` subclasses).
 
 3. Import it in `__init__.py` and add an instance to `ASSERTION_HANDLERS`.
 
diff --git a/src/babel_validation/assertions/__init__.py b/src/babel_validation/assertions/__init__.py
index bc6cecff..a5b9253b 100644
--- a/src/babel_validation/assertions/__init__.py
+++ b/src/babel_validation/assertions/__init__.py
@@ -10,16 +10,16 @@
 
 Adding a new assertion type
 ---------------------------
-1. Create a subclass of AssertionHandler (or NodeNormAssertion / NameResAssertion)
+1. Create a subclass of NodeNormTest or NameResTest (or AssertionHandler for both)
    in the appropriate module (nodenorm.py, nameres.py, or common.py).
 2. Set NAME and DESCRIPTION class attributes.
-3. Override test_with_nodenorm() and/or test_with_nameres().
+3. Override test_param_set().
 4. Import it here and add an instance to ASSERTION_HANDLERS.
 """
 
 from typing import Iterator
 
-from src.babel_validation.core.testrow import TestResult
+from src.babel_validation.core.testrow import TestResult, TestStatus
 
 
 class AssertionHandler:
@@ -27,6 +27,12 @@ class AssertionHandler:
     NAME: str           # lowercase assertion name as used in issue bodies
     DESCRIPTION: str    # one-line human-readable description
 
+    def passed(self, message: str) -> TestResult:
+        return TestResult(status=TestStatus.Passed, message=message)
+
+    def failed(self, message: str) -> TestResult:
+        return TestResult(status=TestStatus.Failed, message=message)
+
     def test_with_nodenorm(self, param_sets: list[list[str]], nodenorm,
                            label: str = "") -> Iterator[TestResult]:
         """Evaluate this assertion against NodeNorm. Returns [] if not applicable."""
@@ -39,24 +45,70 @@ def test_with_nameres(self, param_sets: list[list[str]], nodenorm, nameres,
         return []
 
 
-class NodeNormAssertion(AssertionHandler):
-    """Marker base class for assertions that test NodeNorm.
+class NodeNormTest(AssertionHandler):
+    """Base class for assertions that test NodeNorm.
 
-    Subclasses must override test_with_nodenorm().
-    test_with_nameres() returns [] and need not be overridden.
-    Use isinstance(handler, NodeNormAssertion) to check applicability.
+    Subclasses implement test_param_set() instead of test_with_nodenorm().
     """
-    pass
-
 
-class NameResAssertion(AssertionHandler):
-    """Marker base class for assertions that test NameRes.
-
-    Subclasses must override test_with_nameres().
-    test_with_nodenorm() returns [] and need not be overridden.
-    Use isinstance(handler, NameResAssertion) to check applicability.
+    def test_with_nodenorm(self, param_sets: list[list[str]], nodenorm,
+                           label: str = "") -> Iterator[TestResult]:
+        if not param_sets:
+            yield self.failed(f"No parameters provided in {label}")
+            return
+        # warm the cache for all CURIEs up front
+        nodenorm.normalize_curies([p for params in param_sets for p in params])
+        found = False
+        for index, params in enumerate(param_sets):
+            if not params:
+                yield self.failed(f"No parameters in param_set {index} in {label}")
+                found = True
+                continue
+            for result in self.test_param_set(params, nodenorm, label):
+                found = True
+                yield result
+        if not found:
+            yield self.failed(f"No test results returned in {label}")
+
+    def test_param_set(self, params: list[str], nodenorm, label: str = "") -> Iterator[TestResult]:
+        """Override this to implement the assertion. Called once per param_set."""
+        raise NotImplementedError
+
+    def resolved_message(self, curie: str, result: dict, nodenorm) -> str:
+        """Standard pass-message when a CURIE resolves."""
+        return (f"Resolved {curie} to {result['id']['identifier']} "
+                f"({result['type'][0]}, \"{result['id']['label']}\") "
+                f"with NodeNormalization service {nodenorm}")
+
+
+class NameResTest(AssertionHandler):
+    """Base class for assertions that test NameRes.
+
+    Subclasses implement test_param_set() instead of test_with_nameres().
     """
-    pass
+
+    def test_with_nameres(self, param_sets: list[list[str]], nodenorm, nameres,
+                          pass_if_found_in_top: int = 5,
+                          label: str = "") -> Iterator[TestResult]:
+        if not param_sets:
+            yield self.failed(f"No parameters provided in {label}")
+            return
+        found = False
+        for index, params in enumerate(param_sets):
+            if not params:
+                yield self.failed(f"No parameters in param_set {index} in {label}")
+                found = True
+                continue
+            for result in self.test_param_set(params, nodenorm, nameres, pass_if_found_in_top, label):
+                found = True
+                yield result
+        if not found:
+            yield self.failed(f"No test results returned in {label}")
+
+    def test_param_set(self, params: list[str], nodenorm, nameres,
+                       pass_if_found_in_top: int, label: str = "") -> Iterator[TestResult]:
+        """Override this to implement the assertion. Called once per param_set."""
+        raise NotImplementedError
 
 
 # Registry — import submodules after base classes are defined to avoid circular imports.
diff --git a/src/babel_validation/assertions/common.py b/src/babel_validation/assertions/common.py
index f9f1aabf..1d21f01d 100644
--- a/src/babel_validation/assertions/common.py
+++ b/src/babel_validation/assertions/common.py
@@ -1,5 +1,4 @@
 from src.babel_validation.assertions import AssertionHandler
-from src.babel_validation.core.testrow import TestResult, TestStatus
 
 
 class NeededHandler(AssertionHandler):
@@ -8,7 +7,7 @@ class NeededHandler(AssertionHandler):
     DESCRIPTION = "Marks an issue as needing a test — always fails as a reminder to add real assertions."
 
     def test_with_nodenorm(self, param_sets, nodenorm, label=""):
-        return [TestResult(status=TestStatus.Failed, message=f"Test needed for issue")]
+        yield self.failed("Test needed for issue")
 
     def test_with_nameres(self, param_sets, nodenorm, nameres, pass_if_found_in_top=5, label=""):
-        return [TestResult(status=TestStatus.Failed, message=f"Test needed for issue")]
+        yield self.failed("Test needed for issue")
diff --git a/src/babel_validation/assertions/nameres.py b/src/babel_validation/assertions/nameres.py
index cec0ec17..5afa741f 100644
--- a/src/babel_validation/assertions/nameres.py
+++ b/src/babel_validation/assertions/nameres.py
@@ -1,13 +1,13 @@
 import json
 from typing import Iterator
 
-from src.babel_validation.assertions import NameResAssertion
-from src.babel_validation.core.testrow import TestResult, TestStatus
+from src.babel_validation.assertions import NameResTest
+from src.babel_validation.core.testrow import TestResult
 from src.babel_validation.services.nameres import CachedNameRes
 from src.babel_validation.services.nodenorm import CachedNodeNorm
 
 
-class SearchByNameHandler(NameResAssertion):
+class SearchByNameHandler(NameResTest):
     """Test that a name search returns an expected CURIE in the top-N results in NameRes."""
     NAME = "searchbyname"
     DESCRIPTION = (
@@ -16,50 +16,37 @@ class SearchByNameHandler(NameResAssertion):
         "(default N=5) when NameRes looks up the search query."
     )
 
-    def test_with_nameres(self, param_sets: list[list[str]], nodenorm: CachedNodeNorm,
-                          nameres: CachedNameRes, pass_if_found_in_top: int = 5,
-                          label: str = "") -> Iterator[TestResult]:
-        if not param_sets:
-            return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {label}")]
-
-        yielded_values = False
-        for params in param_sets:
-            if len(params) < 2:
-                yield TestResult(status=TestStatus.Failed, message=f"Two parameters expected for SearchByName in {label}, but params = {params}")
-                yielded_values = True
-                continue
-
-            [search_query, expected_curie_from_test, *args] = params
-            expected_curie_result = nodenorm.normalize_curie(expected_curie_from_test, drug_chemical_conflate='true')
-            if not expected_curie_result:
-                yield TestResult(status=TestStatus.Failed, message=f"Unable to normalize CURIE {expected_curie_from_test} in {label}")
-                yielded_values = True
-                continue
-
-            expected_curie = expected_curie_result['id']['identifier']
-            expected_curie_label = expected_curie_result['id']['label']
-            expected_curie_string = f"Expected CURIE {expected_curie_from_test}, normalized to {expected_curie} '{expected_curie_label}'"
-
-            # Search for the expected CURIE in the first {pass_if_found_in_top} results.
-            results = nameres.lookup(search_query, autocomplete='false', limit=(2 * pass_if_found_in_top))
-            if not results:
-                yield TestResult(status=TestStatus.Failed, message=f"No results found for '{search_query}' on NameRes {nameres} ({expected_curie_string}")
-                yielded_values = True
-                continue
-
-            curies = [result['curie'] for result in results]
-            try:
-                found_index = curies.index(expected_curie)
-            except ValueError:
-                yield TestResult(status=TestStatus.Failed, message=f"{expected_curie_string} not found when searching for '{search_query}' in NameRes {nameres}: {json.dumps(results, indent=2, sort_keys=True)}")
-                yielded_values = True
-                continue
-
-            if found_index <= pass_if_found_in_top:
-                yield TestResult(status=TestStatus.Passed, message=f"{expected_curie_string} found at index {found_index + 1} on NameRes {nameres}")
-            else:
-                yield TestResult(status=TestStatus.Failed, message=f"{expected_curie_string} found at index {found_index + 1} which is greater than {pass_if_found_in_top} on NameRes {nameres}")
-            yielded_values = True
-
-        if not yielded_values:
-            return [TestResult(status=TestStatus.Failed, message=f"No test results returned in {label}")]
+    def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
+                       nameres: CachedNameRes, pass_if_found_in_top: int = 5,
+                       label: str = "") -> Iterator[TestResult]:
+        if len(params) < 2:
+            yield self.failed(f"Two parameters expected for SearchByName in {label}, but params = {params}")
+            return
+
+        [search_query, expected_curie_from_test, *args] = params
+        expected_curie_result = nodenorm.normalize_curie(expected_curie_from_test, drug_chemical_conflate='true')
+        if not expected_curie_result:
+            yield self.failed(f"Unable to normalize CURIE {expected_curie_from_test} in {label}")
+            return
+
+        expected_curie = expected_curie_result['id']['identifier']
+        expected_curie_label = expected_curie_result['id']['label']
+        expected_curie_string = f"Expected CURIE {expected_curie_from_test}, normalized to {expected_curie} '{expected_curie_label}'"
+
+        # Search for the expected CURIE in the first {pass_if_found_in_top} results.
+        results = nameres.lookup(search_query, autocomplete='false', limit=(2 * pass_if_found_in_top))
+        if not results:
+            yield self.failed(f"No results found for '{search_query}' on NameRes {nameres} ({expected_curie_string}")
+            return
+
+        curies = [result['curie'] for result in results]
+        try:
+            found_index = curies.index(expected_curie)
+        except ValueError:
+            yield self.failed(f"{expected_curie_string} not found when searching for '{search_query}' in NameRes {nameres}: {json.dumps(results, indent=2, sort_keys=True)}")
+            return
+
+        if found_index <= pass_if_found_in_top:
+            yield self.passed(f"{expected_curie_string} found at index {found_index + 1} on NameRes {nameres}")
+        else:
+            yield self.failed(f"{expected_curie_string} found at index {found_index + 1} which is greater than {pass_if_found_in_top} on NameRes {nameres}")
diff --git a/src/babel_validation/assertions/nodenorm.py b/src/babel_validation/assertions/nodenorm.py
index e00a9dd0..3eea05c8 100644
--- a/src/babel_validation/assertions/nodenorm.py
+++ b/src/babel_validation/assertions/nodenorm.py
@@ -1,75 +1,42 @@
 import json
 from typing import Iterator
 
-from src.babel_validation.assertions import NodeNormAssertion
-from src.babel_validation.core.testrow import TestResult, TestStatus
+from src.babel_validation.assertions import NodeNormTest
+from src.babel_validation.core.testrow import TestResult
 from src.babel_validation.services.nodenorm import CachedNodeNorm
 
 
-class ResolvesHandler(NodeNormAssertion):
+class ResolvesHandler(NodeNormTest):
     """Test that every CURIE in every param_set resolves in NodeNorm."""
     NAME = "resolves"
     DESCRIPTION = "Each CURIE in each param_set must resolve to a non-null result in NodeNorm."
 
-    def test_with_nodenorm(self, param_sets: list[list[str]], nodenorm: CachedNodeNorm,
-                           label: str = "") -> Iterator[TestResult]:
-        if not param_sets:
-            return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {label}")]
+    def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
+                       label: str = "") -> Iterator[TestResult]:
+        for curie in params:
+            result = nodenorm.normalize_curie(curie)
+            if not result:
+                yield self.failed(f"Could not resolve {curie} with NodeNormalization service {nodenorm}")
+            else:
+                yield self.passed(self.resolved_message(curie, result, nodenorm))
 
-        curies_to_resolve = [param for params in param_sets for param in params]
-        nodenorm.normalize_curies(curies_to_resolve)
 
-        yielded_values = False
-        for index, curies in enumerate(param_sets):
-            if not curies:
-                return TestResult(status=TestStatus.Failed, message=f"No parameters provided in paramset {index} in {label}")
-
-            for curie in curies:
-                result = nodenorm.normalize_curie(curie)
-                if not result:
-                    yield TestResult(status=TestStatus.Failed, message=f"Could not resolve {curie} with NodeNormalization service {nodenorm}")
-                    yielded_values = True
-                else:
-                    yield TestResult(status=TestStatus.Passed, message=f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\") with NodeNormalization service {nodenorm}")
-                    yielded_values = True
-
-        if not yielded_values:
-            return [TestResult(status=TestStatus.Failed, message=f"No test results returned in {label}")]
-
-
-class DoesNotResolveHandler(NodeNormAssertion):
+class DoesNotResolveHandler(NodeNormTest):
     """Test that every CURIE in every param_set does NOT resolve in NodeNorm."""
     NAME = "doesnotresolve"
     DESCRIPTION = "Each CURIE in each param_set must fail to resolve (return null) in NodeNorm."
 
-    def test_with_nodenorm(self, param_sets: list[list[str]], nodenorm: CachedNodeNorm,
-                           label: str = "") -> Iterator[TestResult]:
-        if not param_sets:
-            return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {label}")]
-
-        curies_to_resolve = [param for params in param_sets for param in params]
-        nodenorm.normalize_curies(curies_to_resolve)
-
-        yielded_values = False
-        for index, curies in enumerate(param_sets):
-            if not curies:
-                yield TestResult(status=TestStatus.Failed, message=f"No parameters provided in paramset {index} in {label}")
-                continue
+    def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
+                       label: str = "") -> Iterator[TestResult]:
+        for curie in params:
+            result = nodenorm.normalize_curie(curie)
+            if not result:
+                yield self.passed(f"Could not resolve {curie} with NodeNormalization service {nodenorm} as expected")
+            else:
+                yield self.failed(f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\") with NodeNormalization service {nodenorm}, but expected not to resolve")
 
-            for curie in curies:
-                result = nodenorm.normalize_curie(curie)
-                if not result:
-                    yield TestResult(status=TestStatus.Passed, message=f"Could not resolve {curie} with NodeNormalization service {nodenorm} as expected")
-                    yielded_values = True
-                else:
-                    yield TestResult(status=TestStatus.Failed, message=f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\") with NodeNormalization service {nodenorm}, but expected not to resolve")
-                    yielded_values = True
 
-        if not yielded_values:
-            return [TestResult(status=TestStatus.Failed, message=f"No test results returned in {label}")]
-
-
-class ResolvesWithHandler(NodeNormAssertion):
+class ResolvesWithHandler(NodeNormTest):
     """Test that all CURIEs in a param_set resolve to the same normalized result in NodeNorm."""
     NAME = "resolveswith"
     DESCRIPTION = (
@@ -77,47 +44,32 @@ class ResolvesWithHandler(NodeNormAssertion):
         "Use this to assert that two identifiers are equivalent."
     )
 
-    def test_with_nodenorm(self, param_sets: list[list[str]], nodenorm: CachedNodeNorm,
-                           label: str = "") -> Iterator[TestResult]:
-        if not param_sets:
-            return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {label}")]
-
-        curies_to_resolve = [param for params in param_sets for param in params]
-        nodenorm.normalize_curies(curies_to_resolve)
-
-        yielded_values = False
-        for curies in param_sets:
-            results = nodenorm.normalize_curies(curies)
-
-            # Find the first good result.
-            first_good_result = None
-            for curie, result in results.items():
-                if result is not None and first_good_result is None:
-                    first_good_result = result
-                    break
-
-            if first_good_result is None:
-                return [TestResult(status=TestStatus.Failed, message=f"None of the CURIEs {curies} could be resolved on {nodenorm}")]
+    def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
+                       label: str = "") -> Iterator[TestResult]:
+        results = nodenorm.normalize_curies(params)
 
-            # Check all the results.
-            for curie, result in results.items():
-                if result is None:
-                    yield TestResult(status=TestStatus.Failed, message=f"CURIE {curie} could not be resolved, and so is not equal to the expected result {json.dumps(first_good_result, indent=2, sort_keys=True)} on {nodenorm}")
-                    yielded_values = True
-                    continue
+        # Find the first good result.
+        first_good_result = None
+        for curie, result in results.items():
+            if result is not None and first_good_result is None:
+                first_good_result = result
+                break
 
-                if json.dumps(first_good_result, sort_keys=True) == json.dumps(result, sort_keys=True):
-                    yield TestResult(status=TestStatus.Passed, message=f"Resolved {curie} to the expected result {json.dumps(first_good_result, indent=2, sort_keys=True)}")
-                    yielded_values = True
-                else:
-                    yield TestResult(status=TestStatus.Failed, message=f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\"), but expected {first_good_result['id']['identifier']} ({first_good_result['type'][0]}, \"{first_good_result['id']['label']}\") on {nodenorm}")
-                    yielded_values = True
+        if first_good_result is None:
+            yield self.failed(f"None of the CURIEs {params} could be resolved on {nodenorm}")
+            return
 
-        if not yielded_values:
-            return [TestResult(status=TestStatus.Failed, message=f"No test results returned in {label}")]
+        # Check all the results.
+        for curie, result in results.items():
+            if result is None:
+                yield self.failed(f"CURIE {curie} could not be resolved, and so is not equal to the expected result {json.dumps(first_good_result, indent=2, sort_keys=True)} on {nodenorm}")
+            elif json.dumps(first_good_result, sort_keys=True) == json.dumps(result, sort_keys=True):
+                yield self.passed(f"Resolved {curie} to the expected result {json.dumps(first_good_result, indent=2, sort_keys=True)}")
+            else:
+                yield self.failed(f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\"), but expected {first_good_result['id']['identifier']} ({first_good_result['type'][0]}, \"{first_good_result['id']['label']}\") on {nodenorm}")
 
 
-class ResolvesWithTypeHandler(NodeNormAssertion):
+class ResolvesWithTypeHandler(NodeNormTest):
     """Test that CURIEs resolve with a specific Biolink type in NodeNorm."""
     NAME = "resolveswithtype"
     DESCRIPTION = (
@@ -125,29 +77,19 @@ class ResolvesWithTypeHandler(NodeNormAssertion):
         "(e.g. 'biolink:Gene'), and the remainder are CURIEs that must resolve with that type."
     )
 
-    def test_with_nodenorm(self, param_sets: list[list[str]], nodenorm: CachedNodeNorm,
-                           label: str = "") -> Iterator[TestResult]:
-        if not param_sets:
-            return [TestResult(status=TestStatus.Failed, message=f"No parameters provided in {label}")]
-
-        yielded_values = False
-        for index, params in enumerate(param_sets):
-            if len(params) < 2:
-                yield TestResult(status=TestStatus.Failed, message=f"Too few parameters provided in param set {index} in {label}: {params}")
-                continue
-
-            expected_biolink_type = params[0]
-            curies = params[1:]
-
-            results = nodenorm.normalize_curies(curies)
-            for curie in curies:
-                biolink_types = results[curie]['type']
-                if expected_biolink_type in biolink_types:
-                    yield TestResult(status=TestStatus.Passed, message=f"Biolink types {biolink_types} for CURIE {curie} includes expected Biolink type {expected_biolink_type}")
-                    yielded_values = True
-                else:
-                    yield TestResult(status=TestStatus.Failed, message=f"Biolink types {biolink_types} for CURIE {curie} does not include expected Biolink type {expected_biolink_type}")
-                    yielded_values = True
-
-        if not yielded_values:
-            return [TestResult(status=TestStatus.Failed, message=f"No test results returned in {label}")]
+    def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
+                       label: str = "") -> Iterator[TestResult]:
+        if len(params) < 2:
+            yield self.failed(f"Too few parameters provided in param_set in {label}: {params}")
+            return
+
+        expected_biolink_type = params[0]
+        curies = params[1:]
+
+        results = nodenorm.normalize_curies(curies)
+        for curie in curies:
+            biolink_types = results[curie]['type']
+            if expected_biolink_type in biolink_types:
+                yield self.passed(f"Biolink types {biolink_types} for CURIE {curie} includes expected Biolink type {expected_biolink_type}")
+            else:
+                yield self.failed(f"Biolink types {biolink_types} for CURIE {curie} does not include expected Biolink type {expected_biolink_type}")

From ddaa14fb6243b9fdd623845df74d59cc78a4c9aa Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Fri, 20 Feb 2026 17:44:50 -0500
Subject: [PATCH 029/126] Auto-generate assertions/README.md from handler class
 attributes

Add PARAMETERS, WIKI_EXAMPLES, and YAML_PARAMS doc attributes to every
assertion handler class, making the class body the single source of truth
for documentation. Add gen_docs.py to render README.md from those attributes,
and a freshness test that fails if README.md is out of date with the handlers.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 src/babel_validation/assertions/README.md   |  27 ++--
 src/babel_validation/assertions/__init__.py |   8 +-
 src/babel_validation/assertions/common.py   |   3 +
 src/babel_validation/assertions/gen_docs.py | 133 ++++++++++++++++++++
 src/babel_validation/assertions/nameres.py  |   6 +
 src/babel_validation/assertions/nodenorm.py |  23 +++-
 tests/test_assertions_docs.py               |  11 ++
 7 files changed, 194 insertions(+), 17 deletions(-)
 create mode 100644 src/babel_validation/assertions/gen_docs.py
 create mode 100644 tests/test_assertions_docs.py

diff --git a/src/babel_validation/assertions/README.md b/src/babel_validation/assertions/README.md
index 751e9efb..7dba6113 100644
--- a/src/babel_validation/assertions/README.md
+++ b/src/babel_validation/assertions/README.md
@@ -1,3 +1,6 @@
+<!-- AUTO-GENERATED — do not edit by hand.
+     Regenerate with: uv run python -m src.babel_validation.assertions.gen_docs -->
+
 # BabelTest Assertion Types
 
 This package defines the assertion types that can be embedded in GitHub issue bodies and evaluated against the NodeNorm and NameRes services.
@@ -33,7 +36,7 @@ These assertions test the [NodeNorm](https://nodenorm.transltr.io/docs) service.
 
 **Applies to:** NodeNorm
 
-Verifies that every CURIE in every param_set can be resolved to a non-null result.
+Each CURIE in each param_set must resolve to a non-null result in NodeNorm.
 
 **Parameters:** One or more CURIEs per param_set.
 
@@ -57,7 +60,7 @@ babel_tests:
 
 **Applies to:** NodeNorm
 
-Verifies that every CURIE in every param_set fails to resolve (returns null). Use this to confirm that an identifier is intentionally not normalizable.
+Each CURIE in each param_set must fail to resolve (return null) in NodeNorm. Use this to confirm that an identifier is intentionally not normalizable.
 
 **Parameters:** One or more CURIEs per param_set.
 
@@ -79,9 +82,9 @@ babel_tests:
 
 **Applies to:** NodeNorm
 
-Verifies that all CURIEs in a param_set resolve to the **identical** normalized result. Use this to assert that two or more identifiers are equivalent (same clique in NodeNorm).
+All CURIEs within each param_set must resolve to the identical normalized result. Use this to assert that two identifiers are equivalent.
 
-**Parameters:** Two or more CURIEs per param_set. All must resolve and produce the same result.
+**Parameters:** Two or more CURIEs per param_set. All must resolve to the same result.
 
 **Wiki syntax:**
 ```
@@ -102,9 +105,9 @@ babel_tests:
 
 **Applies to:** NodeNorm
 
-Verifies that one or more CURIEs resolve with a specific Biolink type in their `type` list.
+Each param_set must have at least two elements: the first is the expected Biolink type (e.g. 'biolink:Gene'), and the remainder are CURIEs that must resolve with that type.
 
-**Parameters:** Each param_set must have at least two elements. The **first** element is the expected Biolink type (e.g. `biolink:Gene`); the remaining elements are CURIEs to check.
+**Parameters:** Each param_set: first element is the expected Biolink type (e.g. `biolink:Gene`), remaining elements are CURIEs.
 
 **Wiki syntax:**
 ```
@@ -128,11 +131,9 @@ These assertions test the [NameRes](https://name-lookup.transltr.io/docs) servic
 
 **Applies to:** NameRes
 
-Verifies that a name search returns an expected CURIE within the top-N results (default N=5).
-
-The expected CURIE is first normalized via NodeNorm (with drug/chemical conflation enabled) to find its preferred identifier; that identifier must appear in the top results.
+Each param_set must have at least two elements: a search query string and an expected CURIE. The test passes if the CURIE's normalized identifier appears within the top N results (default N=5) when NameRes looks up the search query.
 
-**Parameters:** Each param_set must have at least two elements: the **search query string** and the **expected CURIE**.
+**Parameters:** Each param_set: the **search query string** and the **expected CURIE**. The CURIE is normalized via NodeNorm (drug/chemical conflation enabled) before matching.
 
 **Wiki syntax:**
 ```
@@ -155,7 +156,7 @@ babel_tests:
 
 **Applies to:** NodeNorm and NameRes
 
-A placeholder that always fails. Use this on issues where you know a test is required but haven't written it yet.
+Marks an issue as needing a test — always fails as a reminder to add real assertions.
 
 **Wiki syntax:**
 ```
@@ -178,8 +179,8 @@ babel_tests:
    - `nameres.py` — for NameRes-only assertions (subclass `NameResTest`, override `test_param_set`)
    - `common.py` — for assertions that apply to both services (subclass `AssertionHandler`, override `test_with_nodenorm` and/or `test_with_nameres`)
 
-2. Define the class with `NAME`, `DESCRIPTION`, and `test_param_set()` (or both `test_with_*` methods for `AssertionHandler` subclasses).
+2. Define the class with `NAME`, `DESCRIPTION`, `PARAMETERS`, `WIKI_EXAMPLES`, `YAML_PARAMS`, and `test_param_set()` (or both `test_with_*` methods for `AssertionHandler` subclasses).
 
 3. Import it in `__init__.py` and add an instance to `ASSERTION_HANDLERS`.
 
-4. Document it in this README.
+4. Run `uv run python -m src.babel_validation.assertions.gen_docs` to regenerate `README.md`.
diff --git a/src/babel_validation/assertions/__init__.py b/src/babel_validation/assertions/__init__.py
index a5b9253b..5a89db32 100644
--- a/src/babel_validation/assertions/__init__.py
+++ b/src/babel_validation/assertions/__init__.py
@@ -6,15 +6,17 @@
 and evaluated against the NodeNorm and NameRes services.
 
 Supported assertion types are registered in ASSERTION_HANDLERS. To see everything
-that is currently supported, scan that dict or read assertions/README.md.
+that is currently supported, scan that dict or read assertions/README.md (auto-generated).
 
 Adding a new assertion type
 ---------------------------
 1. Create a subclass of NodeNormTest or NameResTest (or AssertionHandler for both)
    in the appropriate module (nodenorm.py, nameres.py, or common.py).
 2. Set NAME and DESCRIPTION class attributes.
-3. Override test_param_set().
-4. Import it here and add an instance to ASSERTION_HANDLERS.
+3. Set PARAMETERS, WIKI_EXAMPLES, and YAML_PARAMS class attributes for documentation.
+4. Override test_param_set().
+5. Import it here and add an instance to ASSERTION_HANDLERS.
+6. Run `uv run python -m src.babel_validation.assertions.gen_docs` to regenerate README.md.
 """
 
 from typing import Iterator
diff --git a/src/babel_validation/assertions/common.py b/src/babel_validation/assertions/common.py
index 1d21f01d..ac12daca 100644
--- a/src/babel_validation/assertions/common.py
+++ b/src/babel_validation/assertions/common.py
@@ -5,6 +5,9 @@ class NeededHandler(AssertionHandler):
     """Placeholder assertion indicating that a test still needs to be written for this issue."""
     NAME = "needed"
     DESCRIPTION = "Marks an issue as needing a test — always fails as a reminder to add real assertions."
+    PARAMETERS = ""
+    WIKI_EXAMPLES = ["{{BabelTest|Needed}}"]
+    YAML_PARAMS = "    - placeholder"
 
     def test_with_nodenorm(self, param_sets, nodenorm, label=""):
         yield self.failed("Test needed for issue")
diff --git a/src/babel_validation/assertions/gen_docs.py b/src/babel_validation/assertions/gen_docs.py
new file mode 100644
index 00000000..c2a5ea22
--- /dev/null
+++ b/src/babel_validation/assertions/gen_docs.py
@@ -0,0 +1,133 @@
+"""Generate assertions/README.md from handler class attributes.
+
+Run:
+    uv run python -m src.babel_validation.assertions.gen_docs
+"""
+
+from pathlib import Path
+
+from src.babel_validation.assertions import (
+    ASSERTION_HANDLERS, AssertionHandler, NodeNormTest, NameResTest,
+)
+
+README_PATH = Path(__file__).parent / "README.md"
+
+INTRO = """\
+<!-- AUTO-GENERATED — do not edit by hand.
+     Regenerate with: uv run python -m src.babel_validation.assertions.gen_docs -->
+
+# BabelTest Assertion Types
+
+This package defines the assertion types that can be embedded in GitHub issue bodies and evaluated against the NodeNorm and NameRes services.
+
+## Embedding Tests in Issues
+
+Two syntaxes are supported:
+
+**Wiki syntax** (one assertion per line):
+```
+{{BabelTest|AssertionType|param1|param2|...}}
+```
+
+**YAML syntax** (multiple assertions, multiple param sets):
+````
+```yaml
+babel_tests:
+  AssertionType:
+    - param1
+    - [param1, param2]
+```
+````
+
+Assertion names are case-insensitive.
+
+---
+"""
+
+ADDING_NEW = """\
+## Adding a New Assertion Type
+
+1. Choose the right module:
+   - `nodenorm.py` — for NodeNorm-only assertions (subclass `NodeNormTest`, override `test_param_set`)
+   - `nameres.py` — for NameRes-only assertions (subclass `NameResTest`, override `test_param_set`)
+   - `common.py` — for assertions that apply to both services (subclass `AssertionHandler`, override `test_with_nodenorm` and/or `test_with_nameres`)
+
+2. Define the class with `NAME`, `DESCRIPTION`, `PARAMETERS`, `WIKI_EXAMPLES`, `YAML_PARAMS`, and `test_param_set()` (or both `test_with_*` methods for `AssertionHandler` subclasses).
+
+3. Import it in `__init__.py` and add an instance to `ASSERTION_HANDLERS`.
+
+4. Run `uv run python -m src.babel_validation.assertions.gen_docs` to regenerate `README.md`.
+"""
+
+_GROUP_HEADERS: dict[str, str] = {
+    "NodeNorm": (
+        "## NodeNorm Assertions\n\n"
+        "These assertions test the [NodeNorm](https://nodenorm.transltr.io/docs) service."
+    ),
+    "NameRes": (
+        "## NameRes Assertions\n\n"
+        "These assertions test the [NameRes](https://name-lookup.transltr.io/docs) service."
+    ),
+    "NodeNorm and NameRes": "## Special Assertions",
+}
+
+
+def _display_name(h: AssertionHandler) -> str:
+    return type(h).__name__.removesuffix("Handler")
+
+
+def _applies_to(h: AssertionHandler) -> str:
+    if isinstance(h, NodeNormTest):
+        return "NodeNorm"
+    if isinstance(h, NameResTest):
+        return "NameRes"
+    return "NodeNorm and NameRes"
+
+
+def _render_handler(h: AssertionHandler) -> str:
+    name = _display_name(h)
+    service = _applies_to(h)
+    description = getattr(h, "DESCRIPTION", "")
+    parameters = getattr(h, "PARAMETERS", "")
+    wiki_examples = getattr(h, "WIKI_EXAMPLES", [])
+    yaml_params = getattr(h, "YAML_PARAMS", "")
+
+    parts = []
+    parts.append(f"### {name}\n")
+    parts.append(f"**Applies to:** {service}\n")
+    parts.append(f"{description}\n")
+
+    if parameters:
+        parts.append(f"**Parameters:** {parameters}\n")
+
+    wiki_block = "\n".join(wiki_examples)
+    parts.append(f"**Wiki syntax:**\n```\n{wiki_block}\n```\n")
+
+    parts.append(
+        f"**YAML syntax:**\n```yaml\nbabel_tests:\n  {name}:\n{yaml_params}\n```\n"
+    )
+
+    parts.append("---\n")
+
+    return "\n".join(parts)
+
+
+def generate_readme() -> str:
+    sections = [INTRO]
+    seen_groups: set[str] = set()
+
+    for h in ASSERTION_HANDLERS.values():
+        service = _applies_to(h)
+        if service not in seen_groups:
+            seen_groups.add(service)
+            sections.append(_GROUP_HEADERS[service] + "\n")
+        sections.append(_render_handler(h))
+
+    sections.append(ADDING_NEW)
+    return "\n".join(sections)
+
+
+if __name__ == "__main__":
+    content = generate_readme()
+    README_PATH.write_text(content, encoding="utf-8")
+    print(f"Written to {README_PATH}")
diff --git a/src/babel_validation/assertions/nameres.py b/src/babel_validation/assertions/nameres.py
index 5afa741f..c4a81264 100644
--- a/src/babel_validation/assertions/nameres.py
+++ b/src/babel_validation/assertions/nameres.py
@@ -15,6 +15,12 @@ class SearchByNameHandler(NameResTest):
         "The test passes if the CURIE's normalized identifier appears within the top N results "
         "(default N=5) when NameRes looks up the search query."
     )
+    PARAMETERS = (
+        "Each param_set: the **search query string** and the **expected CURIE**. "
+        "The CURIE is normalized via NodeNorm (drug/chemical conflation enabled) before matching."
+    )
+    WIKI_EXAMPLES = ["{{BabelTest|SearchByName|water|CHEBI:15377}}"]
+    YAML_PARAMS = "    - [water, CHEBI:15377]\n    - [diabetes, MONDO:0005015]"
 
     def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                        nameres: CachedNameRes, pass_if_found_in_top: int = 5,
diff --git a/src/babel_validation/assertions/nodenorm.py b/src/babel_validation/assertions/nodenorm.py
index 3eea05c8..870f68de 100644
--- a/src/babel_validation/assertions/nodenorm.py
+++ b/src/babel_validation/assertions/nodenorm.py
@@ -10,6 +10,12 @@ class ResolvesHandler(NodeNormTest):
     """Test that every CURIE in every param_set resolves in NodeNorm."""
     NAME = "resolves"
     DESCRIPTION = "Each CURIE in each param_set must resolve to a non-null result in NodeNorm."
+    PARAMETERS = "One or more CURIEs per param_set."
+    WIKI_EXAMPLES = [
+        "{{BabelTest|Resolves|CHEBI:15365}}",
+        "{{BabelTest|Resolves|MONDO:0005015|DOID:9351}}",
+    ]
+    YAML_PARAMS = "    - CHEBI:15365\n    - [MONDO:0005015, DOID:9351]"
 
     def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                        label: str = "") -> Iterator[TestResult]:
@@ -24,7 +30,13 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
 class DoesNotResolveHandler(NodeNormTest):
     """Test that every CURIE in every param_set does NOT resolve in NodeNorm."""
     NAME = "doesnotresolve"
-    DESCRIPTION = "Each CURIE in each param_set must fail to resolve (return null) in NodeNorm."
+    DESCRIPTION = (
+        "Each CURIE in each param_set must fail to resolve (return null) in NodeNorm. "
+        "Use this to confirm that an identifier is intentionally not normalizable."
+    )
+    PARAMETERS = "One or more CURIEs per param_set."
+    WIKI_EXAMPLES = ["{{BabelTest|DoesNotResolve|FAKENS:99999}}"]
+    YAML_PARAMS = "    - FAKENS:99999"
 
     def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                        label: str = "") -> Iterator[TestResult]:
@@ -43,6 +55,9 @@ class ResolvesWithHandler(NodeNormTest):
         "All CURIEs within each param_set must resolve to the identical normalized result. "
         "Use this to assert that two identifiers are equivalent."
     )
+    PARAMETERS = "Two or more CURIEs per param_set. All must resolve to the same result."
+    WIKI_EXAMPLES = ["{{BabelTest|ResolvesWith|CHEBI:15365|PUBCHEM.COMPOUND:1}}"]
+    YAML_PARAMS = "    - [CHEBI:15365, PUBCHEM.COMPOUND:1]\n    - [MONDO:0005015, DOID:9351]"
 
     def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                        label: str = "") -> Iterator[TestResult]:
@@ -76,6 +91,12 @@ class ResolvesWithTypeHandler(NodeNormTest):
         "Each param_set must have at least two elements: the first is the expected Biolink type "
         "(e.g. 'biolink:Gene'), and the remainder are CURIEs that must resolve with that type."
     )
+    PARAMETERS = (
+        "Each param_set: first element is the expected Biolink type (e.g. `biolink:Gene`), "
+        "remaining elements are CURIEs."
+    )
+    WIKI_EXAMPLES = ["{{BabelTest|ResolvesWithType|biolink:Gene|NCBIGene:1}}"]
+    YAML_PARAMS = "    - [biolink:Gene, NCBIGene:1, HGNC:5]"
 
     def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                        label: str = "") -> Iterator[TestResult]:
diff --git a/tests/test_assertions_docs.py b/tests/test_assertions_docs.py
new file mode 100644
index 00000000..d98130ff
--- /dev/null
+++ b/tests/test_assertions_docs.py
@@ -0,0 +1,11 @@
+from src.babel_validation.assertions.gen_docs import generate_readme, README_PATH
+
+
+def test_assertions_readme_is_up_to_date():
+    expected = generate_readme()
+    actual = README_PATH.read_text(encoding="utf-8")
+    assert actual == expected, (
+        "assertions/README.md is out of date.\n"
+        "Regenerate it with:\n"
+        "    uv run python -m src.babel_validation.assertions.gen_docs"
+    )

From 4ed60913302181d596a1ae3f4ecb1a35062e1cf0 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Fri, 20 Feb 2026 23:25:44 -0500
Subject: [PATCH 030/126] Speed up GitHub issues test collection with
 pytest_generate_tests hook

Move parametrization from module-level @pytest.mark.parametrize to a
pytest_generate_tests hook in tests/github_issues/conftest.py. This
enables two fast paths: --issue fetches only named issues directly
(near-instant), and the full run pre-filters issues with BabelTest
syntax at collection time rather than creating test items for all issues.

Also fix get_test_issues_from_issue() to avoid a separate GitHub API
call per issue by using repository.full_name instead of
repository.organization.name.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .../github/github_issues_test_cases.py        | 43 +++++++++++++++--
 tests/github_issues/conftest.py               | 42 +++++++++++++++++
 tests/github_issues/test_github_issues.py     | 47 ++-----------------
 3 files changed, 85 insertions(+), 47 deletions(-)
 create mode 100644 tests/github_issues/conftest.py

diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index c3422e88..bec4d50f 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -107,10 +107,7 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
         :return: A list of GitHubIssueTest objects found in the issue body.
         """
 
-        github_org = github_issue.repository.organization.name
-        github_repo = github_issue.repository.name
-
-        github_issue_id = f"{github_org}/{github_repo}#{github_issue.number}"
+        github_issue_id = f"{github_issue.repository.full_name}#{github_issue.number}"
         self.logger.debug(f"Looking for tests in issue {github_issue_id}: {github_issue.title} ({str(github_issue.state)}, {github_issue.html_url})")
 
         # Is there an issue body at all?
@@ -162,6 +159,44 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
 
         return testrows
 
+    def issue_has_tests(self, issue: Issue.Issue) -> bool:
+        """Quick regex check to see if an issue body contains any BabelTest syntax."""
+        if not issue.body or issue.body.strip() == '':
+            return False
+        return bool(self.babeltest_pattern.search(issue.body) or
+                    self.babeltest_yaml_pattern.search(issue.body))
+
+    def get_issues_by_ids(self, issue_ids: list[str]) -> list[Issue.Issue]:
+        """
+        Fetch specific GitHub issues by their ID strings, supporting three formats:
+        - 'org/repo#N'  → direct fetch from that repo
+        - 'repo#N'      → search self.github_repositories for matching repo name
+        - 'N'           → fetch #N from all configured repositories
+        """
+        from github import GithubException
+        issues = []
+        for issue_id in issue_ids:
+            if m := re.match(r'^([^/]+)/([^#]+)#(\d+)$', issue_id):
+                # org/repo#N
+                issue = self.github.get_repo(f"{m.group(1)}/{m.group(2)}").get_issue(int(m.group(3)))
+                issues.append(issue)
+            elif m := re.match(r'^([^/#]+)#(\d+)$', issue_id):
+                # repo#N — find repo in configured list
+                repo_name, num = m.group(1), int(m.group(2))
+                for full_repo in self.github_repositories:
+                    if full_repo.split('/')[1] == repo_name:
+                        issues.append(self.github.get_repo(full_repo).get_issue(num))
+                        break
+            elif m := re.match(r'^(\d+)$', issue_id):
+                # N — try all configured repos
+                num = int(m.group(1))
+                for full_repo in self.github_repositories:
+                    try:
+                        issues.append(self.github.get_repo(full_repo).get_issue(num))
+                    except GithubException:
+                        pass
+        return issues
+
     def get_all_issues(self, github_repositories = None) -> Iterator[Issue.Issue]:
         """
         Get a list of test rows from one or more repositories.
diff --git a/tests/github_issues/conftest.py b/tests/github_issues/conftest.py
new file mode 100644
index 00000000..8b43ca01
--- /dev/null
+++ b/tests/github_issues/conftest.py
@@ -0,0 +1,42 @@
+import os
+
+import dotenv
+import pytest
+from github import Issue
+
+from src.babel_validation.sources.github.github_issues_test_cases import GitHubIssuesTestCases
+
+dotenv.load_dotenv()
+_github_token = os.getenv('GITHUB_TOKEN')
+_repos = [
+    'NCATSTranslator/Babel',
+    'NCATSTranslator/NodeNormalization',
+    'NCATSTranslator/NameResolution',
+    'TranslatorSRI/babel-validation',
+]
+github_issues_test_cases = GitHubIssuesTestCases(_github_token, _repos)
+
+
+def _issue_id(issue: Issue.Issue) -> str:
+    """Derive a test ID from an issue without making extra API calls."""
+    parts = issue.html_url.split('/')
+    return f"{parts[3]}/{parts[4]}#{issue.number}"
+
+
+def pytest_generate_tests(metafunc):
+    if "github_issue" not in metafunc.fixturenames:
+        return
+    issue_ids = metafunc.config.getoption("issue", default=[])
+    if issue_ids:
+        # Fast path: direct API call for each named issue (near-instant)
+        issues = github_issues_test_cases.get_issues_by_ids(issue_ids)
+    else:
+        # Standard path: fetch all, pre-filter to issues that have tests
+        issues = [i for i in github_issues_test_cases.get_all_issues()
+                  if github_issues_test_cases.issue_has_tests(i)]
+    metafunc.parametrize("github_issue", issues, ids=[_issue_id(i) for i in issues])
+
+
+@pytest.fixture(scope="session")
+def github_issues_test_cases_fixture():
+    return github_issues_test_cases
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 497afd71..c4eb06d7 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -1,62 +1,23 @@
 import itertools
-import os
 
-import dotenv
 import pytest
 from github import Issue
 
-from src.babel_validation.sources.github.github_issues_test_cases import GitHubIssuesTestCases
 from src.babel_validation.services.nameres import CachedNameRes
 from src.babel_validation.services.nodenorm import CachedNodeNorm
 from src.babel_validation.core.testrow import TestResult, TestStatus
 
-# Helper functions
-def get_github_issue_id(github_issue: Issue.Issue):
-    parts = github_issue.html_url.split('/')
-    return f"{parts[3]}/{parts[4]}#{github_issue.number}"
-
-# Initialize the test.
-dotenv.load_dotenv()
-github_token = os.getenv('GITHUB_TOKEN')
-github_issues_test_cases = GitHubIssuesTestCases(github_token, [
-    'NCATSTranslator/Babel',                # https://github.com/NCATSTranslator/Babel
-    'NCATSTranslator/NodeNormalization',    # https://github.com/NCATSTranslator/NodeNormalization
-    'NCATSTranslator/NameResolution',       # https://github.com/NCATSTranslator/NameResolution
-    'TranslatorSRI/babel-validation',       # https://github.com/TranslatorSRI/babel-validation
-])
-
-@pytest.mark.parametrize("github_issue", github_issues_test_cases.get_all_issues())
-def test_github_issue(target_info, github_issue, selected_github_issues, subtests):
-    # If github_issues is provided, we can skip all others.
-    if selected_github_issues:
-        # Check all three possible ways in which this issue might be specified.
-        github_issue_matched = False
-        for selected_github_issue in selected_github_issues:
-            if '/' in selected_github_issue:
-                github_issue_matched = (f"{github_issue.repository.organization.name}/{github_issue.repository.name}#{github_issue.number}" == selected_github_issue)
-            elif '#' in selected_github_issue:
-                github_issue_matched = (f"{github_issue.repository.name}#{github_issue.number}" == selected_github_issue)
-            else:
-                github_issue_matched = int(selected_github_issue) == github_issue.number
-            if github_issue_matched:
-                break
 
-        if github_issue_matched:
-            # This issue is one of those that should be tested.
-            pass
-        else:
-            pytest.skip(f"GitHub Issue {str(github_issue)} not included in list of GitHub issues to be tested: {selected_github_issues}.")
-            return
-
-    # Test this issue with NodeNorm.
+def test_github_issue(target_info, github_issue, github_issues_test_cases_fixture, subtests):
     nodenorm = CachedNodeNorm.from_url(target_info['NodeNormURL'])
     nameres = CachedNameRes.from_url(target_info['NameResURL'])
-    tests = github_issues_test_cases.get_test_issues_from_issue(github_issue)
+    tests = github_issues_test_cases_fixture.get_test_issues_from_issue(github_issue)
     if not tests:
         pytest.skip(f"No tests found in issue {github_issue}")
         return
 
-    issue_id = get_github_issue_id(github_issue)
+    parts = github_issue.html_url.split('/')
+    issue_id = f"{parts[3]}/{parts[4]}#{github_issue.number}"
     subtests_passed = 0
     subtests_failed = 0
 

From c63e2d19f44f98f3eee8ef790619b837fb4ff47b Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Fri, 20 Feb 2026 23:43:50 -0500
Subject: [PATCH 031/126] Parallelize GitHub issues tests with pytest-xdist

Add pytest-xdist[psutil] and filelock dependencies. Refactor
github_issues conftest to parametrize with picklable string IDs
instead of PyGithub Issue objects, add a filelock-guarded file cache
for the full issue list (1-hour TTL), and hydrate Issue objects in
a per-test fixture so xdist workers avoid redundant GitHub API scans.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 pyproject.toml                  |  2 +
 tests/github_issues/conftest.py | 45 +++++++++++++++++-----
 uv.lock                         | 68 +++++++++++++++++++++++++++++++++
 3 files changed, 106 insertions(+), 9 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2dca9751..7ccecf5b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,6 +12,8 @@ dependencies = [
     "openapi-spec-validator>=0.7.2",
     "pygithub>=2.8.1",
     "pytest>=9.0",
+    "pytest-xdist[psutil]",
+    "filelock",
     "requests>=2.32.5",
     "tqdm>=4.67.1",
 ]
diff --git a/tests/github_issues/conftest.py b/tests/github_issues/conftest.py
index 8b43ca01..d5739a63 100644
--- a/tests/github_issues/conftest.py
+++ b/tests/github_issues/conftest.py
@@ -1,7 +1,12 @@
+import json
 import os
+import tempfile
+import time
+from pathlib import Path
 
 import dotenv
 import pytest
+from filelock import FileLock
 from github import Issue
 
 from src.babel_validation.sources.github.github_issues_test_cases import GitHubIssuesTestCases
@@ -16,6 +21,10 @@
 ]
 github_issues_test_cases = GitHubIssuesTestCases(_github_token, _repos)
 
+_CACHE_FILE = Path(tempfile.gettempdir()) / "babel_validation_issues_cache.json"
+_LOCK_FILE = _CACHE_FILE.with_suffix(".lock")
+_CACHE_TTL = 3600  # 1 hour
+
 
 def _issue_id(issue: Issue.Issue) -> str:
     """Derive a test ID from an issue without making extra API calls."""
@@ -23,18 +32,36 @@ def _issue_id(issue: Issue.Issue) -> str:
     return f"{parts[3]}/{parts[4]}#{issue.number}"
 
 
+def _get_all_test_issue_ids() -> list[str]:
+    """Return IDs of all issues that contain tests, using a file-based cache."""
+    with FileLock(_LOCK_FILE):
+        if _CACHE_FILE.exists():
+            age = time.time() - _CACHE_FILE.stat().st_mtime
+            if age < _CACHE_TTL:
+                return json.loads(_CACHE_FILE.read_text())
+        issues = [i for i in github_issues_test_cases.get_all_issues()
+                  if github_issues_test_cases.issue_has_tests(i)]
+        ids = [_issue_id(i) for i in issues]
+        _CACHE_FILE.write_text(json.dumps(ids))
+        return ids
+
+
 def pytest_generate_tests(metafunc):
-    if "github_issue" not in metafunc.fixturenames:
+    if "github_issue_id" not in metafunc.fixturenames:
         return
-    issue_ids = metafunc.config.getoption("issue", default=[])
-    if issue_ids:
-        # Fast path: direct API call for each named issue (near-instant)
-        issues = github_issues_test_cases.get_issues_by_ids(issue_ids)
+    issue_id_filter = metafunc.config.getoption("issue", default=[])
+    if issue_id_filter:
+        issues = github_issues_test_cases.get_issues_by_ids(issue_id_filter)
+        ids = [_issue_id(i) for i in issues]
     else:
-        # Standard path: fetch all, pre-filter to issues that have tests
-        issues = [i for i in github_issues_test_cases.get_all_issues()
-                  if github_issues_test_cases.issue_has_tests(i)]
-    metafunc.parametrize("github_issue", issues, ids=[_issue_id(i) for i in issues])
+        ids = _get_all_test_issue_ids()
+    metafunc.parametrize("github_issue_id", ids, ids=ids)
+
+
+@pytest.fixture
+def github_issue(github_issue_id):
+    """Hydrate a GitHub Issue object from its string ID."""
+    return github_issues_test_cases.get_issues_by_ids([github_issue_id])[0]
 
 
 @pytest.fixture(scope="session")
diff --git a/uv.lock b/uv.lock
index 07752575..b6d3c196 100644
--- a/uv.lock
+++ b/uv.lock
@@ -19,9 +19,11 @@ dependencies = [
     { name = "black" },
     { name = "deepdiff" },
     { name = "dotenv" },
+    { name = "filelock" },
     { name = "openapi-spec-validator" },
     { name = "pygithub" },
     { name = "pytest" },
+    { name = "pytest-xdist", extra = ["psutil"] },
     { name = "requests" },
     { name = "tqdm" },
 ]
@@ -31,9 +33,11 @@ requires-dist = [
     { name = "black", specifier = ">=25.9.0" },
     { name = "deepdiff", specifier = ">=8.6.1" },
     { name = "dotenv", specifier = ">=0.9.9" },
+    { name = "filelock" },
     { name = "openapi-spec-validator", specifier = ">=0.7.2" },
     { name = "pygithub", specifier = ">=2.8.1" },
     { name = "pytest", specifier = ">=9.0" },
+    { name = "pytest-xdist", extras = ["psutil"] },
     { name = "requests", specifier = ">=2.32.5" },
     { name = "tqdm", specifier = ">=4.67.1" },
 ]
@@ -325,6 +329,24 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/b2/b7/545d2c10c1fc15e48653c91efde329a790f2eecfbbf2bd16003b5db2bab0/dotenv-0.9.9-py2.py3-none-any.whl", hash = "sha256:29cf74a087b31dafdb5a446b6d7e11cbce8ed2741540e2339c69fbef92c94ce9", size = 1892, upload-time = "2025-02-19T22:15:01.647Z" },
 ]
 
+[[package]]
+name = "execnet"
+version = "2.1.2"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/bf/89/780e11f9588d9e7128a3f87788354c7946a9cbb1401ad38a48c4db9a4f07/execnet-2.1.2.tar.gz", hash = "sha256:63d83bfdd9a23e35b9c6a3261412324f964c2ec8dcd8d3c6916ee9373e0befcd", size = 166622, upload-time = "2025-11-12T09:56:37.75Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/ab/84/02fc1827e8cdded4aa65baef11296a9bbe595c474f0d6d758af082d849fd/execnet-2.1.2-py3-none-any.whl", hash = "sha256:67fba928dd5a544b783f6056f449e5e3931a5c378b128bc18501f7ea79e296ec", size = 40708, upload-time = "2025-11-12T09:56:36.333Z" },
+]
+
+[[package]]
+name = "filelock"
+version = "3.24.3"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/73/92/a8e2479937ff39185d20dd6a851c1a63e55849e447a55e798cc2e1f49c65/filelock-3.24.3.tar.gz", hash = "sha256:011a5644dc937c22699943ebbfc46e969cdde3e171470a6e40b9533e5a72affa", size = 37935, upload-time = "2026-02-19T00:48:20.543Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/9c/0f/5d0c71a1aefeb08efff26272149e07ab922b64f46c63363756224bd6872e/filelock-3.24.3-py3-none-any.whl", hash = "sha256:426e9a4660391f7f8a810d71b0555bce9008b0a1cc342ab1f6947d37639e002d", size = 24331, upload-time = "2026-02-19T00:48:18.465Z" },
+]
+
 [[package]]
 name = "idna"
 version = "3.11"
@@ -516,6 +538,34 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/54/20/4d324d65cc6d9205fabedc306948156824eb9f0ee1633355a8f7ec5c66bf/pluggy-1.6.0-py3-none-any.whl", hash = "sha256:e920276dd6813095e9377c0bc5566d94c932c33b27a3e3945d8389c374dd4746", size = 20538, upload-time = "2025-05-15T12:30:06.134Z" },
 ]
 
+[[package]]
+name = "psutil"
+version = "7.2.2"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/aa/c6/d1ddf4abb55e93cebc4f2ed8b5d6dbad109ecb8d63748dd2b20ab5e57ebe/psutil-7.2.2.tar.gz", hash = "sha256:0746f5f8d406af344fd547f1c8daa5f5c33dbc293bb8d6a16d80b4bb88f59372", size = 493740, upload-time = "2026-01-28T18:14:54.428Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/51/08/510cbdb69c25a96f4ae523f733cdc963ae654904e8db864c07585ef99875/psutil-7.2.2-cp313-cp313t-macosx_10_13_x86_64.whl", hash = "sha256:2edccc433cbfa046b980b0df0171cd25bcaeb3a68fe9022db0979e7aa74a826b", size = 130595, upload-time = "2026-01-28T18:14:57.293Z" },
+    { url = "https://files.pythonhosted.org/packages/d6/f5/97baea3fe7a5a9af7436301f85490905379b1c6f2dd51fe3ecf24b4c5fbf/psutil-7.2.2-cp313-cp313t-macosx_11_0_arm64.whl", hash = "sha256:e78c8603dcd9a04c7364f1a3e670cea95d51ee865e4efb3556a3a63adef958ea", size = 131082, upload-time = "2026-01-28T18:14:59.732Z" },
+    { url = "https://files.pythonhosted.org/packages/37/d6/246513fbf9fa174af531f28412297dd05241d97a75911ac8febefa1a53c6/psutil-7.2.2-cp313-cp313t-manylinux2010_x86_64.manylinux_2_12_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:1a571f2330c966c62aeda00dd24620425d4b0cc86881c89861fbc04549e5dc63", size = 181476, upload-time = "2026-01-28T18:15:01.884Z" },
+    { url = "https://files.pythonhosted.org/packages/b8/b5/9182c9af3836cca61696dabe4fd1304e17bc56cb62f17439e1154f225dd3/psutil-7.2.2-cp313-cp313t-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:917e891983ca3c1887b4ef36447b1e0873e70c933afc831c6b6da078ba474312", size = 184062, upload-time = "2026-01-28T18:15:04.436Z" },
+    { url = "https://files.pythonhosted.org/packages/16/ba/0756dca669f5a9300d0cbcbfae9a4c30e446dfc7440ffe43ded5724bfd93/psutil-7.2.2-cp313-cp313t-win_amd64.whl", hash = "sha256:ab486563df44c17f5173621c7b198955bd6b613fb87c71c161f827d3fb149a9b", size = 139893, upload-time = "2026-01-28T18:15:06.378Z" },
+    { url = "https://files.pythonhosted.org/packages/1c/61/8fa0e26f33623b49949346de05ec1ddaad02ed8ba64af45f40a147dbfa97/psutil-7.2.2-cp313-cp313t-win_arm64.whl", hash = "sha256:ae0aefdd8796a7737eccea863f80f81e468a1e4cf14d926bd9b6f5f2d5f90ca9", size = 135589, upload-time = "2026-01-28T18:15:08.03Z" },
+    { url = "https://files.pythonhosted.org/packages/81/69/ef179ab5ca24f32acc1dac0c247fd6a13b501fd5534dbae0e05a1c48b66d/psutil-7.2.2-cp314-cp314t-macosx_10_15_x86_64.whl", hash = "sha256:eed63d3b4d62449571547b60578c5b2c4bcccc5387148db46e0c2313dad0ee00", size = 130664, upload-time = "2026-01-28T18:15:09.469Z" },
+    { url = "https://files.pythonhosted.org/packages/7b/64/665248b557a236d3fa9efc378d60d95ef56dd0a490c2cd37dafc7660d4a9/psutil-7.2.2-cp314-cp314t-macosx_11_0_arm64.whl", hash = "sha256:7b6d09433a10592ce39b13d7be5a54fbac1d1228ed29abc880fb23df7cb694c9", size = 131087, upload-time = "2026-01-28T18:15:11.724Z" },
+    { url = "https://files.pythonhosted.org/packages/d5/2e/e6782744700d6759ebce3043dcfa661fb61e2fb752b91cdeae9af12c2178/psutil-7.2.2-cp314-cp314t-manylinux2010_x86_64.manylinux_2_12_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:1fa4ecf83bcdf6e6c8f4449aff98eefb5d0604bf88cb883d7da3d8d2d909546a", size = 182383, upload-time = "2026-01-28T18:15:13.445Z" },
+    { url = "https://files.pythonhosted.org/packages/57/49/0a41cefd10cb7505cdc04dab3eacf24c0c2cb158a998b8c7b1d27ee2c1f5/psutil-7.2.2-cp314-cp314t-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:e452c464a02e7dc7822a05d25db4cde564444a67e58539a00f929c51eddda0cf", size = 185210, upload-time = "2026-01-28T18:15:16.002Z" },
+    { url = "https://files.pythonhosted.org/packages/dd/2c/ff9bfb544f283ba5f83ba725a3c5fec6d6b10b8f27ac1dc641c473dc390d/psutil-7.2.2-cp314-cp314t-win_amd64.whl", hash = "sha256:c7663d4e37f13e884d13994247449e9f8f574bc4655d509c3b95e9ec9e2b9dc1", size = 141228, upload-time = "2026-01-28T18:15:18.385Z" },
+    { url = "https://files.pythonhosted.org/packages/f2/fc/f8d9c31db14fcec13748d373e668bc3bed94d9077dbc17fb0eebc073233c/psutil-7.2.2-cp314-cp314t-win_arm64.whl", hash = "sha256:11fe5a4f613759764e79c65cf11ebdf26e33d6dd34336f8a337aa2996d71c841", size = 136284, upload-time = "2026-01-28T18:15:19.912Z" },
+    { url = "https://files.pythonhosted.org/packages/e7/36/5ee6e05c9bd427237b11b3937ad82bb8ad2752d72c6969314590dd0c2f6e/psutil-7.2.2-cp36-abi3-macosx_10_9_x86_64.whl", hash = "sha256:ed0cace939114f62738d808fdcecd4c869222507e266e574799e9c0faa17d486", size = 129090, upload-time = "2026-01-28T18:15:22.168Z" },
+    { url = "https://files.pythonhosted.org/packages/80/c4/f5af4c1ca8c1eeb2e92ccca14ce8effdeec651d5ab6053c589b074eda6e1/psutil-7.2.2-cp36-abi3-macosx_11_0_arm64.whl", hash = "sha256:1a7b04c10f32cc88ab39cbf606e117fd74721c831c98a27dc04578deb0c16979", size = 129859, upload-time = "2026-01-28T18:15:23.795Z" },
+    { url = "https://files.pythonhosted.org/packages/b5/70/5d8df3b09e25bce090399cf48e452d25c935ab72dad19406c77f4e828045/psutil-7.2.2-cp36-abi3-manylinux2010_x86_64.manylinux_2_12_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:076a2d2f923fd4821644f5ba89f059523da90dc9014e85f8e45a5774ca5bc6f9", size = 155560, upload-time = "2026-01-28T18:15:25.976Z" },
+    { url = "https://files.pythonhosted.org/packages/63/65/37648c0c158dc222aba51c089eb3bdfa238e621674dc42d48706e639204f/psutil-7.2.2-cp36-abi3-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:b0726cecd84f9474419d67252add4ac0cd9811b04d61123054b9fb6f57df6e9e", size = 156997, upload-time = "2026-01-28T18:15:27.794Z" },
+    { url = "https://files.pythonhosted.org/packages/8e/13/125093eadae863ce03c6ffdbae9929430d116a246ef69866dad94da3bfbc/psutil-7.2.2-cp36-abi3-musllinux_1_2_aarch64.whl", hash = "sha256:fd04ef36b4a6d599bbdb225dd1d3f51e00105f6d48a28f006da7f9822f2606d8", size = 148972, upload-time = "2026-01-28T18:15:29.342Z" },
+    { url = "https://files.pythonhosted.org/packages/04/78/0acd37ca84ce3ddffaa92ef0f571e073faa6d8ff1f0559ab1272188ea2be/psutil-7.2.2-cp36-abi3-musllinux_1_2_x86_64.whl", hash = "sha256:b58fabe35e80b264a4e3bb23e6b96f9e45a3df7fb7eed419ac0e5947c61e47cc", size = 148266, upload-time = "2026-01-28T18:15:31.597Z" },
+    { url = "https://files.pythonhosted.org/packages/b4/90/e2159492b5426be0c1fef7acba807a03511f97c5f86b3caeda6ad92351a7/psutil-7.2.2-cp37-abi3-win_amd64.whl", hash = "sha256:eb7e81434c8d223ec4a219b5fc1c47d0417b12be7ea866e24fb5ad6e84b3d988", size = 137737, upload-time = "2026-01-28T18:15:33.849Z" },
+    { url = "https://files.pythonhosted.org/packages/8c/c7/7bb2e321574b10df20cbde462a94e2b71d05f9bbda251ef27d104668306a/psutil-7.2.2-cp37-abi3-win_arm64.whl", hash = "sha256:8c233660f575a5a89e6d4cb65d9f938126312bca76d8fe087b947b3a1aaac9ee", size = 134617, upload-time = "2026-01-28T18:15:36.514Z" },
+]
+
 [[package]]
 name = "pycparser"
 version = "2.23"
@@ -615,6 +665,24 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/3b/ab/b3226f0bd7cdcf710fbede2b3548584366da3b19b5021e74f5bde2a8fa3f/pytest-9.0.2-py3-none-any.whl", hash = "sha256:711ffd45bf766d5264d487b917733b453d917afd2b0ad65223959f59089f875b", size = 374801, upload-time = "2025-12-06T21:30:49.154Z" },
 ]
 
+[[package]]
+name = "pytest-xdist"
+version = "3.8.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "execnet" },
+    { name = "pytest" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/78/b4/439b179d1ff526791eb921115fca8e44e596a13efeda518b9d845a619450/pytest_xdist-3.8.0.tar.gz", hash = "sha256:7e578125ec9bc6050861aa93f2d59f1d8d085595d6551c2c90b6f4fad8d3a9f1", size = 88069, upload-time = "2025-07-01T13:30:59.346Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/ca/31/d4e37e9e550c2b92a9cbc2e4d0b7420a27224968580b5a447f420847c975/pytest_xdist-3.8.0-py3-none-any.whl", hash = "sha256:202ca578cfeb7370784a8c33d6d05bc6e13b4f25b5053c30a152269fd10f0b88", size = 46396, upload-time = "2025-07-01T13:30:56.632Z" },
+]
+
+[package.optional-dependencies]
+psutil = [
+    { name = "psutil" },
+]
+
 [[package]]
 name = "python-dotenv"
 version = "1.2.1"

From 75abe00ebf48b3ab68118be0d7dba39b6c48b5ba Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Fri, 20 Feb 2026 23:49:07 -0500
Subject: [PATCH 032/126] Cache Google Sheet CSV to disk so xdist workers share
 one download

Add a filelock-guarded file cache (TTL 1 hour) in GoogleSheetTestCases.__init__
so that when pytest-xdist workers reimport the module they read from the local
temp file instead of each making a redundant HTTP request to Google Sheets.

This enables parallel execution of gsheet tests with -n auto.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .../google_sheets/google_sheet_test_cases.py  | 23 ++++++++++++++++---
 1 file changed, 20 insertions(+), 3 deletions(-)

diff --git a/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py b/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py
index 152af4bb..fcfdb571 100644
--- a/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py
+++ b/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py
@@ -3,15 +3,22 @@
 #
 # This library contains classes and methods for accessing those test cases.
 import csv
+import hashlib
 import io
+import tempfile
+import time
 from collections import Counter
+from pathlib import Path
 
 import pytest
 import requests
 from _pytest.mark import ParameterSet
+from filelock import FileLock
 
 from src.babel_validation.core.testrow import TestRow
 
+_CACHE_TTL = 3600  # 1 hour
+
 
 class GoogleSheetTestCases:
     """
@@ -28,9 +35,19 @@ def __init__(self, google_sheet_id="11zebx8Qs1Tc3ShQR9nh4HRW8QSoo8k65w_xIaftN0no
         """
 
         self.google_sheet_id = google_sheet_id
-        csv_url = f"https://docs.google.com/spreadsheets/d/{google_sheet_id}/gviz/tq?tqx=out:csv&sheet=Tests"
-        response = requests.get(csv_url)
-        self.csv_content = response.text
+
+        sheet_hash = hashlib.md5(google_sheet_id.encode()).hexdigest()[:8]
+        cache_file = Path(tempfile.gettempdir()) / f"babel_validation_gsheet_{sheet_hash}.csv"
+        lock_file = cache_file.with_suffix(".lock")
+
+        with FileLock(lock_file):
+            if cache_file.exists() and (time.time() - cache_file.stat().st_mtime) < _CACHE_TTL:
+                self.csv_content = cache_file.read_text(encoding="utf-8")
+            else:
+                csv_url = f"https://docs.google.com/spreadsheets/d/{google_sheet_id}/gviz/tq?tqx=out:csv&sheet=Tests"
+                response = requests.get(csv_url)
+                self.csv_content = response.text
+                cache_file.write_text(self.csv_content, encoding="utf-8")
 
         self.rows = []
         with io.StringIO(self.csv_content) as f:

From 3bf169e32da50ce3790d74028e83c0f003b7e9d2 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sat, 21 Feb 2026 00:14:44 -0500
Subject: [PATCH 033/126] Fix non-deterministic test ordering under
 pytest-xdist

IDENTIFIERS_WITH_DESCRIPTIONS and IDENTIFIERS_WITHOUT_DESCRIPTIONS were
Python sets, which have unpredictable iteration order across processes.
Workers collected tests in different orders, triggering xdist's
"Different tests were collected" fatal error.

Changed both to lists so parametrize order is stable across all workers.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 tests/nodenorm/test_nodenorm_descriptions.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/nodenorm/test_nodenorm_descriptions.py b/tests/nodenorm/test_nodenorm_descriptions.py
index 75831944..1b82c6ff 100644
--- a/tests/nodenorm/test_nodenorm_descriptions.py
+++ b/tests/nodenorm/test_nodenorm_descriptions.py
@@ -6,15 +6,15 @@
 import pytest
 import requests
 
-IDENTIFIERS_WITH_DESCRIPTIONS = {
+IDENTIFIERS_WITH_DESCRIPTIONS = [
     'MESH:D014867',
     'NCIT:C34373',
     'NCBIGene:1756',
-}
+]
 
-IDENTIFIERS_WITHOUT_DESCRIPTIONS = {
+IDENTIFIERS_WITHOUT_DESCRIPTIONS = [
     'UMLS:C0665297',        # natalizumab
-}
+]
 
 @pytest.mark.parametrize('curie', IDENTIFIERS_WITH_DESCRIPTIONS)
 def test_descriptions(target_info, curie):

From 93753b0943d57cb019ef843b9e2c2fe75de3a2bb Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sat, 21 Feb 2026 00:28:23 -0500
Subject: [PATCH 034/126] Cleaned up code a bit.

---
 src/babel_validation/core/testrow.py                       | 4 ++--
 .../sources/google_sheets/google_sheet_test_cases.py       | 7 ++++---
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/babel_validation/core/testrow.py b/src/babel_validation/core/testrow.py
index 88ae3828..35cd1ca9 100644
--- a/src/babel_validation/core/testrow.py
+++ b/src/babel_validation/core/testrow.py
@@ -37,8 +37,8 @@ def __str__(self):
     def from_data_row(row):
         return TestRow(
             Category=row.get('Category', ''),
-            ExpectPassInNodeNorm=row.get('Passes in NodeNorm', '') == 'y',
-            ExpectPassInNameRes=row.get('Passes in NameRes', '') == 'y',
+            ExpectPassInNodeNorm=row.get('Passes in NodeNorm', '').strip().lower() == 'y',
+            ExpectPassInNameRes=row.get('Passes in NameRes', '').strip().lower() == 'y',
             Flags=set(row.get('Flags', '').split('|')),
             QueryLabel=row.get('Query Label', ''),
             QueryID=row.get('Query ID', ''),
diff --git a/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py b/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py
index fcfdb571..9ebdca79 100644
--- a/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py
+++ b/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py
@@ -71,7 +71,8 @@ def has_nonempty_value(d: dict):
         for count, row in enumerate(self.rows):
             # Note that count is off by two: presumably one for the header row and one because we count from zero
             # but Google Sheets counts from one.
-            row_id = f"{test_id_prefix}:row={count + 2}"
+            row_count = count + 2
+            row_id = f"{test_id_prefix}:row={row_count}"
 
             if has_nonempty_value(row):
                 tr = TestRow.from_data_row(row)
@@ -83,7 +84,7 @@ def has_nonempty_value(d: dict):
                         trows.append(pytest.param(
                             tr,
                             marks=pytest.mark.xfail(
-                                reason=f"Test row {count + 2} is marked as not expected to pass NodeNorm in the "
+                                reason=f"Test row {row_count} is marked as not expected to pass NodeNorm in the "
                                        f"Google Sheet: {tr}",
                                 strict=True),
                             id=row_id
@@ -96,7 +97,7 @@ def has_nonempty_value(d: dict):
                         trows.append(pytest.param(
                             tr,
                             marks=pytest.mark.xfail(
-                                reason=f"Test row {count + 2} is marked as not expected to pass NameRes in the "
+                                reason=f"Test row {row_count} is marked as not expected to pass NameRes in the "
                                        f"Google Sheet: {tr}",
                                 strict=True),
                             id=row_id

From 2e3b93a3cfa4152de840c600707524364e976286 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sat, 21 Feb 2026 01:14:46 -0500
Subject: [PATCH 035/126] Improved outputs.

---
 src/babel_validation/assertions/nameres.py | 3 ++-
 tests/github_issues/test_github_issues.py  | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/babel_validation/assertions/nameres.py b/src/babel_validation/assertions/nameres.py
index c4a81264..ce1b25d1 100644
--- a/src/babel_validation/assertions/nameres.py
+++ b/src/babel_validation/assertions/nameres.py
@@ -49,7 +49,8 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
         try:
             found_index = curies.index(expected_curie)
         except ValueError:
-            yield self.failed(f"{expected_curie_string} not found when searching for '{search_query}' in NameRes {nameres}: {json.dumps(results, indent=2, sort_keys=True)}")
+            print(f"{expected_curie_string} not found when searching for '{search_query}' in NameRes {nameres}: {json.dumps(results, indent=2, sort_keys=True)}")
+            yield self.failed(f"{expected_curie_string} not found when searching for '{search_query}' in NameRes {nameres}")
             return
 
         if found_index <= pass_if_found_in_top:
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index c4eb06d7..5f4b113d 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -26,7 +26,7 @@ def test_github_issue(target_info, github_issue, github_issues_test_cases_fixtur
         results_nameres = test_issue.test_with_nameres(nodenorm, nameres)
 
         for result in itertools.chain(results_nodenorm, results_nameres):
-            with subtests.test(msg=f"{issue_id} ({github_issue.state}): {result.message}"):
+            with subtests.test(msg=issue_id):
                 match result:
                     case TestResult(status=TestStatus.Passed, message=message):
                         subtests_passed += 1

From db7933b9e96f3bc7dd6d9ddec1f12f7356bea7b7 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sat, 21 Feb 2026 01:27:25 -0500
Subject: [PATCH 036/126] Always download fresh Google Sheet data on each test
 run
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Replace the 1-hour TTL with per-run invalidation:
- pytest_configure hook in conftest.py deletes the gsheet CSV cache at the
  start of each run (controller only, not xdist workers).
- GoogleSheetTestCases.__init__ now just checks whether the cache file exists;
  no more time-based TTL.

Result: the controller downloads once, workers share that file — but the next
pytest invocation always starts fresh, so edits to the Google Sheet are
immediately reflected.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .../google_sheets/google_sheet_test_cases.py      |  5 +----
 tests/conftest.py                                 | 15 +++++++++++++++
 2 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py b/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py
index 9ebdca79..af076a7b 100644
--- a/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py
+++ b/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py
@@ -6,7 +6,6 @@
 import hashlib
 import io
 import tempfile
-import time
 from collections import Counter
 from pathlib import Path
 
@@ -17,8 +16,6 @@
 
 from src.babel_validation.core.testrow import TestRow
 
-_CACHE_TTL = 3600  # 1 hour
-
 
 class GoogleSheetTestCases:
     """
@@ -41,7 +38,7 @@ def __init__(self, google_sheet_id="11zebx8Qs1Tc3ShQR9nh4HRW8QSoo8k65w_xIaftN0no
         lock_file = cache_file.with_suffix(".lock")
 
         with FileLock(lock_file):
-            if cache_file.exists() and (time.time() - cache_file.stat().st_mtime) < _CACHE_TTL:
+            if cache_file.exists():
                 self.csv_content = cache_file.read_text(encoding="utf-8")
             else:
                 csv_url = f"https://docs.google.com/spreadsheets/d/{google_sheet_id}/gviz/tq?tqx=out:csv&sheet=Tests"
diff --git a/tests/conftest.py b/tests/conftest.py
index bf5d233c..69c5008f 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,7 +1,10 @@
 #
 # conftest.py - pytest configuration settings
 #
+import glob
+import os
 import os.path
+import tempfile
 
 import pytest
 import configparser
@@ -25,6 +28,18 @@ def get_targets_ini_path(config):
     return config_path
 
 
+def pytest_configure(config):
+    # Delete the Google Sheet CSV cache at the start of each run so tests always
+    # use a fresh download. Only the controller does this — xdist workers skip it
+    # so they can share the cache file written by the controller.
+    if not os.environ.get('PYTEST_XDIST_WORKER'):
+        for f in glob.glob(os.path.join(tempfile.gettempdir(), 'babel_validation_gsheet_*.csv')):
+            try:
+                os.unlink(f)
+            except FileNotFoundError:
+                pass
+
+
 def pytest_addoption(parser):
     # The target environment(s) to target.
     parser.addoption(

From 768cf917e1946f88337f16da2835f61368fe3624 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sat, 21 Feb 2026 01:38:45 -0500
Subject: [PATCH 037/126] xfail open GitHub issues so failures don't block CI
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Apply pytest.mark.xfail(strict=False) dynamically to each test when the
GitHub issue is still open:
- Open issue + any subtest fails  → XFAIL  (x) — known outstanding issue
- Open issue + all subtests pass  → XPASS  (X) — issue ready to be closed
- Closed issue + any subtest fails → FAIL  (F) — regression, needs attention
- Closed issue + all subtests pass → PASS  (.) — as expected

Removes the ad-hoc issue-state consistency subtests at the bottom, which
are now fully covered by the xfail mechanism. Also drops the unused
`from github import Issue` import.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 tests/github_issues/test_github_issues.py | 31 +++++++----------------
 1 file changed, 9 insertions(+), 22 deletions(-)

diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 5f4b113d..80c97dcd 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -1,14 +1,13 @@
 import itertools
 
 import pytest
-from github import Issue
 
 from src.babel_validation.services.nameres import CachedNameRes
 from src.babel_validation.services.nodenorm import CachedNodeNorm
 from src.babel_validation.core.testrow import TestResult, TestStatus
 
 
-def test_github_issue(target_info, github_issue, github_issues_test_cases_fixture, subtests):
+def test_github_issue(request, target_info, github_issue, github_issues_test_cases_fixture, subtests):
     nodenorm = CachedNodeNorm.from_url(target_info['NodeNormURL'])
     nameres = CachedNameRes.from_url(target_info['NameResURL'])
     tests = github_issues_test_cases_fixture.get_test_issues_from_issue(github_issue)
@@ -18,8 +17,14 @@ def test_github_issue(target_info, github_issue, github_issues_test_cases_fixtur
 
     parts = github_issue.html_url.split('/')
     issue_id = f"{parts[3]}/{parts[4]}#{github_issue.number}"
-    subtests_passed = 0
-    subtests_failed = 0
+
+    # Open issues are expected to have failing tests. Mark as xfail(strict=False) so
+    # that failures show as XFAIL (x) and unexpected full passes show as XPASS (X).
+    if github_issue.state == "open":
+        request.node.add_marker(pytest.mark.xfail(
+            reason=f"Issue {issue_id} is still open",
+            strict=False,
+        ))
 
     for test_issue in tests:
         results_nodenorm = test_issue.test_with_nodenorm(nodenorm)
@@ -29,31 +34,13 @@ def test_github_issue(target_info, github_issue, github_issues_test_cases_fixtur
             with subtests.test(msg=issue_id):
                 match result:
                     case TestResult(status=TestStatus.Passed, message=message):
-                        subtests_passed += 1
                         assert True, f"{issue_id} ({github_issue.state}): {message}"
 
                     case TestResult(status=TestStatus.Failed, message=message):
-                        subtests_failed += 1
                         assert False, f"{issue_id} ({github_issue.state}): {message}"
 
                     case TestResult(status=TestStatus.Skipped, message=message):
                         pytest.skip(f"{issue_id} ({github_issue.state}): {message}")
 
                     case _:
-                        subtests_failed += 1
                         assert False, f"Unknown result from {issue_id}: {result}"
-
-    # Issue state vs. test results consistency checks
-    if github_issue.state == "closed" and subtests_failed > 0:
-        with subtests.test(msg=f"Issue state: {issue_id} is closed but has failing tests"):
-            assert False, (
-                f"Issue {issue_id} is closed but {subtests_failed} subtest(s) failed. "
-                f"Consider reopening: {github_issue.html_url}"
-            )
-
-    if github_issue.state == "open" and subtests_passed > 0 and subtests_failed == 0:
-        with subtests.test(msg=f"Issue state: {issue_id} is open but all tests pass"):
-            pytest.xfail(
-                f"Issue {issue_id} is open but all {subtests_passed} subtest(s) passed. "
-                f"Consider closing: {github_issue.html_url}"
-            )

From 6ee74413c94f424784c4feb33c121ca5f48cacf8 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sat, 21 Feb 2026 01:41:48 -0500
Subject: [PATCH 038/126] Wipe GitHub issues cache at the start of every test
 run

Same pattern as the Google Sheet cache: the pytest_configure hook in
tests/conftest.py now also deletes babel_validation_issues_cache.json on
startup (controller only, not xdist workers). The TTL check in
_get_all_test_issue_ids() is replaced with a plain existence check, so
workers share the file the controller wrote without re-fetching.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 tests/conftest.py               | 4 ++++
 tests/github_issues/conftest.py | 6 +-----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 69c5008f..7de6e13b 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -38,6 +38,10 @@ def pytest_configure(config):
                 os.unlink(f)
             except FileNotFoundError:
                 pass
+        try:
+            os.unlink(os.path.join(tempfile.gettempdir(), 'babel_validation_issues_cache.json'))
+        except FileNotFoundError:
+            pass
 
 
 def pytest_addoption(parser):
diff --git a/tests/github_issues/conftest.py b/tests/github_issues/conftest.py
index d5739a63..6e9f74df 100644
--- a/tests/github_issues/conftest.py
+++ b/tests/github_issues/conftest.py
@@ -1,7 +1,6 @@
 import json
 import os
 import tempfile
-import time
 from pathlib import Path
 
 import dotenv
@@ -23,7 +22,6 @@
 
 _CACHE_FILE = Path(tempfile.gettempdir()) / "babel_validation_issues_cache.json"
 _LOCK_FILE = _CACHE_FILE.with_suffix(".lock")
-_CACHE_TTL = 3600  # 1 hour
 
 
 def _issue_id(issue: Issue.Issue) -> str:
@@ -36,9 +34,7 @@ def _get_all_test_issue_ids() -> list[str]:
     """Return IDs of all issues that contain tests, using a file-based cache."""
     with FileLock(_LOCK_FILE):
         if _CACHE_FILE.exists():
-            age = time.time() - _CACHE_FILE.stat().st_mtime
-            if age < _CACHE_TTL:
-                return json.loads(_CACHE_FILE.read_text())
+            return json.loads(_CACHE_FILE.read_text())
         issues = [i for i in github_issues_test_cases.get_all_issues()
                   if github_issues_test_cases.issue_has_tests(i)]
         ids = [_issue_id(i) for i in issues]

From 74c5e3584e651f5cc83870e1a586802b80b2bd92 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sat, 21 Feb 2026 02:04:25 -0500
Subject: [PATCH 039/126] Add system tests for invalid BabelTest assertion name
 detection

Documents and verifies that unknown assertion names are silently parsed
but raise ValueError at execution time for both wiki and YAML syntaxes.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 tests/github_issues/test_system.py | 61 ++++++++++++++++++++++++++++++
 1 file changed, 61 insertions(+)
 create mode 100644 tests/github_issues/test_system.py

diff --git a/tests/github_issues/test_system.py b/tests/github_issues/test_system.py
new file mode 100644
index 00000000..ae1fe4f3
--- /dev/null
+++ b/tests/github_issues/test_system.py
@@ -0,0 +1,61 @@
+"""System tests for BabelTest trigger detection in GitHub issue bodies."""
+
+from unittest.mock import MagicMock
+import pytest
+
+INVALID_NAME = "NotARealAssertion"
+
+
+def _mock_issue(body: str, number: int = 999) -> MagicMock:
+    """Minimal mock GitHub Issue for get_test_issues_from_issue()."""
+    issue = MagicMock()
+    issue.body = body
+    issue.number = number
+    issue.repository.full_name = "test-org/test-repo"
+    return issue
+
+
+class TestInvalidAssertionNameDetection:
+    """Invalid assertion names are parsed but raise ValueError at execution time."""
+
+    def _wiki_issue(self):
+        return _mock_issue(f"{{{{BabelTest|{INVALID_NAME}|CHEBI:90926}}}}")
+
+    def _yaml_issue(self):
+        return _mock_issue(
+            f"```yaml\nbabel_tests:\n  {INVALID_NAME}:\n  - CHEBI:90926\n```"
+        )
+
+    # --- parsing: invalid names are extracted, not rejected ---
+
+    def test_wiki_syntax_parses_invalid_name(self, github_issues_test_cases_fixture):
+        tests = github_issues_test_cases_fixture.get_test_issues_from_issue(self._wiki_issue())
+        assert len(tests) == 1
+        assert tests[0].assertion == INVALID_NAME
+
+    def test_yaml_syntax_parses_invalid_name(self, github_issues_test_cases_fixture):
+        tests = github_issues_test_cases_fixture.get_test_issues_from_issue(self._yaml_issue())
+        assert len(tests) == 1
+        assert tests[0].assertion == INVALID_NAME
+
+    # --- execution: invalid names raise ValueError before any service call ---
+
+    def test_wiki_invalid_name_raises_on_nodenorm(self, github_issues_test_cases_fixture):
+        tests = github_issues_test_cases_fixture.get_test_issues_from_issue(self._wiki_issue())
+        with pytest.raises(ValueError, match="Unknown assertion type"):
+            list(tests[0].test_with_nodenorm(None))
+
+    def test_wiki_invalid_name_raises_on_nameres(self, github_issues_test_cases_fixture):
+        tests = github_issues_test_cases_fixture.get_test_issues_from_issue(self._wiki_issue())
+        with pytest.raises(ValueError, match="Unknown assertion type"):
+            list(tests[0].test_with_nameres(None, None))
+
+    def test_yaml_invalid_name_raises_on_nodenorm(self, github_issues_test_cases_fixture):
+        tests = github_issues_test_cases_fixture.get_test_issues_from_issue(self._yaml_issue())
+        with pytest.raises(ValueError, match="Unknown assertion type"):
+            list(tests[0].test_with_nodenorm(None))
+
+    def test_yaml_invalid_name_raises_on_nameres(self, github_issues_test_cases_fixture):
+        tests = github_issues_test_cases_fixture.get_test_issues_from_issue(self._yaml_issue())
+        with pytest.raises(ValueError, match="Unknown assertion type"):
+            list(tests[0].test_with_nameres(None, None))

From 33aa773c293c875c7e7b8986bd65499855e4fa0e Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sat, 28 Feb 2026 00:20:22 -0500
Subject: [PATCH 040/126] Report failing subtests of open issues as XFAIL
 instead of FAIL

When an issue is open, individual failing subtests now call pytest.xfail()
imperatively so they show as x (XFAIL) rather than F (FAIL) in the output.
A parent-level pytest.xfail() is also called after all subtests complete
(when any xfailed) to ensure the parent shows as XFAIL rather than XPASS.
This preserves the XPASS signal for the case where all subtests pass on an
open issue, indicating the issue may be ready to close.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 tests/github_issues/test_github_issues.py | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 80c97dcd..4aaa151c 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -17,15 +17,17 @@ def test_github_issue(request, target_info, github_issue, github_issues_test_cas
 
     parts = github_issue.html_url.split('/')
     issue_id = f"{parts[3]}/{parts[4]}#{github_issue.number}"
+    is_open = github_issue.state == "open"
 
     # Open issues are expected to have failing tests. Mark as xfail(strict=False) so
-    # that failures show as XFAIL (x) and unexpected full passes show as XPASS (X).
-    if github_issue.state == "open":
+    # that if all subtests pass, the parent shows as XPASS (X) — issue ready to close.
+    if is_open:
         request.node.add_marker(pytest.mark.xfail(
             reason=f"Issue {issue_id} is still open",
             strict=False,
         ))
 
+    any_subtest_xfailed = False
     for test_issue in tests:
         results_nodenorm = test_issue.test_with_nodenorm(nodenorm)
         results_nameres = test_issue.test_with_nameres(nodenorm, nameres)
@@ -37,10 +39,19 @@ def test_github_issue(request, target_info, github_issue, github_issues_test_cas
                         assert True, f"{issue_id} ({github_issue.state}): {message}"
 
                     case TestResult(status=TestStatus.Failed, message=message):
-                        assert False, f"{issue_id} ({github_issue.state}): {message}"
+                        if is_open:
+                            any_subtest_xfailed = True
+                            pytest.xfail(f"Issue {issue_id} is still open: {message}")
+                        else:
+                            assert False, f"{issue_id} ({github_issue.state}): {message}"
 
                     case TestResult(status=TestStatus.Skipped, message=message):
                         pytest.skip(f"{issue_id} ({github_issue.state}): {message}")
 
                     case _:
                         assert False, f"Unknown result from {issue_id}: {result}"
+
+    # If any subtest xfailed, also xfail the parent — otherwise the parent would show
+    # as XPASS (masking the distinction between "all pass" and "some fail").
+    if is_open and any_subtest_xfailed:
+        pytest.xfail(f"Issue {issue_id} has failing subtests (issue is still open)")

From d238f38d0ae36fdf7d2919158b07a1368f8e0b5a Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sat, 28 Feb 2026 00:30:43 -0500
Subject: [PATCH 041/126] Improved outputs.

---
 tests/github_issues/test_github_issues.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 4aaa151c..03ba3752 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -27,12 +27,15 @@ def test_github_issue(request, target_info, github_issue, github_issues_test_cas
             strict=False,
         ))
 
-    any_subtest_xfailed = False
+    count_subtests = 0
+    count_subtests_xfailed = 0
     for test_issue in tests:
         results_nodenorm = test_issue.test_with_nodenorm(nodenorm)
         results_nameres = test_issue.test_with_nameres(nodenorm, nameres)
 
         for result in itertools.chain(results_nodenorm, results_nameres):
+            count_subtests += 1
+
             with subtests.test(msg=issue_id):
                 match result:
                     case TestResult(status=TestStatus.Passed, message=message):
@@ -40,8 +43,8 @@ def test_github_issue(request, target_info, github_issue, github_issues_test_cas
 
                     case TestResult(status=TestStatus.Failed, message=message):
                         if is_open:
-                            any_subtest_xfailed = True
-                            pytest.xfail(f"Issue {issue_id} is still open: {message}")
+                            count_subtests_xfailed += 1
+                            pytest.xfail(message)
                         else:
                             assert False, f"{issue_id} ({github_issue.state}): {message}"
 
@@ -53,5 +56,5 @@ def test_github_issue(request, target_info, github_issue, github_issues_test_cas
 
     # If any subtest xfailed, also xfail the parent — otherwise the parent would show
     # as XPASS (masking the distinction between "all pass" and "some fail").
-    if is_open and any_subtest_xfailed:
-        pytest.xfail(f"Issue {issue_id} has failing subtests (issue is still open)")
+    if is_open and (count_subtests_xfailed > 0):
+        pytest.xfail(f"Open issue {issue_id} has {count_subtests_xfailed:,} failing subtests out of {count_subtests:,} ({count_subtests_xfailed/count_subtests:.0%})")

From 8807972533198c275e0f3c6d37df7452233c0d36 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sat, 28 Feb 2026 00:47:47 -0500
Subject: [PATCH 042/126] Speed up GitHub issues test collection via Search API

Replace full-repo pagination with GitHub Search API in
get_issues_with_tests(), reducing collection from O(all issues) fetches
to O(matching issues). Add a module-level _fetched_issues_cache to avoid
re-fetching issues already retrieved during collection.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .../github/github_issues_test_cases.py        | 26 ++++++++++++++++++-
 tests/github_issues/conftest.py               | 12 +++++++--
 2 files changed, 35 insertions(+), 3 deletions(-)

diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index bec4d50f..3f88fdd3 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -197,7 +197,31 @@ def get_issues_by_ids(self, issue_ids: list[str]) -> list[Issue.Issue]:
                         pass
         return issues
 
-    def get_all_issues(self, github_repositories = None) -> Iterator[Issue.Issue]:
+    def get_issues_with_tests(self, github_repositories=None) -> Iterator[Issue.Issue]:
+        """Use GitHub search API to find only issues containing BabelTest syntax.
+
+        This is much faster than get_all_issues() + issue_has_tests() filtering because
+        it only fetches issues that match the search query rather than paginating through
+        every issue in each repository.
+
+        Note: GitHub's search index has a ~60-second lag for very recent edits. For
+        immediate testing of freshly-edited issues, use --issue which calls
+        get_issues_by_ids() directly.
+        """
+        if github_repositories is None:
+            github_repositories = self.github_repositories
+        for repo_id in github_repositories:
+            seen_numbers = set()
+            for keyword in ['{{BabelTest', 'babel_tests:']:
+                query = f'"{keyword}" is:issue in:body repo:{repo_id}'
+                self.logger.info(f"Searching GitHub issues with query: {query}")
+                for issue in self.github.search_issues(query):
+                    if issue.number not in seen_numbers:
+                        seen_numbers.add(issue.number)
+                        if self.issue_has_tests(issue):
+                            yield issue
+
+    def get_all_issues(self, github_repositories=None) -> Iterator[Issue.Issue]:
         """
         Get a list of test rows from one or more repositories.
 
diff --git a/tests/github_issues/conftest.py b/tests/github_issues/conftest.py
index 6e9f74df..bf5343ac 100644
--- a/tests/github_issues/conftest.py
+++ b/tests/github_issues/conftest.py
@@ -23,6 +23,9 @@
 _CACHE_FILE = Path(tempfile.gettempdir()) / "babel_validation_issues_cache.json"
 _LOCK_FILE = _CACHE_FILE.with_suffix(".lock")
 
+# Module-level cache to avoid re-fetching issues already retrieved during collection.
+_fetched_issues_cache: dict[str, Issue.Issue] = {}
+
 
 def _issue_id(issue: Issue.Issue) -> str:
     """Derive a test ID from an issue without making extra API calls."""
@@ -35,9 +38,10 @@ def _get_all_test_issue_ids() -> list[str]:
     with FileLock(_LOCK_FILE):
         if _CACHE_FILE.exists():
             return json.loads(_CACHE_FILE.read_text())
-        issues = [i for i in github_issues_test_cases.get_all_issues()
-                  if github_issues_test_cases.issue_has_tests(i)]
+        issues = list(github_issues_test_cases.get_issues_with_tests())
         ids = [_issue_id(i) for i in issues]
+        for issue, id_ in zip(issues, ids):
+            _fetched_issues_cache[id_] = issue
         _CACHE_FILE.write_text(json.dumps(ids))
         return ids
 
@@ -49,6 +53,8 @@ def pytest_generate_tests(metafunc):
     if issue_id_filter:
         issues = github_issues_test_cases.get_issues_by_ids(issue_id_filter)
         ids = [_issue_id(i) for i in issues]
+        for issue, id_ in zip(issues, ids):
+            _fetched_issues_cache[id_] = issue
     else:
         ids = _get_all_test_issue_ids()
     metafunc.parametrize("github_issue_id", ids, ids=ids)
@@ -57,6 +63,8 @@ def pytest_generate_tests(metafunc):
 @pytest.fixture
 def github_issue(github_issue_id):
     """Hydrate a GitHub Issue object from its string ID."""
+    if github_issue_id in _fetched_issues_cache:
+        return _fetched_issues_cache[github_issue_id]
     return github_issues_test_cases.get_issues_by_ids([github_issue_id])[0]
 
 

From 056e168e82e2d176e0aa56fd2e4af152d79f6ff5 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 1 Mar 2026 01:37:27 -0500
Subject: [PATCH 043/126] Fail hard on unknown assertion types instead of XFAIL
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

When a GitHub issue embeds a BabelTest with an unrecognised assertion
type, the test previously showed as XFAIL (misleading — implies the
service is at fault, not the test itself). Now a pre-flight check runs
before the xfail marker is applied: if any assertion type is unknown,
pytest.fail() is called immediately, producing a hard FAIL with a
clear message listing the bad type(s) and valid alternatives.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 tests/github_issues/test_github_issues.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 03ba3752..da28fbc6 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -2,6 +2,7 @@
 
 import pytest
 
+from src.babel_validation.assertions import ASSERTION_HANDLERS
 from src.babel_validation.services.nameres import CachedNameRes
 from src.babel_validation.services.nodenorm import CachedNodeNorm
 from src.babel_validation.core.testrow import TestResult, TestStatus
@@ -19,6 +20,16 @@ def test_github_issue(request, target_info, github_issue, github_issues_test_cas
     issue_id = f"{parts[3]}/{parts[4]}#{github_issue.number}"
     is_open = github_issue.state == "open"
 
+    # Unknown assertion types must fail hard, not XFAIL.
+    unknown = [f"'{t.assertion}'" for t in tests
+               if t.assertion.lower() not in ASSERTION_HANDLERS]
+    if unknown:
+        pytest.fail(
+            f"Issue {issue_id} uses unknown assertion type(s): "
+            f"{', '.join(unknown)}. "
+            f"Valid types (case-insensitive): {sorted(ASSERTION_HANDLERS.keys())}"
+        )
+
     # Open issues are expected to have failing tests. Mark as xfail(strict=False) so
     # that if all subtests pass, the parent shows as XPASS (X) — issue ready to close.
     if is_open:

From 79fab58b1cdc93fd72ca5f7db148d3056c49df85 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 1 Mar 2026 01:39:02 -0500
Subject: [PATCH 044/126] Removed default repo list.

---
 .../sources/github/github_issues_test_cases.py        | 11 +++--------
 tests/github_issues/conftest.py                       |  1 +
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index 3f88fdd3..ebf07bac 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -53,7 +53,7 @@ class GitHubIssuesTestCases:
     - A closed issue has test cases that are now failing (and so should be reopened).
     """
 
-    def __init__(self, github_token: str, github_repositories=None):
+    def __init__(self, github_token: str, github_repositories):
         """
         Create a GitHubIssuesTestCase object.
 
@@ -72,13 +72,8 @@ def __init__(self, github_token: str, github_repositories=None):
         self.logger = logging.getLogger(self.__class__.__name__)
         self.logger.info("Set up GitHub object ({self.github})")
 
-        if github_repositories is None:
-            github_repositories = [
-                'NCATSTranslator/Babel',                # https://github.com/NCATSTranslator/Babel
-                'NCATSTranslator/NodeNormalization',    # https://github.com/NCATSTranslator/NodeNormalization
-                'NCATSTranslator/NameResolution',       # https://github.com/NCATSTranslator/NameResolution
-                'TranslatorSRI/babel-validation',       # https://github.com/TranslatorSRI/babel-validation
-            ]
+        if not github_repositories:
+            raise ValueError("No GitHub repositories specified in `github_repositories`.")
         self.github_repositories = github_repositories
 
         # Prepare regular expressions.
diff --git a/tests/github_issues/conftest.py b/tests/github_issues/conftest.py
index bf5343ac..82f78a34 100644
--- a/tests/github_issues/conftest.py
+++ b/tests/github_issues/conftest.py
@@ -17,6 +17,7 @@
     'NCATSTranslator/NodeNormalization',
     'NCATSTranslator/NameResolution',
     'TranslatorSRI/babel-validation',
+    'TranslatorSRI/babel-explorer',
 ]
 github_issues_test_cases = GitHubIssuesTestCases(_github_token, _repos)
 

From fc158e405f1efef6b946ae50b6f4ebb59a2ff51c Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 1 Mar 2026 02:14:21 -0500
Subject: [PATCH 045/126] Add DoesNotResolveWith assertion handler
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Adds DoesNotResolveWithHandler, the inverse of ResolvesWith: asserts
that a set of CURIEs do NOT all normalize to the same canonical
identifier in NodeNorm.

Also extracts _compare_resolutions() helper shared by both handlers,
and fixes both ResolvesWith and DoesNotResolveWith to compare by
result['id']['identifier'] rather than full JSON dumps — which is
more robust and semantically correct (equality of the canonical
identifier, not byte-for-byte JSON equality).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 src/babel_validation/assertions/__init__.py |  4 +-
 src/babel_validation/assertions/nodenorm.py | 91 +++++++++++++++++----
 2 files changed, 79 insertions(+), 16 deletions(-)

diff --git a/src/babel_validation/assertions/__init__.py b/src/babel_validation/assertions/__init__.py
index 5a89db32..78a62d73 100644
--- a/src/babel_validation/assertions/__init__.py
+++ b/src/babel_validation/assertions/__init__.py
@@ -115,7 +115,8 @@ def test_param_set(self, params: list[str], nodenorm, nameres,
 
 # Registry — import submodules after base classes are defined to avoid circular imports.
 from src.babel_validation.assertions.nodenorm import (  # noqa: E402
-    ResolvesHandler, DoesNotResolveHandler, ResolvesWithHandler, ResolvesWithTypeHandler,
+    ResolvesHandler, DoesNotResolveHandler, ResolvesWithHandler,
+    ResolvesWithTypeHandler, DoesNotResolveWithHandler,
 )
 from src.babel_validation.assertions.nameres import SearchByNameHandler  # noqa: E402
 from src.babel_validation.assertions.common import NeededHandler  # noqa: E402
@@ -125,6 +126,7 @@ def test_param_set(self, params: list[str], nodenorm, nameres,
         ResolvesHandler(),
         DoesNotResolveHandler(),
         ResolvesWithHandler(),
+        DoesNotResolveWithHandler(),
         ResolvesWithTypeHandler(),
         SearchByNameHandler(),
         NeededHandler(),
diff --git a/src/babel_validation/assertions/nodenorm.py b/src/babel_validation/assertions/nodenorm.py
index 870f68de..197283bd 100644
--- a/src/babel_validation/assertions/nodenorm.py
+++ b/src/babel_validation/assertions/nodenorm.py
@@ -1,4 +1,3 @@
-import json
 from typing import Iterator
 
 from src.babel_validation.assertions import NodeNormTest
@@ -48,6 +47,19 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                 yield self.failed(f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\") with NodeNormalization service {nodenorm}, but expected not to resolve")
 
 
+def _compare_resolutions(
+    params: list[str], nodenorm: CachedNodeNorm
+) -> tuple[dict | None, dict[str, dict | None]]:
+    """Resolve all params; return (first_good_result, per_curie_results).
+
+    first_good_result is None if every CURIE failed to resolve.
+    per_curie_results maps each CURIE to its result (None if unresolvable).
+    """
+    per_curie = nodenorm.normalize_curies(params)
+    first_good = next((r for r in per_curie.values() if r is not None), None)
+    return first_good, per_curie
+
+
 class ResolvesWithHandler(NodeNormTest):
     """Test that all CURIEs in a param_set resolve to the same normalized result in NodeNorm."""
     NAME = "resolveswith"
@@ -61,27 +73,76 @@ class ResolvesWithHandler(NodeNormTest):
 
     def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                        label: str = "") -> Iterator[TestResult]:
-        results = nodenorm.normalize_curies(params)
-
-        # Find the first good result.
-        first_good_result = None
-        for curie, result in results.items():
-            if result is not None and first_good_result is None:
-                first_good_result = result
-                break
+        first_good, results = _compare_resolutions(params, nodenorm)
 
-        if first_good_result is None:
+        if first_good is None:
             yield self.failed(f"None of the CURIEs {params} could be resolved on {nodenorm}")
             return
 
-        # Check all the results.
+        canonical_id = first_good['id']['identifier']
+
         for curie, result in results.items():
             if result is None:
-                yield self.failed(f"CURIE {curie} could not be resolved, and so is not equal to the expected result {json.dumps(first_good_result, indent=2, sort_keys=True)} on {nodenorm}")
-            elif json.dumps(first_good_result, sort_keys=True) == json.dumps(result, sort_keys=True):
-                yield self.passed(f"Resolved {curie} to the expected result {json.dumps(first_good_result, indent=2, sort_keys=True)}")
+                yield self.failed(
+                    f"CURIE {curie} could not be resolved on {nodenorm}"
+                )
+            elif result['id']['identifier'] == canonical_id:
+                yield self.passed(
+                    f"Resolved {curie} to the expected canonical identifier {canonical_id}"
+                )
             else:
-                yield self.failed(f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\"), but expected {first_good_result['id']['identifier']} ({first_good_result['type'][0]}, \"{first_good_result['id']['label']}\") on {nodenorm}")
+                yield self.failed(
+                    f"Resolved {curie} to {result['id']['identifier']} "
+                    f"({result['type'][0]}, \"{result['id']['label']}\"), but expected "
+                    f"{canonical_id} "
+                    f"({first_good['type'][0]}, \"{first_good['id']['label']}\") on {nodenorm}"
+                )
+
+
+class DoesNotResolveWithHandler(NodeNormTest):
+    """Test that not all CURIEs in a param_set resolve to the same result in NodeNorm."""
+    NAME = "doesnotresolveswith"
+    DESCRIPTION = (
+        "The CURIEs within each param_set must NOT all resolve to the same normalized "
+        "result. Use this to assert that two identifiers are intentionally distinct entities."
+    )
+    PARAMETERS = "Two or more CURIEs per param_set. They must not all resolve to the same result."
+    WIKI_EXAMPLES = ["{{BabelTest|DoesNotResolveWith|CHEBI:15365|CHEBI:16856}}"]
+    YAML_PARAMS = "    - [CHEBI:15365, CHEBI:16856]"
+
+    def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
+                       label: str = "") -> Iterator[TestResult]:
+        first_good, results = _compare_resolutions(params, nodenorm)
+
+        # Every CURIE must resolve — an unresolved CURIE is a configuration error.
+        unresolved = [curie for curie, result in results.items() if result is None]
+        if unresolved:
+            yield self.failed(
+                f"CURIEs {unresolved} could not be resolved on {nodenorm}; "
+                f"all CURIEs in a DoesNotResolveWith param_set must resolve"
+            )
+            return
+
+        # All resolved — check that they don't all map to the same canonical identifier.
+        canonical_ids = {result['id']['identifier'] for result in results.values()}
+
+        if len(canonical_ids) == 1:
+            # Every CURIE maps to the same result — assertion fails.
+            shared = first_good
+            yield self.failed(
+                f"All CURIEs {params} resolved to the same result "
+                f"{shared['id']['identifier']} "
+                f"({shared['type'][0]}, \"{shared['id']['label']}\") on {nodenorm}, "
+                f"but expected them to resolve differently"
+            )
+        else:
+            summary = ", ".join(
+                f"{curie} → {result['id']['identifier']}"
+                for curie, result in results.items()
+            )
+            yield self.passed(
+                f"CURIEs resolve to different results as expected: {summary} on {nodenorm}"
+            )
 
 
 class ResolvesWithTypeHandler(NodeNormTest):

From 4b77e98b63825d4f5ec0a87c72ef15113d193201 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 1 Mar 2026 02:20:48 -0500
Subject: [PATCH 046/126] Fixed Claude typo.

---
 src/babel_validation/assertions/nodenorm.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/babel_validation/assertions/nodenorm.py b/src/babel_validation/assertions/nodenorm.py
index 197283bd..88d6ad65 100644
--- a/src/babel_validation/assertions/nodenorm.py
+++ b/src/babel_validation/assertions/nodenorm.py
@@ -101,7 +101,7 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
 
 class DoesNotResolveWithHandler(NodeNormTest):
     """Test that not all CURIEs in a param_set resolve to the same result in NodeNorm."""
-    NAME = "doesnotresolveswith"
+    NAME = "doesnotresolvewith"
     DESCRIPTION = (
         "The CURIEs within each param_set must NOT all resolve to the same normalized "
         "result. Use this to assert that two identifiers are intentionally distinct entities."

From d3fb921af59704f629b6f11bb786e37f8a174dfb Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 1 Mar 2026 02:25:33 -0500
Subject: [PATCH 047/126] Improve error message.

---
 tests/github_issues/test_github_issues.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index da28fbc6..1491f7e0 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -1,4 +1,5 @@
 import itertools
+import json
 
 import pytest
 
@@ -26,7 +27,7 @@ def test_github_issue(request, target_info, github_issue, github_issues_test_cas
     if unknown:
         pytest.fail(
             f"Issue {issue_id} uses unknown assertion type(s): "
-            f"{', '.join(unknown)}. "
+            f"{', '.join(unknown)} with param sets {json.dumps([t.param_set for t in tests])}. "
             f"Valid types (case-insensitive): {sorted(ASSERTION_HANDLERS.keys())}"
         )
 

From 4d272f16215dc79ff5d6aa0765c19a27a7941bec Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 1 Mar 2026 02:31:31 -0500
Subject: [PATCH 048/126] Add HasLabel assertion handler

Adds a new `HasLabel` assertion that checks a CURIE resolves to a
specific primary label in NodeNorm (id.label), enabling label regression
tests. Syntax: {{BabelTest|HasLabel|CHEBI:15365|aspirin}}.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 src/babel_validation/assertions/__init__.py |  3 +-
 src/babel_validation/assertions/nodenorm.py | 42 +++++++++++++++++++++
 2 files changed, 44 insertions(+), 1 deletion(-)

diff --git a/src/babel_validation/assertions/__init__.py b/src/babel_validation/assertions/__init__.py
index 78a62d73..becc948e 100644
--- a/src/babel_validation/assertions/__init__.py
+++ b/src/babel_validation/assertions/__init__.py
@@ -116,7 +116,7 @@ def test_param_set(self, params: list[str], nodenorm, nameres,
 # Registry — import submodules after base classes are defined to avoid circular imports.
 from src.babel_validation.assertions.nodenorm import (  # noqa: E402
     ResolvesHandler, DoesNotResolveHandler, ResolvesWithHandler,
-    ResolvesWithTypeHandler, DoesNotResolveWithHandler,
+    ResolvesWithTypeHandler, DoesNotResolveWithHandler, HasLabelHandler,
 )
 from src.babel_validation.assertions.nameres import SearchByNameHandler  # noqa: E402
 from src.babel_validation.assertions.common import NeededHandler  # noqa: E402
@@ -127,6 +127,7 @@ def test_param_set(self, params: list[str], nodenorm, nameres,
         DoesNotResolveHandler(),
         ResolvesWithHandler(),
         DoesNotResolveWithHandler(),
+        HasLabelHandler(),
         ResolvesWithTypeHandler(),
         SearchByNameHandler(),
         NeededHandler(),
diff --git a/src/babel_validation/assertions/nodenorm.py b/src/babel_validation/assertions/nodenorm.py
index 88d6ad65..3ebba113 100644
--- a/src/babel_validation/assertions/nodenorm.py
+++ b/src/babel_validation/assertions/nodenorm.py
@@ -145,6 +145,48 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
             )
 
 
+class HasLabelHandler(NodeNormTest):
+    """Test that a CURIE resolves to a specific primary label in NodeNorm."""
+    NAME = "haslabel"
+    DESCRIPTION = (
+        "The CURIE must resolve in NodeNorm and its primary label (id.label) must "
+        "match the expected label exactly (case-sensitive)."
+    )
+    PARAMETERS = "Exactly two elements per param_set: a CURIE, then the expected label string."
+    WIKI_EXAMPLES = ["{{BabelTest|HasLabel|CHEBI:15365|aspirin}}"]
+    YAML_PARAMS = "    - [CHEBI:15365, aspirin]"
+
+    def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
+                       label: str = "") -> Iterator[TestResult]:
+        if len(params) < 2:
+            yield self.failed(
+                f"HasLabel requires two parameters (CURIE, expected label) in {label}, "
+                f"but got: {params}"
+            )
+            return
+
+        curie = params[0]
+        expected_label = params[1].strip()
+
+        result = nodenorm.normalize_curie(curie)
+        if not result:
+            yield self.failed(
+                f"Could not resolve {curie} on {nodenorm}"
+            )
+            return
+
+        actual_label = result['id']['label']
+        if actual_label == expected_label:
+            yield self.passed(
+                f"CURIE {curie} has expected label '{actual_label}' on {nodenorm}"
+            )
+        else:
+            yield self.failed(
+                f"CURIE {curie} has label '{actual_label}', "
+                f"but expected '{expected_label}' on {nodenorm}"
+            )
+
+
 class ResolvesWithTypeHandler(NodeNormTest):
     """Test that CURIEs resolve with a specific Biolink type in NodeNorm."""
     NAME = "resolveswithtype"

From a9c0842225c970db1a6e61bf989d14af3c184c82 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 1 Mar 2026 02:32:09 -0500
Subject: [PATCH 049/126] Fixed typo in my code.

---
 tests/github_issues/test_github_issues.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 1491f7e0..429eef09 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -27,7 +27,7 @@ def test_github_issue(request, target_info, github_issue, github_issues_test_cas
     if unknown:
         pytest.fail(
             f"Issue {issue_id} uses unknown assertion type(s): "
-            f"{', '.join(unknown)} with param sets {json.dumps([t.param_set for t in tests])}. "
+            f"{', '.join(unknown)} with param sets {json.dumps([t.param_sets for t in tests])}. "
             f"Valid types (case-insensitive): {sorted(ASSERTION_HANDLERS.keys())}"
         )
 

From 4b6ea9182dc93e7229cd5acacc037c497635b6f0 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 1 Mar 2026 03:32:26 -0500
Subject: [PATCH 050/126] XPASS tests now correctly complain.

---
 tests/github_issues/test_github_issues.py | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 429eef09..e43639b3 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -31,12 +31,12 @@ def test_github_issue(request, target_info, github_issue, github_issues_test_cas
             f"Valid types (case-insensitive): {sorted(ASSERTION_HANDLERS.keys())}"
         )
 
-    # Open issues are expected to have failing tests. Mark as xfail(strict=False) so
-    # that if all subtests pass, the parent shows as XPASS (X) — issue ready to close.
+    # Open issues are assumed to fail, so we set an xfail marker (but we set it to strict so
+    # that XPASSes are reported loudly).
     if is_open:
         request.node.add_marker(pytest.mark.xfail(
             reason=f"Issue {issue_id} is still open",
-            strict=False,
+            strict=True,
         ))
 
     count_subtests = 0
@@ -66,7 +66,11 @@ def test_github_issue(request, target_info, github_issue, github_issues_test_cas
                     case _:
                         assert False, f"Unknown result from {issue_id}: {result}"
 
-    # If any subtest xfailed, also xfail the parent — otherwise the parent would show
-    # as XPASS (masking the distinction between "all pass" and "some fail").
-    if is_open and (count_subtests_xfailed > 0):
-        pytest.xfail(f"Open issue {issue_id} has {count_subtests_xfailed:,} failing subtests out of {count_subtests:,} ({count_subtests_xfailed/count_subtests:.0%})")
+    # Always xfail open issues so the result stays in the xfail family.
+    # If all subtests pass the message signals the issue is ready to close;
+    # if some failed it reports the failure count.
+    if is_open:
+        if count_subtests_xfailed > 0:
+            pytest.xfail(f"Open issue {issue_id} has {count_subtests_xfailed:,} failing subtests out of {count_subtests:,} ({count_subtests_xfailed/count_subtests:.0%})")
+        else:
+            assert True, f"Open issue {issue_id} has all {count_subtests:,} subtests passing -- ready to close?"

From 84143501ea03c04c483bd0668adbba7e674b696f Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 5 Mar 2026 19:06:47 -0500
Subject: [PATCH 051/126] Regenerated BabelTest assertions documentation.

---
 src/babel_validation/assertions/README.md | 44 +++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/src/babel_validation/assertions/README.md b/src/babel_validation/assertions/README.md
index 7dba6113..1d0c6124 100644
--- a/src/babel_validation/assertions/README.md
+++ b/src/babel_validation/assertions/README.md
@@ -101,6 +101,50 @@ babel_tests:
 
 ---
 
+### DoesNotResolveWith
+
+**Applies to:** NodeNorm
+
+The CURIEs within each param_set must NOT all resolve to the same normalized result. Use this to assert that two identifiers are intentionally distinct entities.
+
+**Parameters:** Two or more CURIEs per param_set. They must not all resolve to the same result.
+
+**Wiki syntax:**
+```
+{{BabelTest|DoesNotResolveWith|CHEBI:15365|CHEBI:16856}}
+```
+
+**YAML syntax:**
+```yaml
+babel_tests:
+  DoesNotResolveWith:
+    - [CHEBI:15365, CHEBI:16856]
+```
+
+---
+
+### HasLabel
+
+**Applies to:** NodeNorm
+
+The CURIE must resolve in NodeNorm and its primary label (id.label) must match the expected label exactly (case-sensitive).
+
+**Parameters:** Exactly two elements per param_set: a CURIE, then the expected label string.
+
+**Wiki syntax:**
+```
+{{BabelTest|HasLabel|CHEBI:15365|aspirin}}
+```
+
+**YAML syntax:**
+```yaml
+babel_tests:
+  HasLabel:
+    - [CHEBI:15365, aspirin]
+```
+
+---
+
 ### ResolvesWithType
 
 **Applies to:** NodeNorm

From 1c75b08164a11e52226f9042deb0079b82aaedd9 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 5 Mar 2026 19:10:41 -0500
Subject: [PATCH 052/126] Fixed timeout.

---
 tests/pytest.ini | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/pytest.ini b/tests/pytest.ini
index 498c5634..934f3369 100644
--- a/tests/pytest.ini
+++ b/tests/pytest.ini
@@ -1,3 +1,4 @@
 # pytest.ini settings
 [pytest]
-timeout = 300 # 5 minutes
+timeout = 300
+# - 300 seconds = 5 mins

From 3eeeccfb0d15451e45ecade7603404e096b30fb0 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 5 Mar 2026 19:28:44 -0500
Subject: [PATCH 053/126] Add unit test marker and GitHub Actions workflow for
 PRs

- Register pytest 'unit' marker in pyproject.toml
- Move test_assertions_docs.py to tests/test_environment/ and mark it @pytest.mark.unit
- Mark tests/github_issues/test_system.py with pytestmark = pytest.mark.unit
- Add .github/workflows/tests.yaml to run unit tests (pytest -m unit) on pull_request

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .github/workflows/tests.yaml                      | 15 +++++++++++++++
 pyproject.toml                                    |  5 +++++
 tests/github_issues/test_system.py                |  2 ++
 .../test_assertions_docs.py                       |  3 +++
 4 files changed, 25 insertions(+)
 create mode 100644 .github/workflows/tests.yaml
 rename tests/{ => test_environment}/test_assertions_docs.py (92%)

diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
new file mode 100644
index 00000000..cca42051
--- /dev/null
+++ b/.github/workflows/tests.yaml
@@ -0,0 +1,15 @@
+name: Tests
+
+on:
+  pull_request:
+
+jobs:
+  unit-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: astral-sh/setup-uv@v6
+
+      - name: Run unit tests
+        run: uv run pytest -m unit -v
diff --git a/pyproject.toml b/pyproject.toml
index 271d7c12..490f9eaa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,5 +19,10 @@ dependencies = [
     "pytest-xdist[psutil]",
 ]
 
+[tool.pytest.ini_options]
+markers = [
+    "unit: unit tests that do not require network access",
+]
+
 [project.urls]
 Repository = "https://github.com/TranslatorSRI/babel-validation"
diff --git a/tests/github_issues/test_system.py b/tests/github_issues/test_system.py
index ae1fe4f3..8420320f 100644
--- a/tests/github_issues/test_system.py
+++ b/tests/github_issues/test_system.py
@@ -3,6 +3,8 @@
 from unittest.mock import MagicMock
 import pytest
 
+pytestmark = pytest.mark.unit
+
 INVALID_NAME = "NotARealAssertion"
 
 
diff --git a/tests/test_assertions_docs.py b/tests/test_environment/test_assertions_docs.py
similarity index 92%
rename from tests/test_assertions_docs.py
rename to tests/test_environment/test_assertions_docs.py
index d98130ff..d1000c70 100644
--- a/tests/test_assertions_docs.py
+++ b/tests/test_environment/test_assertions_docs.py
@@ -1,6 +1,9 @@
+import pytest
+
 from src.babel_validation.assertions.gen_docs import generate_readme, README_PATH
 
 
+@pytest.mark.unit
 def test_assertions_readme_is_up_to_date():
     expected = generate_readme()
     actual = README_PATH.read_text(encoding="utf-8")

From bccde0700596f9d67b75f64729815f3475aae06e Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Sun, 15 Mar 2026 02:56:33 -0400
Subject: [PATCH 054/126] Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 490f9eaa..4fa87ef4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,7 +11,7 @@ dependencies = [
     "tqdm>=4.67.1",
     "filelock",
     "deepdiff>=8.6.1",
-    "dotenv>=0.9.9",
+    "python-dotenv>=0.9.9",
     "openapi-spec-validator>=0.7.2",
     "pygithub>=2.8.1",
     "pytest>=8.4.2",

From f7338582aeee0463b209e51a4f420e7a083858cc Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Sun, 15 Mar 2026 02:57:14 -0400
Subject: [PATCH 055/126] Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
---
 src/babel_validation/sources/github/github_issues_test_cases.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index ebf07bac..f62e2666 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -70,7 +70,7 @@ def __init__(self, github_token: str, github_repositories):
 
         self.github = Github(auth=Auth.Token(self.github_token))
         self.logger = logging.getLogger(self.__class__.__name__)
-        self.logger.info("Set up GitHub object ({self.github})")
+        self.logger.info(f"Set up GitHub object ({self.github})")
 
         if not github_repositories:
             raise ValueError("No GitHub repositories specified in `github_repositories`.")

From 79c01f7d4adab414a2e9f2d589ee520e5317f834 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Sun, 15 Mar 2026 02:57:41 -0400
Subject: [PATCH 056/126] Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
---
 src/babel_validation/assertions/nodenorm.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/babel_validation/assertions/nodenorm.py b/src/babel_validation/assertions/nodenorm.py
index 3ebba113..920572d0 100644
--- a/src/babel_validation/assertions/nodenorm.py
+++ b/src/babel_validation/assertions/nodenorm.py
@@ -212,7 +212,11 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
 
         results = nodenorm.normalize_curies(curies)
         for curie in curies:
-            biolink_types = results[curie]['type']
+            node = results.get(curie)
+            if not node:
+                yield self.failed(f"Could not resolve {curie} with NodeNormalization service {nodenorm}")
+                continue
+            biolink_types = node['type']
             if expected_biolink_type in biolink_types:
                 yield self.passed(f"Biolink types {biolink_types} for CURIE {curie} includes expected Biolink type {expected_biolink_type}")
             else:

From 9163671b329883aae54642b4e2dcf4fd4bf3ec0a Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Sun, 15 Mar 2026 02:58:56 -0400
Subject: [PATCH 057/126] Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
---
 src/babel_validation/assertions/nodenorm.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/babel_validation/assertions/nodenorm.py b/src/babel_validation/assertions/nodenorm.py
index 920572d0..01ddf426 100644
--- a/src/babel_validation/assertions/nodenorm.py
+++ b/src/babel_validation/assertions/nodenorm.py
@@ -217,6 +217,10 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                 yield self.failed(f"Could not resolve {curie} with NodeNormalization service {nodenorm}")
                 continue
             biolink_types = node['type']
+            if not node:
+                yield self.failed(f"Could not resolve {curie} with NodeNormalization service {nodenorm}")
+                continue
+            biolink_types = node['type']
             if expected_biolink_type in biolink_types:
                 yield self.passed(f"Biolink types {biolink_types} for CURIE {curie} includes expected Biolink type {expected_biolink_type}")
             else:

From 79a0b5c492cc48ffc91c4d6750493dfd38695638 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Sun, 15 Mar 2026 02:59:36 -0400
Subject: [PATCH 058/126] Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
---
 tests/github_issues/conftest.py | 24 +++++++++++++++++++-----
 1 file changed, 19 insertions(+), 5 deletions(-)

diff --git a/tests/github_issues/conftest.py b/tests/github_issues/conftest.py
index 82f78a34..ff615f29 100644
--- a/tests/github_issues/conftest.py
+++ b/tests/github_issues/conftest.py
@@ -19,7 +19,7 @@
     'TranslatorSRI/babel-validation',
     'TranslatorSRI/babel-explorer',
 ]
-github_issues_test_cases = GitHubIssuesTestCases(_github_token, _repos)
+github_issues_test_cases = None
 
 _CACHE_FILE = Path(tempfile.gettempdir()) / "babel_validation_issues_cache.json"
 _LOCK_FILE = _CACHE_FILE.with_suffix(".lock")
@@ -28,6 +28,20 @@
 _fetched_issues_cache: dict[str, Issue.Issue] = {}
 
 
+def _get_github_issues_test_cases() -> GitHubIssuesTestCases:
+    """Lazily construct GitHubIssuesTestCases, skipping tests if no token is available."""
+    global github_issues_test_cases
+    if github_issues_test_cases is not None:
+        return github_issues_test_cases
+    if not _github_token:
+        pytest.skip(
+            "GITHUB_TOKEN environment variable not set; skipping GitHub issues tests.",
+            allow_module_level=True,
+        )
+    github_issues_test_cases = GitHubIssuesTestCases(_github_token, _repos)
+    return github_issues_test_cases
+
+
 def _issue_id(issue: Issue.Issue) -> str:
     """Derive a test ID from an issue without making extra API calls."""
     parts = issue.html_url.split('/')
@@ -39,7 +53,7 @@ def _get_all_test_issue_ids() -> list[str]:
     with FileLock(_LOCK_FILE):
         if _CACHE_FILE.exists():
             return json.loads(_CACHE_FILE.read_text())
-        issues = list(github_issues_test_cases.get_issues_with_tests())
+        issues = list(_get_github_issues_test_cases().get_issues_with_tests())
         ids = [_issue_id(i) for i in issues]
         for issue, id_ in zip(issues, ids):
             _fetched_issues_cache[id_] = issue
@@ -52,7 +66,7 @@ def pytest_generate_tests(metafunc):
         return
     issue_id_filter = metafunc.config.getoption("issue", default=[])
     if issue_id_filter:
-        issues = github_issues_test_cases.get_issues_by_ids(issue_id_filter)
+        issues = _get_github_issues_test_cases().get_issues_by_ids(issue_id_filter)
         ids = [_issue_id(i) for i in issues]
         for issue, id_ in zip(issues, ids):
             _fetched_issues_cache[id_] = issue
@@ -66,9 +80,9 @@ def github_issue(github_issue_id):
     """Hydrate a GitHub Issue object from its string ID."""
     if github_issue_id in _fetched_issues_cache:
         return _fetched_issues_cache[github_issue_id]
-    return github_issues_test_cases.get_issues_by_ids([github_issue_id])[0]
+    return _get_github_issues_test_cases().get_issues_by_ids([github_issue_id])[0]
 
 
 @pytest.fixture(scope="session")
 def github_issues_test_cases_fixture():
-    return github_issues_test_cases
+    return _get_github_issues_test_cases()

From 8e90722e7c1abcdbe1a9c8ea1f05e6d8a55f685b Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Sun, 15 Mar 2026 03:00:11 -0400
Subject: [PATCH 059/126] Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
---
 src/babel_validation/assertions/nameres.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/babel_validation/assertions/nameres.py b/src/babel_validation/assertions/nameres.py
index ce1b25d1..18d8d528 100644
--- a/src/babel_validation/assertions/nameres.py
+++ b/src/babel_validation/assertions/nameres.py
@@ -53,7 +53,7 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
             yield self.failed(f"{expected_curie_string} not found when searching for '{search_query}' in NameRes {nameres}")
             return
 
-        if found_index <= pass_if_found_in_top:
+        if found_index < pass_if_found_in_top:
             yield self.passed(f"{expected_curie_string} found at index {found_index + 1} on NameRes {nameres}")
         else:
             yield self.failed(f"{expected_curie_string} found at index {found_index + 1} which is greater than {pass_if_found_in_top} on NameRes {nameres}")

From 4a399e684fa7d7b6544e2fcafdd349b752b01d8b Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Sun, 15 Mar 2026 03:00:30 -0400
Subject: [PATCH 060/126] Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
---
 src/babel_validation/assertions/nameres.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/babel_validation/assertions/nameres.py b/src/babel_validation/assertions/nameres.py
index 18d8d528..a7179ffd 100644
--- a/src/babel_validation/assertions/nameres.py
+++ b/src/babel_validation/assertions/nameres.py
@@ -42,7 +42,7 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
         # Search for the expected CURIE in the first {pass_if_found_in_top} results.
         results = nameres.lookup(search_query, autocomplete='false', limit=(2 * pass_if_found_in_top))
         if not results:
-            yield self.failed(f"No results found for '{search_query}' on NameRes {nameres} ({expected_curie_string}")
+            yield self.failed(f"No results found for '{search_query}' on NameRes {nameres} ({expected_curie_string})")
             return
 
         curies = [result['curie'] for result in results]

From 224cd42c0645aa77c3414d3cdad440681e51028b Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 15 Mar 2026 03:13:56 -0400
Subject: [PATCH 061/126] Fix CURIE prewarming to only normalize CURIE
 parameters

- Add `curie_params()` to `NodeNormTest` so handlers can declare which
  params are CURIEs (default: all params)
- Prewarm NodeNorm cache only for CURIE params instead of all params
- Validate CURIE format (PREFIX:LOCAL_ID) before calling test_param_set,
  yielding a clear failure for malformed CURIEs
- Override `curie_params()` in HasLabelHandler (params[:1]) and
  ResolvesWithTypeHandler (params[1:]) to exclude non-CURIE params

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 src/babel_validation/assertions/__init__.py | 20 ++++++++++++++++++--
 src/babel_validation/assertions/nodenorm.py |  6 ++++++
 2 files changed, 24 insertions(+), 2 deletions(-)

diff --git a/src/babel_validation/assertions/__init__.py b/src/babel_validation/assertions/__init__.py
index becc948e..7b74457a 100644
--- a/src/babel_validation/assertions/__init__.py
+++ b/src/babel_validation/assertions/__init__.py
@@ -19,6 +19,7 @@
 6. Run `uv run python -m src.babel_validation.assertions.gen_docs` to regenerate README.md.
 """
 
+import re
 from typing import Iterator
 
 from src.babel_validation.core.testrow import TestResult, TestStatus
@@ -53,19 +54,34 @@ class NodeNormTest(AssertionHandler):
     Subclasses implement test_param_set() instead of test_with_nodenorm().
     """
 
+    _CURIE_RE = re.compile(r'^[A-Za-z][A-Za-z0-9._-]*:[^\s]+$')
+
+    def curie_params(self, params: list[str]) -> list[str]:
+        """Return the subset of params that are CURIEs (for prewarming and validation).
+        Default: all params are CURIEs. Subclasses override when some params are non-CURIEs."""
+        return params
+
     def test_with_nodenorm(self, param_sets: list[list[str]], nodenorm,
                            label: str = "") -> Iterator[TestResult]:
         if not param_sets:
             yield self.failed(f"No parameters provided in {label}")
             return
-        # warm the cache for all CURIEs up front
-        nodenorm.normalize_curies([p for params in param_sets for p in params])
+        # warm the cache only for params that are CURIEs
+        nodenorm.normalize_curies([p for params in param_sets for p in self.curie_params(params)])
         found = False
         for index, params in enumerate(param_sets):
             if not params:
                 yield self.failed(f"No parameters in param_set {index} in {label}")
                 found = True
                 continue
+            invalid = [c for c in self.curie_params(params) if not self._CURIE_RE.match(c)]
+            if invalid:
+                yield self.failed(
+                    f"Malformed CURIE(s) {invalid} in param_set {index} in {label}: "
+                    f"expected format PREFIX:LOCAL_ID (e.g. CHEBI:15365)"
+                )
+                found = True
+                continue
             for result in self.test_param_set(params, nodenorm, label):
                 found = True
                 yield result
diff --git a/src/babel_validation/assertions/nodenorm.py b/src/babel_validation/assertions/nodenorm.py
index 01ddf426..172b03ec 100644
--- a/src/babel_validation/assertions/nodenorm.py
+++ b/src/babel_validation/assertions/nodenorm.py
@@ -148,6 +148,9 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
 class HasLabelHandler(NodeNormTest):
     """Test that a CURIE resolves to a specific primary label in NodeNorm."""
     NAME = "haslabel"
+
+    def curie_params(self, params: list[str]) -> list[str]:
+        return params[:1]
     DESCRIPTION = (
         "The CURIE must resolve in NodeNorm and its primary label (id.label) must "
         "match the expected label exactly (case-sensitive)."
@@ -190,6 +193,9 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
 class ResolvesWithTypeHandler(NodeNormTest):
     """Test that CURIEs resolve with a specific Biolink type in NodeNorm."""
     NAME = "resolveswithtype"
+
+    def curie_params(self, params: list[str]) -> list[str]:
+        return params[1:]
     DESCRIPTION = (
         "Each param_set must have at least two elements: the first is the expected Biolink type "
         "(e.g. 'biolink:Gene'), and the remainder are CURIEs that must resolve with that type."

From 2628f5004bdf11553e3ff55fba718eca2baa0ff0 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Sun, 15 Mar 2026 03:14:46 -0400
Subject: [PATCH 062/126] Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

From 32248b2cb910e61e9c29faf52dc26167330c5366 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 15 Mar 2026 03:27:55 -0400
Subject: [PATCH 063/126] Move pytest marker config from pyproject.toml to
 tests/pytest.ini

tests/pytest.ini takes precedence over pyproject.toml when running
tests under tests/, so the [tool.pytest.ini_options] block was never
read. Register the `unit` mark in tests/pytest.ini and remove the
now-redundant section from pyproject.toml.

Also fixes python-dotenv dependency name (was incorrectly listed as
`dotenv`, a thin wrapper package).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 pyproject.toml   |  5 -----
 tests/pytest.ini |  2 ++
 uv.lock          | 15 ++-------------
 3 files changed, 4 insertions(+), 18 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4fa87ef4..90b630ca 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,10 +19,5 @@ dependencies = [
     "pytest-xdist[psutil]",
 ]
 
-[tool.pytest.ini_options]
-markers = [
-    "unit: unit tests that do not require network access",
-]
-
 [project.urls]
 Repository = "https://github.com/TranslatorSRI/babel-validation"
diff --git a/tests/pytest.ini b/tests/pytest.ini
index 934f3369..a84b1690 100644
--- a/tests/pytest.ini
+++ b/tests/pytest.ini
@@ -2,3 +2,5 @@
 [pytest]
 timeout = 300
 # - 300 seconds = 5 mins
+markers =
+    unit: unit tests that do not require network access
diff --git a/uv.lock b/uv.lock
index 6406328a..9e76d081 100644
--- a/uv.lock
+++ b/uv.lock
@@ -27,13 +27,13 @@ source = { virtual = "." }
 dependencies = [
     { name = "black" },
     { name = "deepdiff" },
-    { name = "dotenv" },
     { name = "filelock" },
     { name = "openapi-spec-validator" },
     { name = "pygithub" },
     { name = "pytest" },
     { name = "pytest-timeout" },
     { name = "pytest-xdist", extra = ["psutil"] },
+    { name = "python-dotenv" },
     { name = "requests" },
     { name = "tqdm" },
 ]
@@ -42,13 +42,13 @@ dependencies = [
 requires-dist = [
     { name = "black", specifier = ">=25.9.0" },
     { name = "deepdiff", specifier = ">=8.6.1" },
-    { name = "dotenv", specifier = ">=0.9.9" },
     { name = "filelock" },
     { name = "openapi-spec-validator", specifier = ">=0.7.2" },
     { name = "pygithub", specifier = ">=2.8.1" },
     { name = "pytest", specifier = ">=8.4.2" },
     { name = "pytest-timeout", specifier = ">=2.4.0" },
     { name = "pytest-xdist", extras = ["psutil"] },
+    { name = "python-dotenv", specifier = ">=0.9.9" },
     { name = "requests", specifier = ">=2.32.5" },
     { name = "tqdm", specifier = ">=4.67.1" },
 ]
@@ -334,17 +334,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/f7/e6/efe534ef0952b531b630780e19cabd416e2032697019d5295defc6ef9bd9/deepdiff-8.6.1-py3-none-any.whl", hash = "sha256:ee8708a7f7d37fb273a541fa24ad010ed484192cd0c4ffc0fa0ed5e2d4b9e78b", size = 91378, upload-time = "2025-09-03T19:40:39.679Z" },
 ]
 
-[[package]]
-name = "dotenv"
-version = "0.9.9"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
-    { name = "python-dotenv" },
-]
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/b2/b7/545d2c10c1fc15e48653c91efde329a790f2eecfbbf2bd16003b5db2bab0/dotenv-0.9.9-py2.py3-none-any.whl", hash = "sha256:29cf74a087b31dafdb5a446b6d7e11cbce8ed2741540e2339c69fbef92c94ce9", size = 1892, upload-time = "2025-02-19T22:15:01.647Z" },
-]
-
 [[package]]
 name = "execnet"
 version = "2.1.2"

From c175f67a172a51d2cce4b4b2a862facc1d9c452f Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 15 Mar 2026 15:55:10 -0400
Subject: [PATCH 064/126] Tweaked error message.

---
 tests/github_issues/test_github_issues.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index e43639b3..f826f94c 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -35,7 +35,7 @@ def test_github_issue(request, target_info, github_issue, github_issues_test_cas
     # that XPASSes are reported loudly).
     if is_open:
         request.node.add_marker(pytest.mark.xfail(
-            reason=f"Issue {issue_id} is still open",
+            reason=f"Issue {github_issue.html_url} is expected to fail because the issue is open.",
             strict=True,
         ))
 

From 1db38aacb9f0da65c2e514a27f52a8715aa8c93b Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 15 Mar 2026 16:38:24 -0400
Subject: [PATCH 065/126] Simplify: remove dead code and minor cleanup

- Remove unreachable duplicate block in ResolvesWithTypeHandler.test_param_set
- Use github_issue_id fixture param directly instead of re-parsing the URL
- Replace unused *args with *_ in SearchByNameHandler

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 src/babel_validation/assertions/nameres.py  | 2 +-
 src/babel_validation/assertions/nodenorm.py | 4 ----
 tests/github_issues/test_github_issues.py   | 5 ++---
 3 files changed, 3 insertions(+), 8 deletions(-)

diff --git a/src/babel_validation/assertions/nameres.py b/src/babel_validation/assertions/nameres.py
index a7179ffd..360c7236 100644
--- a/src/babel_validation/assertions/nameres.py
+++ b/src/babel_validation/assertions/nameres.py
@@ -29,7 +29,7 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
             yield self.failed(f"Two parameters expected for SearchByName in {label}, but params = {params}")
             return
 
-        [search_query, expected_curie_from_test, *args] = params
+        [search_query, expected_curie_from_test, *_] = params
         expected_curie_result = nodenorm.normalize_curie(expected_curie_from_test, drug_chemical_conflate='true')
         if not expected_curie_result:
             yield self.failed(f"Unable to normalize CURIE {expected_curie_from_test} in {label}")
diff --git a/src/babel_validation/assertions/nodenorm.py b/src/babel_validation/assertions/nodenorm.py
index 172b03ec..93386c35 100644
--- a/src/babel_validation/assertions/nodenorm.py
+++ b/src/babel_validation/assertions/nodenorm.py
@@ -223,10 +223,6 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                 yield self.failed(f"Could not resolve {curie} with NodeNormalization service {nodenorm}")
                 continue
             biolink_types = node['type']
-            if not node:
-                yield self.failed(f"Could not resolve {curie} with NodeNormalization service {nodenorm}")
-                continue
-            biolink_types = node['type']
             if expected_biolink_type in biolink_types:
                 yield self.passed(f"Biolink types {biolink_types} for CURIE {curie} includes expected Biolink type {expected_biolink_type}")
             else:
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index f826f94c..87ff59eb 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -9,7 +9,7 @@
 from src.babel_validation.core.testrow import TestResult, TestStatus
 
 
-def test_github_issue(request, target_info, github_issue, github_issues_test_cases_fixture, subtests):
+def test_github_issue(request, target_info, github_issue_id, github_issue, github_issues_test_cases_fixture, subtests):
     nodenorm = CachedNodeNorm.from_url(target_info['NodeNormURL'])
     nameres = CachedNameRes.from_url(target_info['NameResURL'])
     tests = github_issues_test_cases_fixture.get_test_issues_from_issue(github_issue)
@@ -17,8 +17,7 @@ def test_github_issue(request, target_info, github_issue, github_issues_test_cas
         pytest.skip(f"No tests found in issue {github_issue}")
         return
 
-    parts = github_issue.html_url.split('/')
-    issue_id = f"{parts[3]}/{parts[4]}#{github_issue.number}"
+    issue_id = github_issue_id
     is_open = github_issue.state == "open"
 
     # Unknown assertion types must fail hard, not XFAIL.

From 2251884a7095d4d46651be79f4924ebb486fc37f Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 15 Mar 2026 16:58:27 -0400
Subject: [PATCH 066/126] Handle corrupted GitHub issues cache file gracefully

If the cache file exists but contains invalid JSON (e.g. from a killed
process mid-write), delete it and re-fetch rather than crashing with an
unhelpful JSONDecodeError.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 tests/github_issues/conftest.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/github_issues/conftest.py b/tests/github_issues/conftest.py
index ff615f29..7c063660 100644
--- a/tests/github_issues/conftest.py
+++ b/tests/github_issues/conftest.py
@@ -52,7 +52,10 @@ def _get_all_test_issue_ids() -> list[str]:
     """Return IDs of all issues that contain tests, using a file-based cache."""
     with FileLock(_LOCK_FILE):
         if _CACHE_FILE.exists():
-            return json.loads(_CACHE_FILE.read_text())
+            try:
+                return json.loads(_CACHE_FILE.read_text())
+            except (json.JSONDecodeError, OSError):
+                _CACHE_FILE.unlink(missing_ok=True)
         issues = list(_get_github_issues_test_cases().get_issues_with_tests())
         ids = [_issue_id(i) for i in issues]
         for issue, id_ in zip(issues, ids):

From 90bc845b8809fe7fca3fb1bb203ae20392611716 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 15 Mar 2026 17:03:54 -0400
Subject: [PATCH 067/126] Replace print() with debug logging in
 SearchByNameHandler

The full NameRes results dump belongs at DEBUG level, not on stdout,
where it would bypass pytest's output capture and could produce large
noise in test runs.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 src/babel_validation/assertions/nameres.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/babel_validation/assertions/nameres.py b/src/babel_validation/assertions/nameres.py
index 360c7236..6781c550 100644
--- a/src/babel_validation/assertions/nameres.py
+++ b/src/babel_validation/assertions/nameres.py
@@ -1,4 +1,5 @@
 import json
+import logging
 from typing import Iterator
 
 from src.babel_validation.assertions import NameResTest
@@ -49,7 +50,10 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
         try:
             found_index = curies.index(expected_curie)
         except ValueError:
-            print(f"{expected_curie_string} not found when searching for '{search_query}' in NameRes {nameres}: {json.dumps(results, indent=2, sort_keys=True)}")
+            logging.getLogger(__name__).debug(
+                "%s not found when searching for '%s' in NameRes %s: %s",
+                expected_curie_string, search_query, nameres, json.dumps(results, indent=2, sort_keys=True)
+            )
             yield self.failed(f"{expected_curie_string} not found when searching for '{search_query}' in NameRes {nameres}")
             return
 

From d474b18f345fa61dbfa11c6a12b6f922490a091a Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Sun, 15 Mar 2026 22:49:07 -0400
Subject: [PATCH 068/126] Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
---
 src/babel_validation/sources/google_sheets/blocklist.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/babel_validation/sources/google_sheets/blocklist.py b/src/babel_validation/sources/google_sheets/blocklist.py
index 6e349d46..b2eab6c1 100644
--- a/src/babel_validation/sources/google_sheets/blocklist.py
+++ b/src/babel_validation/sources/google_sheets/blocklist.py
@@ -54,7 +54,8 @@ def load_blocklist_from_gsheet():
     google_sheet_id = '1UR2eplHBvFRwaSIVOhlB44wpfNPY1z7AVzUkqzDqIWA'
     csv_url = f"https://docs.google.com/spreadsheets/d/{google_sheet_id}/gviz/tq?tqx=out:csv&sheet=Tests"
 
-    response = requests.get(csv_url)
+    response = requests.get(csv_url, timeout=10)
+    response.raise_for_status()
     csv_content = response.text
 
     rows = []

From 14d230c89ef8b66b48f0f99b4633a147fa8c993d Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 15 Mar 2026 22:50:44 -0400
Subject: [PATCH 069/126] Fixed comment.

---
 tests/conftest.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 7de6e13b..cd923996 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -66,7 +66,7 @@ def pytest_addoption(parser):
         help="The categories of tests to exclude."
     )
 
-    # The issue option is only used by
+    # Only test particular GitHub issues.
     parser.addoption(
         '--issue',
         default=[],

From ae9ed8deb8b406bac03ee185b394239acb5053c0 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 15 Mar 2026 22:56:35 -0400
Subject: [PATCH 070/126] Move pytest config from tests/pytest.ini to
 pyproject.toml

tests/pytest.ini was never picked up when running pytest from the repo
root (pytest searches upward, not into subdirectories). The timeout
and unit marker registration were silently ignored.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 pyproject.toml   | 6 ++++++
 tests/pytest.ini | 6 ------
 2 files changed, 6 insertions(+), 6 deletions(-)
 delete mode 100644 tests/pytest.ini

diff --git a/pyproject.toml b/pyproject.toml
index 90b630ca..4747dccb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,3 +21,9 @@ dependencies = [
 
 [project.urls]
 Repository = "https://github.com/TranslatorSRI/babel-validation"
+
+[tool.pytest.ini_options]
+timeout = 300
+markers = [
+    "unit: unit tests that do not require network access",
+]
diff --git a/tests/pytest.ini b/tests/pytest.ini
deleted file mode 100644
index a84b1690..00000000
--- a/tests/pytest.ini
+++ /dev/null
@@ -1,6 +0,0 @@
-# pytest.ini settings
-[pytest]
-timeout = 300
-# - 300 seconds = 5 mins
-markers =
-    unit: unit tests that do not require network access

From dc51c0be5d5e783af669e0a2a824bc2380d9798a Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 15 Mar 2026 23:39:37 -0400
Subject: [PATCH 071/126] Updated pytest to 9.0+ so we can use subtests.

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4747dccb..3cc1b9a8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -14,7 +14,7 @@ dependencies = [
     "python-dotenv>=0.9.9",
     "openapi-spec-validator>=0.7.2",
     "pygithub>=2.8.1",
-    "pytest>=8.4.2",
+    "pytest>=9.0.2",
     "pytest-timeout>=2.4.0",
     "pytest-xdist[psutil]",
 ]

From 552d53a47a79cdd3624a6d9cc21caab09bb62170 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Mon, 16 Mar 2026 00:48:00 -0400
Subject: [PATCH 072/126] Move GitHub repo list from conftest.py to targets.ini
 [DEFAULT]

The list of repositories to scan for BabelTest assertions is now
configuration rather than code. It lives in [DEFAULT] so it applies
globally and can be overridden per-section if ever needed.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 tests/github_issues/conftest.py | 12 +++++++-----
 tests/targets.ini               |  8 ++++++++
 2 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/tests/github_issues/conftest.py b/tests/github_issues/conftest.py
index 7c063660..f1774166 100644
--- a/tests/github_issues/conftest.py
+++ b/tests/github_issues/conftest.py
@@ -1,3 +1,4 @@
+import configparser
 import json
 import os
 import tempfile
@@ -12,12 +13,13 @@
 
 dotenv.load_dotenv()
 _github_token = os.getenv('GITHUB_TOKEN')
+
+_targets_config = configparser.ConfigParser()
+_targets_config.read(Path(__file__).parent.parent / 'targets.ini')
 _repos = [
-    'NCATSTranslator/Babel',
-    'NCATSTranslator/NodeNormalization',
-    'NCATSTranslator/NameResolution',
-    'TranslatorSRI/babel-validation',
-    'TranslatorSRI/babel-explorer',
+    r.strip()
+    for r in _targets_config['DEFAULT']['Repositories'].splitlines()
+    if r.strip()
 ]
 github_issues_test_cases = None
 
diff --git a/tests/targets.ini b/tests/targets.ini
index 5580aebe..73fd324c 100644
--- a/tests/targets.ini
+++ b/tests/targets.ini
@@ -14,6 +14,14 @@
 [DEFAULT]
 NameResLimit = 20
 NameResXFailIfInTop = 5
+# GitHub repositories to scan for embedded BabelTest assertions.
+# One "org/repo" per line. Can be overridden per-environment section if needed.
+Repositories =
+    NCATSTranslator/Babel
+    NCATSTranslator/NodeNormalization
+    NCATSTranslator/NameResolution
+    TranslatorSRI/babel-validation
+    TranslatorSRI/babel-explorer
 
 [ci-es]
 NodeNormURL = https://biothings.ci.transltr.io/nodenorm/

From 2de6e09b3b28e6dd629766e3dcacfc646c826d43 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Mon, 16 Mar 2026 00:54:11 -0400
Subject: [PATCH 073/126] Updated uv.lock.

---
 uv.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/uv.lock b/uv.lock
index 9e76d081..3559d52f 100644
--- a/uv.lock
+++ b/uv.lock
@@ -45,7 +45,7 @@ requires-dist = [
     { name = "filelock" },
     { name = "openapi-spec-validator", specifier = ">=0.7.2" },
     { name = "pygithub", specifier = ">=2.8.1" },
-    { name = "pytest", specifier = ">=8.4.2" },
+    { name = "pytest", specifier = ">=9.0.2" },
     { name = "pytest-timeout", specifier = ">=2.4.0" },
     { name = "pytest-xdist", extras = ["psutil"] },
     { name = "python-dotenv", specifier = ">=0.9.9" },

From 870f1f9da9884371a8c385c807f63b7f8131f2ef Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Mon, 16 Mar 2026 01:10:09 -0400
Subject: [PATCH 074/126] Document param_set/param_sets terminology across
 assertions package

Add module docstring to github_issues_test_cases.py defining assertion,
param_set, and param_sets; document GitHubIssueTest class and __init__
params; add inline comments showing how Wiki/YAML syntax maps to
param_sets. Add param_sets/:param params: notes to base class methods in
__init__.py. Add inline comments to HasLabelHandler,
ResolvesWithTypeHandler, and SearchByNameHandler clarifying special
element positions. Add "Param Sets" section to gen_docs.py INTRO and
regenerate README.md.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 src/babel_validation/assertions/README.md     | 13 +++++++
 src/babel_validation/assertions/__init__.py   | 24 ++++++++++--
 src/babel_validation/assertions/gen_docs.py   | 13 +++++++
 src/babel_validation/assertions/nameres.py    |  1 +
 src/babel_validation/assertions/nodenorm.py   |  3 ++
 .../github/github_issues_test_cases.py        | 39 +++++++++++++++++++
 6 files changed, 89 insertions(+), 4 deletions(-)

diff --git a/src/babel_validation/assertions/README.md b/src/babel_validation/assertions/README.md
index 1d0c6124..813394bb 100644
--- a/src/babel_validation/assertions/README.md
+++ b/src/babel_validation/assertions/README.md
@@ -26,6 +26,19 @@ babel_tests:
 
 Assertion names are case-insensitive.
 
+## Param Sets
+
+Each assertion can be invoked with one or more **param sets** — independent groups of
+parameters that are each evaluated separately.
+
+- **Wiki syntax** — each `{{BabelTest|...}}` line is one param set.
+- **YAML syntax** — each list entry under an assertion key is one param set; a bare string
+  is a single-element param set, a YAML list is a multi-element param set.
+
+The meaning of each element in a param set depends on the assertion type (see below).
+For most assertions the elements are CURIEs; for `HasLabel` the second element is a
+label string; for `ResolvesWithType` the first element is a Biolink type.
+
 ---
 
 ## NodeNorm Assertions
diff --git a/src/babel_validation/assertions/__init__.py b/src/babel_validation/assertions/__init__.py
index 7b74457a..53fc5583 100644
--- a/src/babel_validation/assertions/__init__.py
+++ b/src/babel_validation/assertions/__init__.py
@@ -38,13 +38,21 @@ def failed(self, message: str) -> TestResult:
 
     def test_with_nodenorm(self, param_sets: list[list[str]], nodenorm,
                            label: str = "") -> Iterator[TestResult]:
-        """Evaluate this assertion against NodeNorm. Returns [] if not applicable."""
+        """Evaluate this assertion against NodeNorm. Returns [] if not applicable.
+
+        :param param_sets: list[list[str]] — see github_issues_test_cases.py module
+                           docstring for the full definition of param_set / param_sets.
+        """
         return []
 
     def test_with_nameres(self, param_sets: list[list[str]], nodenorm, nameres,
                           pass_if_found_in_top: int = 5,
                           label: str = "") -> Iterator[TestResult]:
-        """Evaluate this assertion against NameRes. Returns [] if not applicable."""
+        """Evaluate this assertion against NameRes. Returns [] if not applicable.
+
+        :param param_sets: list[list[str]] — see github_issues_test_cases.py module
+                           docstring for the full definition of param_set / param_sets.
+        """
         return []
 
 
@@ -89,7 +97,11 @@ def test_with_nodenorm(self, param_sets: list[list[str]], nodenorm,
             yield self.failed(f"No test results returned in {label}")
 
     def test_param_set(self, params: list[str], nodenorm, label: str = "") -> Iterator[TestResult]:
-        """Override this to implement the assertion. Called once per param_set."""
+        """Override this to implement the assertion. Called once per param_set.
+
+        :param params: A single param_set — one element of the outer param_sets list.
+                       See github_issues_test_cases.py for the full terminology.
+        """
         raise NotImplementedError
 
     def resolved_message(self, curie: str, result: dict, nodenorm) -> str:
@@ -125,7 +137,11 @@ def test_with_nameres(self, param_sets: list[list[str]], nodenorm, nameres,
 
     def test_param_set(self, params: list[str], nodenorm, nameres,
                        pass_if_found_in_top: int, label: str = "") -> Iterator[TestResult]:
-        """Override this to implement the assertion. Called once per param_set."""
+        """Override this to implement the assertion. Called once per param_set.
+
+        :param params: A single param_set — one element of the outer param_sets list.
+                       See github_issues_test_cases.py for the full terminology.
+        """
         raise NotImplementedError
 
 
diff --git a/src/babel_validation/assertions/gen_docs.py b/src/babel_validation/assertions/gen_docs.py
index c2a5ea22..b6e90270 100644
--- a/src/babel_validation/assertions/gen_docs.py
+++ b/src/babel_validation/assertions/gen_docs.py
@@ -41,6 +41,19 @@
 
 Assertion names are case-insensitive.
 
+## Param Sets
+
+Each assertion can be invoked with one or more **param sets** — independent groups of
+parameters that are each evaluated separately.
+
+- **Wiki syntax** — each `{{BabelTest|...}}` line is one param set.
+- **YAML syntax** — each list entry under an assertion key is one param set; a bare string
+  is a single-element param set, a YAML list is a multi-element param set.
+
+The meaning of each element in a param set depends on the assertion type (see below).
+For most assertions the elements are CURIEs; for `HasLabel` the second element is a
+label string; for `ResolvesWithType` the first element is a Biolink type.
+
 ---
 """
 
diff --git a/src/babel_validation/assertions/nameres.py b/src/babel_validation/assertions/nameres.py
index 6781c550..9178df9e 100644
--- a/src/babel_validation/assertions/nameres.py
+++ b/src/babel_validation/assertions/nameres.py
@@ -26,6 +26,7 @@ class SearchByNameHandler(NameResTest):
     def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                        nameres: CachedNameRes, pass_if_found_in_top: int = 5,
                        label: str = "") -> Iterator[TestResult]:
+        # params[0] is the search query string; params[1] is the expected CURIE.
         if len(params) < 2:
             yield self.failed(f"Two parameters expected for SearchByName in {label}, but params = {params}")
             return
diff --git a/src/babel_validation/assertions/nodenorm.py b/src/babel_validation/assertions/nodenorm.py
index 93386c35..fba52954 100644
--- a/src/babel_validation/assertions/nodenorm.py
+++ b/src/babel_validation/assertions/nodenorm.py
@@ -161,6 +161,7 @@ def curie_params(self, params: list[str]) -> list[str]:
 
     def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                        label: str = "") -> Iterator[TestResult]:
+        # params[0] is the CURIE to resolve; params[1] is the expected label string.
         if len(params) < 2:
             yield self.failed(
                 f"HasLabel requires two parameters (CURIE, expected label) in {label}, "
@@ -209,6 +210,8 @@ def curie_params(self, params: list[str]) -> list[str]:
 
     def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                        label: str = "") -> Iterator[TestResult]:
+        # params[0] is the expected Biolink type (e.g. "biolink:Gene");
+        # params[1:] are the CURIEs that must resolve with that type.
         if len(params) < 2:
             yield self.failed(f"Too few parameters provided in param_set in {label}: {params}")
             return
diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index f62e2666..34670a5f 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -1,3 +1,28 @@
+"""
+Parse and evaluate BabelTest assertions embedded in GitHub issue bodies.
+
+Terminology
+-----------
+assertion   — The name of the test type, e.g. "Resolves" or "ResolvesWith".
+              Case-insensitive. Maps to a key in ASSERTION_HANDLERS.
+
+param_set   — One set of parameters for a single invocation of an assertion.
+              Represented as a list of strings. Each Wiki-syntax line produces
+              exactly one param_set; each entry under a YAML assertion key
+              produces one param_set.
+
+              Often the first element is "special" (e.g. an expected label or
+              Biolink type) and the remaining elements are CURIEs to test,
+              but the interpretation is assertion-specific.
+              Example: ["CHEBI:15365", "PUBCHEM.COMPOUND:1"]
+
+param_sets  — The full list of param_sets for one assertion in one issue.
+              A list of lists (list[list[str]]). YAML syntax allows many
+              param_sets for one assertion type in a single block.
+              Example: [["CHEBI:15365", "PUBCHEM.COMPOUND:1"],
+                        ["MONDO:0005015", "DOID:9351"]]
+"""
+
 import json
 import logging
 import re
@@ -15,7 +40,17 @@
 
 
 class GitHubIssueTest:
+    """Represents one assertion extracted from a GitHub issue body — an assertion name paired with a list of param_sets to evaluate."""
+
     def __init__(self, github_issue_id: str, github_issue: Issue.Issue, assertion: str, param_sets: list[list[str]] = None):
+        """
+        :param github_issue_id: Human-readable issue identifier, e.g. "org/repo#42".
+        :param github_issue: The PyGitHub Issue object this test was extracted from.
+        :param assertion: The assertion name (case-insensitive), e.g. "Resolves" or "HasLabel".
+                          Must match a key in ASSERTION_HANDLERS.
+        :param param_sets: A list of param_sets (list[list[str]]) to evaluate for this assertion.
+                           Each inner list is one param_set — see module docstring for details.
+        """
         self.github_issue = github_issue
         self.assertion = assertion
         if param_sets is None:
@@ -127,6 +162,8 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
                 if len(params) < 2:
                     raise ValueError(f"Too few parameters found in BabelTest in issue {github_issue_id}: {match}")
                 else:
+                    # Wiki syntax: params[0] is the assertion name; params[1:] form a single
+                    # param_set, so param_sets is a one-element list: [params[1:]].
                     testrows.append(GitHubIssueTest(github_issue_id, github_issue, params[0], [params[1:]]))
 
         babeltest_yaml_matches = re.findall(self.babeltest_yaml_pattern, github_issue.body)
@@ -142,6 +179,8 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
                 yaml_dict = yaml.safe_load(match)
 
                 for assertion, original_param_sets in yaml_dict['babel_tests'].items():
+                    # YAML syntax: each entry under an assertion key becomes one param_set.
+                    # A bare string becomes a single-element param_set; a list is used as-is.
                     param_sets = []
                     for param_set in original_param_sets:
                         if isinstance(param_set, str):

From d6077eaa18cd78980a89802523de0f71d0014725 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Mon, 16 Mar 2026 01:39:31 -0400
Subject: [PATCH 075/126] Reject extra params in HasLabel and SearchByName
 assertions

Both handlers previously silently discarded extra parameters. They now
yield a failed TestResult when more than 2 params are supplied, making
malformed assertions visible rather than silently tolerated. Added unit
tests to cover the new behaviour.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 src/babel_validation/assertions/nameres.py  |  8 ++++-
 src/babel_validation/assertions/nodenorm.py |  6 ++++
 tests/github_issues/test_system.py          | 35 +++++++++++++++++++++
 3 files changed, 48 insertions(+), 1 deletion(-)

diff --git a/src/babel_validation/assertions/nameres.py b/src/babel_validation/assertions/nameres.py
index 9178df9e..acf05c6f 100644
--- a/src/babel_validation/assertions/nameres.py
+++ b/src/babel_validation/assertions/nameres.py
@@ -30,8 +30,14 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
         if len(params) < 2:
             yield self.failed(f"Two parameters expected for SearchByName in {label}, but params = {params}")
             return
+        elif len(params) > 2:
+            yield self.failed(
+                f"SearchByName requires exactly two parameters (search query, expected CURIE) in {label}, "
+                f"but got {len(params)}: {params}"
+            )
+            return
 
-        [search_query, expected_curie_from_test, *_] = params
+        [search_query, expected_curie_from_test] = params
         expected_curie_result = nodenorm.normalize_curie(expected_curie_from_test, drug_chemical_conflate='true')
         if not expected_curie_result:
             yield self.failed(f"Unable to normalize CURIE {expected_curie_from_test} in {label}")
diff --git a/src/babel_validation/assertions/nodenorm.py b/src/babel_validation/assertions/nodenorm.py
index fba52954..60cd194a 100644
--- a/src/babel_validation/assertions/nodenorm.py
+++ b/src/babel_validation/assertions/nodenorm.py
@@ -168,6 +168,12 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                 f"but got: {params}"
             )
             return
+        elif len(params) > 2:
+            yield self.failed(
+                f"HasLabel requires exactly two parameters (CURIE, expected label) in {label}, "
+                f"but got {len(params)}: {params}"
+            )
+            return
 
         curie = params[0]
         expected_label = params[1].strip()
diff --git a/tests/github_issues/test_system.py b/tests/github_issues/test_system.py
index 8420320f..d0f8b961 100644
--- a/tests/github_issues/test_system.py
+++ b/tests/github_issues/test_system.py
@@ -3,6 +3,8 @@
 from unittest.mock import MagicMock
 import pytest
 
+from src.babel_validation.core.testrow import TestStatus
+
 pytestmark = pytest.mark.unit
 
 INVALID_NAME = "NotARealAssertion"
@@ -61,3 +63,36 @@ def test_yaml_invalid_name_raises_on_nameres(self, github_issues_test_cases_fixt
         tests = github_issues_test_cases_fixture.get_test_issues_from_issue(self._yaml_issue())
         with pytest.raises(ValueError, match="Unknown assertion type"):
             list(tests[0].test_with_nameres(None, None))
+
+
+@pytest.mark.unit
+class TestTooManyParams:
+    """Extra params for fixed-arity assertions should yield a failed result, not silently pass."""
+
+    def _results(self, fixture, wiki_syntax, service="nodenorm"):
+        mock = _mock_issue(wiki_syntax)
+        tests = fixture.get_test_issues_from_issue(mock)
+        assert len(tests) == 1
+        if service == "nodenorm":
+            return list(tests[0].test_with_nodenorm(MagicMock()))
+        else:
+            return list(tests[0].test_with_nameres(None, None))
+
+    def test_haslabel_too_many_params(self, github_issues_test_cases_fixture):
+        results = self._results(
+            github_issues_test_cases_fixture,
+            "{{BabelTest|HasLabel|CHEBI:15365|aspirin|unexpected}}"
+        )
+        assert len(results) == 1
+        assert results[0].status == TestStatus.Failed
+        assert "exactly two" in results[0].message
+
+    def test_searchbyname_too_many_params(self, github_issues_test_cases_fixture):
+        results = self._results(
+            github_issues_test_cases_fixture,
+            "{{BabelTest|SearchByName|water|CHEBI:15377|unexpected}}",
+            service="nameres"
+        )
+        assert len(results) == 1
+        assert results[0].status == TestStatus.Failed
+        assert "exactly two" in results[0].message

From d7fde855726f96e7ea6064892294e2835a34b075 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Mon, 16 Mar 2026 01:46:08 -0400
Subject: [PATCH 076/126] Add unit test documenting yaml.YAMLError on malformed
 YAML block

Covers the unhandled path in get_test_issues_from_issue() where a YAML
block matches the detection regex but contains invalid YAML.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 tests/github_issues/test_system.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/tests/github_issues/test_system.py b/tests/github_issues/test_system.py
index d0f8b961..39dccb96 100644
--- a/tests/github_issues/test_system.py
+++ b/tests/github_issues/test_system.py
@@ -2,6 +2,7 @@
 
 from unittest.mock import MagicMock
 import pytest
+import yaml
 
 from src.babel_validation.core.testrow import TestStatus
 
@@ -96,3 +97,15 @@ def test_searchbyname_too_many_params(self, github_issues_test_cases_fixture):
         assert len(results) == 1
         assert results[0].status == TestStatus.Failed
         assert "exactly two" in results[0].message
+
+
+@pytest.mark.unit
+class TestMalformedYaml:
+    """A YAML block that matches the detection regex but is not valid YAML raises yaml.YAMLError."""
+
+    MALFORMED_BODY = "```yaml\nbabel_tests:\n  Resolves:\n  - [unclosed bracket\n```"
+
+    def test_malformed_yaml_raises(self, github_issues_test_cases_fixture):
+        mock = _mock_issue(self.MALFORMED_BODY)
+        with pytest.raises(yaml.YAMLError):
+            github_issues_test_cases_fixture.get_test_issues_from_issue(mock)

From 688ef36e886634a34b0e1344196e935fdff4912b Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Mon, 16 Mar 2026 01:55:20 -0400
Subject: [PATCH 077/126] Add TestEmptyOrNullBabelTests to document current
 behaviour for empty/null babel test content

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 tests/github_issues/test_system.py | 43 ++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/tests/github_issues/test_system.py b/tests/github_issues/test_system.py
index 39dccb96..53aec906 100644
--- a/tests/github_issues/test_system.py
+++ b/tests/github_issues/test_system.py
@@ -109,3 +109,46 @@ def test_malformed_yaml_raises(self, github_issues_test_cases_fixture):
         mock = _mock_issue(self.MALFORMED_BODY)
         with pytest.raises(yaml.YAMLError):
             github_issues_test_cases_fixture.get_test_issues_from_issue(mock)
+
+
+@pytest.mark.unit
+class TestEmptyOrNullBabelTests:
+    """Documents behaviour when issue bodies contain empty or null babel test content."""
+
+    # --- empty/null body (already handled gracefully) ---
+
+    def test_none_body_returns_empty(self, github_issues_test_cases_fixture):
+        mock = _mock_issue(None)
+        assert github_issues_test_cases_fixture.get_test_issues_from_issue(mock) == []
+
+    def test_whitespace_body_returns_empty(self, github_issues_test_cases_fixture):
+        mock = _mock_issue("   ")
+        assert github_issues_test_cases_fixture.get_test_issues_from_issue(mock) == []
+
+    # --- wiki syntax: assertion name only, no curie params ---
+
+    def test_wiki_no_curie_params_raises(self, github_issues_test_cases_fixture):
+        mock = _mock_issue("{{BabelTest|Resolves}}")
+        with pytest.raises(ValueError, match="Too few parameters"):
+            github_issues_test_cases_fixture.get_test_issues_from_issue(mock)
+
+    # --- YAML syntax: null / empty values ---
+
+    def test_yaml_null_babel_tests_raises(self, github_issues_test_cases_fixture):
+        # babel_tests: null → AttributeError calling .items() on None
+        mock = _mock_issue("```yaml\nbabel_tests:\n\n```")
+        with pytest.raises((AttributeError, TypeError)):
+            github_issues_test_cases_fixture.get_test_issues_from_issue(mock)
+
+    def test_yaml_null_assertion_params_raises(self, github_issues_test_cases_fixture):
+        # Resolves: null → TypeError iterating over None
+        mock = _mock_issue("```yaml\nbabel_tests:\n  Resolves:\n```")
+        with pytest.raises(TypeError):
+            github_issues_test_cases_fixture.get_test_issues_from_issue(mock)
+
+    def test_yaml_empty_assertion_params(self, github_issues_test_cases_fixture):
+        # Resolves: [] → GitHubIssueTest with empty param_sets (no crash)
+        mock = _mock_issue("```yaml\nbabel_tests:\n  Resolves: []\n```")
+        tests = github_issues_test_cases_fixture.get_test_issues_from_issue(mock)
+        assert len(tests) == 1
+        assert tests[0].param_sets == []

From a02909319af63db45a2fcfcf1ccd0399a4054401 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Mon, 16 Mar 2026 02:04:14 -0400
Subject: [PATCH 078/126] Add unit tests for issue_has_tests() and
 get_issues_with_tests()

Adds TestIssueHasTests (5 tests) and TestGetIssuesWithTests (4 tests)
covering the regex gate, deduplication logic, and search false-positive
filtering in GitHubIssuesTestCases.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 tests/github_issues/test_system.py | 77 +++++++++++++++++++++++++++++-
 1 file changed, 76 insertions(+), 1 deletion(-)

diff --git a/tests/github_issues/test_system.py b/tests/github_issues/test_system.py
index 53aec906..919dae00 100644
--- a/tests/github_issues/test_system.py
+++ b/tests/github_issues/test_system.py
@@ -1,6 +1,6 @@
 """System tests for BabelTest trigger detection in GitHub issue bodies."""
 
-from unittest.mock import MagicMock
+from unittest.mock import MagicMock, patch
 import pytest
 import yaml
 
@@ -152,3 +152,78 @@ def test_yaml_empty_assertion_params(self, github_issues_test_cases_fixture):
         tests = github_issues_test_cases_fixture.get_test_issues_from_issue(mock)
         assert len(tests) == 1
         assert tests[0].param_sets == []
+
+
+@pytest.mark.unit
+class TestIssueHasTests:
+    """Documents issue_has_tests() behaviour for various body contents."""
+
+    def test_none_body_returns_false(self, github_issues_test_cases_fixture):
+        assert github_issues_test_cases_fixture.issue_has_tests(_mock_issue(None)) is False
+
+    def test_whitespace_body_returns_false(self, github_issues_test_cases_fixture):
+        assert github_issues_test_cases_fixture.issue_has_tests(_mock_issue("   ")) is False
+
+    def test_wiki_syntax_detected(self, github_issues_test_cases_fixture):
+        assert github_issues_test_cases_fixture.issue_has_tests(
+            _mock_issue("{{BabelTest|Resolves|CHEBI:12345}}")
+        ) is True
+
+    def test_yaml_syntax_detected(self, github_issues_test_cases_fixture):
+        assert github_issues_test_cases_fixture.issue_has_tests(
+            _mock_issue("```yaml\nbabel_tests:\n  Resolves:\n  - CHEBI:12345\n```")
+        ) is True
+
+    def test_plain_text_not_detected(self, github_issues_test_cases_fixture):
+        assert github_issues_test_cases_fixture.issue_has_tests(
+            _mock_issue("Just some text without babel tests.")
+        ) is False
+
+
+@pytest.mark.unit
+class TestGetIssuesWithTests:
+    """Documents the search-API path of get_issues_with_tests()."""
+
+    _REPOS = ["test-org/test-repo"]
+
+    def test_no_results_yields_nothing(self, github_issues_test_cases_fixture):
+        with patch.object(github_issues_test_cases_fixture.github, "search_issues",
+                          return_value=[]):
+            results = list(
+                github_issues_test_cases_fixture.get_issues_with_tests(self._REPOS)
+            )
+        assert results == []
+
+    def test_matching_issue_is_yielded(self, github_issues_test_cases_fixture):
+        mock = _mock_issue("{{BabelTest|Resolves|CHEBI:12345}}", number=1)
+        # Two keyword searches per repo; first returns our issue, second returns nothing.
+        with patch.object(github_issues_test_cases_fixture.github, "search_issues",
+                          side_effect=[[mock], []]):
+            results = list(
+                github_issues_test_cases_fixture.get_issues_with_tests(self._REPOS)
+            )
+        assert results == [mock]
+
+    def test_duplicate_across_keywords_deduplicated(self, github_issues_test_cases_fixture):
+        # Issue contains both syntaxes → appears in both keyword searches → yielded once.
+        body = (
+            "{{BabelTest|Resolves|CHEBI:12345}}\n"
+            "```yaml\nbabel_tests:\n  Resolves:\n  - CHEBI:12345\n```"
+        )
+        mock = _mock_issue(body, number=42)
+        with patch.object(github_issues_test_cases_fixture.github, "search_issues",
+                          side_effect=[[mock], [mock]]):
+            results = list(
+                github_issues_test_cases_fixture.get_issues_with_tests(self._REPOS)
+            )
+        assert results == [mock]
+
+    def test_search_false_positive_filtered(self, github_issues_test_cases_fixture):
+        # GitHub returns an issue that mentions the keyword in prose (no real BabelTest block).
+        mock = _mock_issue("This issue discusses babel_tests: in passing.", number=99)
+        with patch.object(github_issues_test_cases_fixture.github, "search_issues",
+                          side_effect=[[mock], []]):
+            results = list(
+                github_issues_test_cases_fixture.get_issues_with_tests(self._REPOS)
+            )
+        assert results == []

From fd44d66c5ba5900b3fca90c2e167e2aca051e12f Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 1 Apr 2026 12:13:41 -0400
Subject: [PATCH 079/126] Simplify: remove dead code, fix string parsing,
 rename fixture

- Remove unused TestResult.github_issue_test field
- Replace magic-number string slicing with removeprefix/removesuffix
- Update stale TODO comment in CachedNameRes to describe actual limitation
- Deduplicate CURIEs with set comprehension before bulk prewarm call
- Rename github_issues_test_cases_fixture -> github_issues_test_cases

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 src/babel_validation/assertions/__init__.py   |   4 +-
 src/babel_validation/core/testrow.py          |   1 -
 src/babel_validation/services/nameres.py      |   3 +-
 .../github/github_issues_test_cases.py        |  12 +-
 tests/github_issues/conftest.py               |  14 +--
 tests/github_issues/test_github_issues.py     |   4 +-
 tests/github_issues/test_system.py            | 104 +++++++++---------
 7 files changed, 67 insertions(+), 75 deletions(-)

diff --git a/src/babel_validation/assertions/__init__.py b/src/babel_validation/assertions/__init__.py
index 53fc5583..80ab1e5f 100644
--- a/src/babel_validation/assertions/__init__.py
+++ b/src/babel_validation/assertions/__init__.py
@@ -74,8 +74,8 @@ def test_with_nodenorm(self, param_sets: list[list[str]], nodenorm,
         if not param_sets:
             yield self.failed(f"No parameters provided in {label}")
             return
-        # warm the cache only for params that are CURIEs
-        nodenorm.normalize_curies([p for params in param_sets for p in self.curie_params(params)])
+        # warm the cache only for params that are CURIEs (deduplicated)
+        nodenorm.normalize_curies(list({p for params in param_sets for p in self.curie_params(params)}))
         found = False
         for index, params in enumerate(param_sets):
             if not params:
diff --git a/src/babel_validation/core/testrow.py b/src/babel_validation/core/testrow.py
index 35cd1ca9..b03a55ee 100644
--- a/src/babel_validation/core/testrow.py
+++ b/src/babel_validation/core/testrow.py
@@ -66,7 +66,6 @@ class TestStatus(Enum):
 class TestResult:
     status: TestStatus
     message: str = ""
-    github_issue_test: 'GitHubIssueTest' = None
 
     # Mark as not a test despite starting with Test*.
     __test__ = False
diff --git a/src/babel_validation/services/nameres.py b/src/babel_validation/services/nameres.py
index 5dcee5c1..251b0fcb 100644
--- a/src/babel_validation/services/nameres.py
+++ b/src/babel_validation/services/nameres.py
@@ -6,7 +6,8 @@
 cached_nameres_by_url = {}
 
 class CachedNameRes:
-    # TODO: actually cache once we've implemented a param-based cache.
+    # Note: caching ignores extra **params (e.g. autocomplete, limit), so callers should use
+    # a consistent set of params or call delete_query() to invalidate before changing params.
     def __init__(self, nameres_url: str):
         self.nameres_url = nameres_url
         self.logger = logging.getLogger(str(self))
diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index 34670a5f..73538b0b 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -153,11 +153,7 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
                 self.logger.info(f"Found BabelTest in issue {github_issue_id}: {match}")
 
                 # Figure out parameters.
-                test_string = match
-                if test_string.startswith("{{BabelTest|"):
-                    test_string = test_string[12:]
-                if test_string.endswith("}}"):
-                    test_string = test_string[:-2]
+                test_string = match.removeprefix("{{BabelTest|").removesuffix("}}")
                 params = test_string.split("|")
                 if len(params) < 2:
                     raise ValueError(f"Too few parameters found in BabelTest in issue {github_issue_id}: {match}")
@@ -172,11 +168,7 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
                 self.logger.info(f"Found BabelTest YAML in issue {github_issue_id}: {match}")
 
                 # Parse string as YAML.
-                if match.startswith("```yaml"):
-                    match = match[7:]
-                if match.endswith("```"):
-                    match = match[:-3]
-                yaml_dict = yaml.safe_load(match)
+                yaml_dict = yaml.safe_load(match.removeprefix("```yaml").removesuffix("```"))
 
                 for assertion, original_param_sets in yaml_dict['babel_tests'].items():
                     # YAML syntax: each entry under an assertion key becomes one param_set.
diff --git a/tests/github_issues/conftest.py b/tests/github_issues/conftest.py
index f1774166..482f0828 100644
--- a/tests/github_issues/conftest.py
+++ b/tests/github_issues/conftest.py
@@ -21,7 +21,7 @@
     for r in _targets_config['DEFAULT']['Repositories'].splitlines()
     if r.strip()
 ]
-github_issues_test_cases = None
+_github_issues_test_cases = None
 
 _CACHE_FILE = Path(tempfile.gettempdir()) / "babel_validation_issues_cache.json"
 _LOCK_FILE = _CACHE_FILE.with_suffix(".lock")
@@ -32,16 +32,16 @@
 
 def _get_github_issues_test_cases() -> GitHubIssuesTestCases:
     """Lazily construct GitHubIssuesTestCases, skipping tests if no token is available."""
-    global github_issues_test_cases
-    if github_issues_test_cases is not None:
-        return github_issues_test_cases
+    global _github_issues_test_cases
+    if _github_issues_test_cases is not None:
+        return _github_issues_test_cases
     if not _github_token:
         pytest.skip(
             "GITHUB_TOKEN environment variable not set; skipping GitHub issues tests.",
             allow_module_level=True,
         )
-    github_issues_test_cases = GitHubIssuesTestCases(_github_token, _repos)
-    return github_issues_test_cases
+    _github_issues_test_cases = GitHubIssuesTestCases(_github_token, _repos)
+    return _github_issues_test_cases
 
 
 def _issue_id(issue: Issue.Issue) -> str:
@@ -89,5 +89,5 @@ def github_issue(github_issue_id):
 
 
 @pytest.fixture(scope="session")
-def github_issues_test_cases_fixture():
+def github_issues_test_cases():
     return _get_github_issues_test_cases()
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 87ff59eb..a82dbd1f 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -9,10 +9,10 @@
 from src.babel_validation.core.testrow import TestResult, TestStatus
 
 
-def test_github_issue(request, target_info, github_issue_id, github_issue, github_issues_test_cases_fixture, subtests):
+def test_github_issue(request, target_info, github_issue_id, github_issue, github_issues_test_cases, subtests):
     nodenorm = CachedNodeNorm.from_url(target_info['NodeNormURL'])
     nameres = CachedNameRes.from_url(target_info['NameResURL'])
-    tests = github_issues_test_cases_fixture.get_test_issues_from_issue(github_issue)
+    tests = github_issues_test_cases.get_test_issues_from_issue(github_issue)
     if not tests:
         pytest.skip(f"No tests found in issue {github_issue}")
         return
diff --git a/tests/github_issues/test_system.py b/tests/github_issues/test_system.py
index 919dae00..008d613a 100644
--- a/tests/github_issues/test_system.py
+++ b/tests/github_issues/test_system.py
@@ -33,35 +33,35 @@ def _yaml_issue(self):
 
     # --- parsing: invalid names are extracted, not rejected ---
 
-    def test_wiki_syntax_parses_invalid_name(self, github_issues_test_cases_fixture):
-        tests = github_issues_test_cases_fixture.get_test_issues_from_issue(self._wiki_issue())
+    def test_wiki_syntax_parses_invalid_name(self, github_issues_test_cases):
+        tests = github_issues_test_cases.get_test_issues_from_issue(self._wiki_issue())
         assert len(tests) == 1
         assert tests[0].assertion == INVALID_NAME
 
-    def test_yaml_syntax_parses_invalid_name(self, github_issues_test_cases_fixture):
-        tests = github_issues_test_cases_fixture.get_test_issues_from_issue(self._yaml_issue())
+    def test_yaml_syntax_parses_invalid_name(self, github_issues_test_cases):
+        tests = github_issues_test_cases.get_test_issues_from_issue(self._yaml_issue())
         assert len(tests) == 1
         assert tests[0].assertion == INVALID_NAME
 
     # --- execution: invalid names raise ValueError before any service call ---
 
-    def test_wiki_invalid_name_raises_on_nodenorm(self, github_issues_test_cases_fixture):
-        tests = github_issues_test_cases_fixture.get_test_issues_from_issue(self._wiki_issue())
+    def test_wiki_invalid_name_raises_on_nodenorm(self, github_issues_test_cases):
+        tests = github_issues_test_cases.get_test_issues_from_issue(self._wiki_issue())
         with pytest.raises(ValueError, match="Unknown assertion type"):
             list(tests[0].test_with_nodenorm(None))
 
-    def test_wiki_invalid_name_raises_on_nameres(self, github_issues_test_cases_fixture):
-        tests = github_issues_test_cases_fixture.get_test_issues_from_issue(self._wiki_issue())
+    def test_wiki_invalid_name_raises_on_nameres(self, github_issues_test_cases):
+        tests = github_issues_test_cases.get_test_issues_from_issue(self._wiki_issue())
         with pytest.raises(ValueError, match="Unknown assertion type"):
             list(tests[0].test_with_nameres(None, None))
 
-    def test_yaml_invalid_name_raises_on_nodenorm(self, github_issues_test_cases_fixture):
-        tests = github_issues_test_cases_fixture.get_test_issues_from_issue(self._yaml_issue())
+    def test_yaml_invalid_name_raises_on_nodenorm(self, github_issues_test_cases):
+        tests = github_issues_test_cases.get_test_issues_from_issue(self._yaml_issue())
         with pytest.raises(ValueError, match="Unknown assertion type"):
             list(tests[0].test_with_nodenorm(None))
 
-    def test_yaml_invalid_name_raises_on_nameres(self, github_issues_test_cases_fixture):
-        tests = github_issues_test_cases_fixture.get_test_issues_from_issue(self._yaml_issue())
+    def test_yaml_invalid_name_raises_on_nameres(self, github_issues_test_cases):
+        tests = github_issues_test_cases.get_test_issues_from_issue(self._yaml_issue())
         with pytest.raises(ValueError, match="Unknown assertion type"):
             list(tests[0].test_with_nameres(None, None))
 
@@ -79,18 +79,18 @@ def _results(self, fixture, wiki_syntax, service="nodenorm"):
         else:
             return list(tests[0].test_with_nameres(None, None))
 
-    def test_haslabel_too_many_params(self, github_issues_test_cases_fixture):
+    def test_haslabel_too_many_params(self, github_issues_test_cases):
         results = self._results(
-            github_issues_test_cases_fixture,
+            github_issues_test_cases,
             "{{BabelTest|HasLabel|CHEBI:15365|aspirin|unexpected}}"
         )
         assert len(results) == 1
         assert results[0].status == TestStatus.Failed
         assert "exactly two" in results[0].message
 
-    def test_searchbyname_too_many_params(self, github_issues_test_cases_fixture):
+    def test_searchbyname_too_many_params(self, github_issues_test_cases):
         results = self._results(
-            github_issues_test_cases_fixture,
+            github_issues_test_cases,
             "{{BabelTest|SearchByName|water|CHEBI:15377|unexpected}}",
             service="nameres"
         )
@@ -105,10 +105,10 @@ class TestMalformedYaml:
 
     MALFORMED_BODY = "```yaml\nbabel_tests:\n  Resolves:\n  - [unclosed bracket\n```"
 
-    def test_malformed_yaml_raises(self, github_issues_test_cases_fixture):
+    def test_malformed_yaml_raises(self, github_issues_test_cases):
         mock = _mock_issue(self.MALFORMED_BODY)
         with pytest.raises(yaml.YAMLError):
-            github_issues_test_cases_fixture.get_test_issues_from_issue(mock)
+            github_issues_test_cases.get_test_issues_from_issue(mock)
 
 
 @pytest.mark.unit
@@ -117,39 +117,39 @@ class TestEmptyOrNullBabelTests:
 
     # --- empty/null body (already handled gracefully) ---
 
-    def test_none_body_returns_empty(self, github_issues_test_cases_fixture):
+    def test_none_body_returns_empty(self, github_issues_test_cases):
         mock = _mock_issue(None)
-        assert github_issues_test_cases_fixture.get_test_issues_from_issue(mock) == []
+        assert github_issues_test_cases.get_test_issues_from_issue(mock) == []
 
-    def test_whitespace_body_returns_empty(self, github_issues_test_cases_fixture):
+    def test_whitespace_body_returns_empty(self, github_issues_test_cases):
         mock = _mock_issue("   ")
-        assert github_issues_test_cases_fixture.get_test_issues_from_issue(mock) == []
+        assert github_issues_test_cases.get_test_issues_from_issue(mock) == []
 
     # --- wiki syntax: assertion name only, no curie params ---
 
-    def test_wiki_no_curie_params_raises(self, github_issues_test_cases_fixture):
+    def test_wiki_no_curie_params_raises(self, github_issues_test_cases):
         mock = _mock_issue("{{BabelTest|Resolves}}")
         with pytest.raises(ValueError, match="Too few parameters"):
-            github_issues_test_cases_fixture.get_test_issues_from_issue(mock)
+            github_issues_test_cases.get_test_issues_from_issue(mock)
 
     # --- YAML syntax: null / empty values ---
 
-    def test_yaml_null_babel_tests_raises(self, github_issues_test_cases_fixture):
+    def test_yaml_null_babel_tests_raises(self, github_issues_test_cases):
         # babel_tests: null → AttributeError calling .items() on None
         mock = _mock_issue("```yaml\nbabel_tests:\n\n```")
         with pytest.raises((AttributeError, TypeError)):
-            github_issues_test_cases_fixture.get_test_issues_from_issue(mock)
+            github_issues_test_cases.get_test_issues_from_issue(mock)
 
-    def test_yaml_null_assertion_params_raises(self, github_issues_test_cases_fixture):
+    def test_yaml_null_assertion_params_raises(self, github_issues_test_cases):
         # Resolves: null → TypeError iterating over None
         mock = _mock_issue("```yaml\nbabel_tests:\n  Resolves:\n```")
         with pytest.raises(TypeError):
-            github_issues_test_cases_fixture.get_test_issues_from_issue(mock)
+            github_issues_test_cases.get_test_issues_from_issue(mock)
 
-    def test_yaml_empty_assertion_params(self, github_issues_test_cases_fixture):
+    def test_yaml_empty_assertion_params(self, github_issues_test_cases):
         # Resolves: [] → GitHubIssueTest with empty param_sets (no crash)
         mock = _mock_issue("```yaml\nbabel_tests:\n  Resolves: []\n```")
-        tests = github_issues_test_cases_fixture.get_test_issues_from_issue(mock)
+        tests = github_issues_test_cases.get_test_issues_from_issue(mock)
         assert len(tests) == 1
         assert tests[0].param_sets == []
 
@@ -158,24 +158,24 @@ def test_yaml_empty_assertion_params(self, github_issues_test_cases_fixture):
 class TestIssueHasTests:
     """Documents issue_has_tests() behaviour for various body contents."""
 
-    def test_none_body_returns_false(self, github_issues_test_cases_fixture):
-        assert github_issues_test_cases_fixture.issue_has_tests(_mock_issue(None)) is False
+    def test_none_body_returns_false(self, github_issues_test_cases):
+        assert github_issues_test_cases.issue_has_tests(_mock_issue(None)) is False
 
-    def test_whitespace_body_returns_false(self, github_issues_test_cases_fixture):
-        assert github_issues_test_cases_fixture.issue_has_tests(_mock_issue("   ")) is False
+    def test_whitespace_body_returns_false(self, github_issues_test_cases):
+        assert github_issues_test_cases.issue_has_tests(_mock_issue("   ")) is False
 
-    def test_wiki_syntax_detected(self, github_issues_test_cases_fixture):
-        assert github_issues_test_cases_fixture.issue_has_tests(
+    def test_wiki_syntax_detected(self, github_issues_test_cases):
+        assert github_issues_test_cases.issue_has_tests(
             _mock_issue("{{BabelTest|Resolves|CHEBI:12345}}")
         ) is True
 
-    def test_yaml_syntax_detected(self, github_issues_test_cases_fixture):
-        assert github_issues_test_cases_fixture.issue_has_tests(
+    def test_yaml_syntax_detected(self, github_issues_test_cases):
+        assert github_issues_test_cases.issue_has_tests(
             _mock_issue("```yaml\nbabel_tests:\n  Resolves:\n  - CHEBI:12345\n```")
         ) is True
 
-    def test_plain_text_not_detected(self, github_issues_test_cases_fixture):
-        assert github_issues_test_cases_fixture.issue_has_tests(
+    def test_plain_text_not_detected(self, github_issues_test_cases):
+        assert github_issues_test_cases.issue_has_tests(
             _mock_issue("Just some text without babel tests.")
         ) is False
 
@@ -186,44 +186,44 @@ class TestGetIssuesWithTests:
 
     _REPOS = ["test-org/test-repo"]
 
-    def test_no_results_yields_nothing(self, github_issues_test_cases_fixture):
-        with patch.object(github_issues_test_cases_fixture.github, "search_issues",
+    def test_no_results_yields_nothing(self, github_issues_test_cases):
+        with patch.object(github_issues_test_cases.github, "search_issues",
                           return_value=[]):
             results = list(
-                github_issues_test_cases_fixture.get_issues_with_tests(self._REPOS)
+                github_issues_test_cases.get_issues_with_tests(self._REPOS)
             )
         assert results == []
 
-    def test_matching_issue_is_yielded(self, github_issues_test_cases_fixture):
+    def test_matching_issue_is_yielded(self, github_issues_test_cases):
         mock = _mock_issue("{{BabelTest|Resolves|CHEBI:12345}}", number=1)
         # Two keyword searches per repo; first returns our issue, second returns nothing.
-        with patch.object(github_issues_test_cases_fixture.github, "search_issues",
+        with patch.object(github_issues_test_cases.github, "search_issues",
                           side_effect=[[mock], []]):
             results = list(
-                github_issues_test_cases_fixture.get_issues_with_tests(self._REPOS)
+                github_issues_test_cases.get_issues_with_tests(self._REPOS)
             )
         assert results == [mock]
 
-    def test_duplicate_across_keywords_deduplicated(self, github_issues_test_cases_fixture):
+    def test_duplicate_across_keywords_deduplicated(self, github_issues_test_cases):
         # Issue contains both syntaxes → appears in both keyword searches → yielded once.
         body = (
             "{{BabelTest|Resolves|CHEBI:12345}}\n"
             "```yaml\nbabel_tests:\n  Resolves:\n  - CHEBI:12345\n```"
         )
         mock = _mock_issue(body, number=42)
-        with patch.object(github_issues_test_cases_fixture.github, "search_issues",
+        with patch.object(github_issues_test_cases.github, "search_issues",
                           side_effect=[[mock], [mock]]):
             results = list(
-                github_issues_test_cases_fixture.get_issues_with_tests(self._REPOS)
+                github_issues_test_cases.get_issues_with_tests(self._REPOS)
             )
         assert results == [mock]
 
-    def test_search_false_positive_filtered(self, github_issues_test_cases_fixture):
+    def test_search_false_positive_filtered(self, github_issues_test_cases):
         # GitHub returns an issue that mentions the keyword in prose (no real BabelTest block).
         mock = _mock_issue("This issue discusses babel_tests: in passing.", number=99)
-        with patch.object(github_issues_test_cases_fixture.github, "search_issues",
+        with patch.object(github_issues_test_cases.github, "search_issues",
                           side_effect=[[mock], []]):
             results = list(
-                github_issues_test_cases_fixture.get_issues_with_tests(self._REPOS)
+                github_issues_test_cases.get_issues_with_tests(self._REPOS)
             )
         assert results == []

From 0c46ce9be44f82619b4bb40783f0b3fb265f11b0 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 1 Apr 2026 12:14:46 -0400
Subject: [PATCH 080/126] Handle missing labels in NodeNorm.

---
 src/babel_validation/assertions/nodenorm.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/babel_validation/assertions/nodenorm.py b/src/babel_validation/assertions/nodenorm.py
index 60cd194a..8a3981d6 100644
--- a/src/babel_validation/assertions/nodenorm.py
+++ b/src/babel_validation/assertions/nodenorm.py
@@ -185,6 +185,12 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
             )
             return
 
+        if 'label' not in result['id']:
+            yield self.failed(
+                f"CURIE {curie} has no label but expected '{expected_label}' on {nodenorm}"
+            )
+            return
+
         actual_label = result['id']['label']
         if actual_label == expected_label:
             yield self.passed(

From aa94099936954c87727d20fa6f40cda02500b7ae Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 1 Apr 2026 12:18:51 -0400
Subject: [PATCH 081/126] Fixed level lookup in NodeNorm result.

---
 src/babel_validation/assertions/nodenorm.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/babel_validation/assertions/nodenorm.py b/src/babel_validation/assertions/nodenorm.py
index 8a3981d6..23142780 100644
--- a/src/babel_validation/assertions/nodenorm.py
+++ b/src/babel_validation/assertions/nodenorm.py
@@ -93,7 +93,7 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
             else:
                 yield self.failed(
                     f"Resolved {curie} to {result['id']['identifier']} "
-                    f"({result['type'][0]}, \"{result['id']['label']}\"), but expected "
+                    f"({result['type'][0]}, \"{result['id'].get('label', '')}\"), but expected "
                     f"{canonical_id} "
                     f"({first_good['type'][0]}, \"{first_good['id']['label']}\") on {nodenorm}"
                 )

From 4f74880010e02bb54c355655e8e561f065cb9f01 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 23 Apr 2026 16:32:11 -0400
Subject: [PATCH 082/126] Reverted NameRes to Solr instead of ElasticSearch.

---
 tests/targets.ini | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tests/targets.ini b/tests/targets.ini
index 1bece5c0..f1499134 100644
--- a/tests/targets.ini
+++ b/tests/targets.ini
@@ -41,7 +41,9 @@ NameResURL = https://name-lookup.ci.transltr.io/
 
 [ci]
 NodeNormURL = https://nodenorm-es.ci.transltr.io/
-NameResURL = https://namelookup-es.ci.transltr.io/
+NameResURL = https://name-lookup.ci.transltr.io/
+# If you want to test NameRes ElasticSearch, you'll need to uncomment this:
+# NameResURL = https://namelookup-es.ci.transltr.io/
 
 [dev]
 NodeNormURL = https://nodenormalization-sri.renci.org/

From 714d4bbdf72dc47bf1dd7cd360e3c1b80e25b606 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Mon, 27 Apr 2026 13:53:46 -0400
Subject: [PATCH 083/126] Reconfigured ci-es.

---
 tests/targets.ini | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/tests/targets.ini b/tests/targets.ini
index f1499134..be12baf3 100644
--- a/tests/targets.ini
+++ b/tests/targets.ini
@@ -23,10 +23,6 @@ Repositories =
     TranslatorSRI/babel-validation
     TranslatorSRI/babel-explorer
 
-[ci-es]
-NodeNormURL = https://biothings.ci.transltr.io/nodenorm/
-NameResURL = https://name-lookup.ci.transltr.io/
-
 [prod]
 NodeNormURL = https://nodenorm.transltr.io/
 NameResURL = https://name-lookup.transltr.io/
@@ -42,8 +38,10 @@ NameResURL = https://name-lookup.ci.transltr.io/
 [ci]
 NodeNormURL = https://nodenorm-es.ci.transltr.io/
 NameResURL = https://name-lookup.ci.transltr.io/
-# If you want to test NameRes ElasticSearch, you'll need to uncomment this:
-# NameResURL = https://namelookup-es.ci.transltr.io/
+
+[ci-es]
+NodeNormURL = https://nodenorm-es.ci.transltr.io/
+NameResURL = https://namelookup-es.ci.transltr.io/
 
 [dev]
 NodeNormURL = https://nodenormalization-sri.renci.org/

From 1e9c42f7383da75a6b9d33fafb8dfbe917f66ccb Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Thu, 30 Apr 2026 15:25:43 -0400
Subject: [PATCH 084/126] Changed Biolink Type param to a list.

---
 tests/nameres/test_nameres_from_gsheet.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/nameres/test_nameres_from_gsheet.py b/tests/nameres/test_nameres_from_gsheet.py
index 5c5993d5..78118bf1 100644
--- a/tests/nameres/test_nameres_from_gsheet.py
+++ b/tests/nameres/test_nameres_from_gsheet.py
@@ -56,8 +56,10 @@ def test_label(target_info, test_row, test_category):
             request = {
                 "string": label,
                 "autocomplete": autocomplete_flag,
-                "biolink_type": biolink_class,
-                "limit": limit
+                "biolink_type": [
+                    # Turned it into a list to support multiple Biolink types.
+                    biolink_class,
+                ], "limit": limit
             }
             if test_row.Prefixes:
                 only_prefixes = []

From 5ee0efa6ec61a24c6488cdb51362b327da409b18 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Mon, 4 May 2026 15:25:38 -0400
Subject: [PATCH 085/126] Add csv-to-babeltests CLI for converting CSV assets
 into BabelTests YAML.

Translator collaborators sometimes circulate spreadsheets pairing a CURIE
column with a label, equivalent CURIE, or Biolink type. This adds a click
CLI that ingests such CSVs and emits a paste-ready YAML babel_tests block
for a GitHub issue, optionally validating each row against a NodeNorm
target from tests/targets.ini and reporting failures on stderr.

The tool reuses ASSERTION_HANDLERS and CachedNodeNorm directly so the
emitted YAML is guaranteed to match what GitHubIssuesTestCases parses,
and per-assertion semantics never drift between the two code paths.

Wires hatchling as the build backend (packaging src/ as-is so existing
`from src.babel_validation.X` imports keep working) so the
csv-to-babeltests console script can be exposed via [project.scripts].

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
---
 pyproject.toml                                |  14 +
 src/babel_validation/tools/__init__.py        |   0
 .../tools/csv_to_babeltests.py                | 428 ++++++++++++++++++
 tests/tools/test_csv_to_babeltests.py         | 227 ++++++++++
 uv.lock                                       |   6 +-
 5 files changed, 674 insertions(+), 1 deletion(-)
 create mode 100644 src/babel_validation/tools/__init__.py
 create mode 100644 src/babel_validation/tools/csv_to_babeltests.py
 create mode 100644 tests/tools/test_csv_to_babeltests.py

diff --git a/pyproject.toml b/pyproject.toml
index 3cc1b9a8..0f193861 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,6 +7,8 @@ readme = "README.md"
 requires-python = ">=3.11"
 dependencies = [
     "black>=25.9.0",
+    "click>=8.1",
+    "pyyaml>=6.0",
     "requests>=2.32.5",
     "tqdm>=4.67.1",
     "filelock",
@@ -22,6 +24,18 @@ dependencies = [
 [project.urls]
 Repository = "https://github.com/TranslatorSRI/babel-validation"
 
+[project.scripts]
+csv-to-babeltests = "src.babel_validation.tools.csv_to_babeltests:main"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+# Package the entire `src/` directory so existing imports
+# (`from src.babel_validation.X import Y`) continue to work after install.
+packages = ["src"]
+
 [tool.pytest.ini_options]
 timeout = 300
 markers = [
diff --git a/src/babel_validation/tools/__init__.py b/src/babel_validation/tools/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/babel_validation/tools/csv_to_babeltests.py b/src/babel_validation/tools/csv_to_babeltests.py
new file mode 100644
index 00000000..668456d3
--- /dev/null
+++ b/src/babel_validation/tools/csv_to_babeltests.py
@@ -0,0 +1,428 @@
+"""csv-to-babeltests
+====================
+
+Convert a CSV of (CURIE, label/type/equivalent-CURIE) rows into a YAML
+``babel_tests:`` block suitable for pasting into a GitHub issue, optionally
+validating each row against a NodeNorm endpoint defined in
+``tests/targets.ini``.
+
+The emitted YAML is the same format consumed by
+``GitHubIssuesTestCases.get_test_issues_from_issue`` — assertion handlers and
+YAML schema are reused, not duplicated.
+
+Run:
+    uv run csv-to-babeltests INPUT.csv --curie-column OutputID \\
+        --label-column "Expected Result / Suggested Comparator" --target dev
+"""
+
+from __future__ import annotations
+
+import configparser
+import csv
+import io
+import sys
+from collections import defaultdict
+from dataclasses import dataclass, field
+from pathlib import Path
+
+import click
+import yaml
+
+from src.babel_validation.assertions import ASSERTION_HANDLERS
+from src.babel_validation.core.testrow import TestStatus
+from src.babel_validation.services.nodenorm import CachedNodeNorm
+
+
+# --- YAML emission ---------------------------------------------------------
+
+class _FlowList(list):
+    """List subclass that yaml.safe_dump emits in inline flow style."""
+
+
+def _represent_flow_list(dumper, data):
+    return dumper.represent_sequence(
+        "tag:yaml.org,2002:seq", data, flow_style=True
+    )
+
+
+yaml.SafeDumper.add_representer(_FlowList, _represent_flow_list)
+
+
+# --- Data structures -------------------------------------------------------
+
+@dataclass
+class BlockEntry:
+    """One assertion invocation: a param_set with provenance back to a CSV row."""
+    row_idx: int           # 1-based; header is row 1, first data row is row 2.
+    param_set: list[str]
+
+
+@dataclass
+class ValidationResult:
+    assertion: str
+    row_idx: int
+    param_set: list[str]
+    status: TestStatus
+    messages: list[str] = field(default_factory=list)
+
+
+# --- Pure functions (testable without network) -----------------------------
+
+def read_csv(path: Path | str, delimiter: str | None = None) -> list[dict[str, str]]:
+    """Read a CSV file (or '-' for stdin) into a list of dict rows.
+
+    If ``delimiter`` is None we let csv.Sniffer guess from the first 4KiB,
+    falling back to ',' on failure.
+    """
+    if str(path) == "-":
+        text = sys.stdin.read()
+    else:
+        text = Path(path).read_text(encoding="utf-8-sig")  # strip any BOM
+
+    if delimiter is None:
+        try:
+            delimiter = csv.Sniffer().sniff(text[:4096], delimiters=",\t;|").delimiter
+        except csv.Error:
+            delimiter = ","
+
+    reader = csv.DictReader(io.StringIO(text), delimiter=delimiter)
+    return list(reader)
+
+
+def build_blocks(
+    rows: list[dict[str, str]],
+    *,
+    curie_column: str,
+    label_column: str | None,
+    type_column: str | None,
+    equivalent_curie_column: str | None,
+    emit_resolves: bool,
+    dedupe: bool,
+    skip_empty: bool,
+) -> tuple[dict[str, list[BlockEntry]], list[str]]:
+    """Turn CSV rows into ``{assertion_name: [BlockEntry, ...]}``.
+
+    Returns ``(blocks, warnings)``. Warnings is a list of human-readable
+    strings the caller can dump to stderr (e.g. "row 17: empty OutputID").
+    """
+    blocks: dict[str, list[BlockEntry]] = defaultdict(list)
+    warnings: list[str] = []
+    seen: dict[str, set[tuple[str, ...]]] = defaultdict(set)
+
+    def add(assertion: str, param_set: list[str], row_idx: int) -> None:
+        key = tuple(param_set)
+        if dedupe and key in seen[assertion]:
+            return
+        seen[assertion].add(key)
+        blocks[assertion].append(BlockEntry(row_idx=row_idx, param_set=param_set))
+
+    for offset, row in enumerate(rows):
+        row_idx = offset + 2  # match what spreadsheet UIs show: header is row 1.
+
+        curie = (row.get(curie_column) or "").strip()
+        if not curie:
+            warnings.append(f"row {row_idx}: empty {curie_column!r} — skipping")
+            continue
+
+        if label_column is not None:
+            label = (row.get(label_column) or "").strip()
+            if not label and skip_empty:
+                warnings.append(f"row {row_idx}: empty {label_column!r} — skipping HasLabel")
+            else:
+                add("HasLabel", [curie, label], row_idx)
+
+        if type_column is not None:
+            biolink_type = (row.get(type_column) or "").strip()
+            if not biolink_type and skip_empty:
+                warnings.append(f"row {row_idx}: empty {type_column!r} — skipping ResolvesWithType")
+            else:
+                add("ResolvesWithType", [biolink_type, curie], row_idx)
+
+        if equivalent_curie_column is not None:
+            equiv = (row.get(equivalent_curie_column) or "").strip()
+            if not equiv and skip_empty:
+                warnings.append(f"row {row_idx}: empty {equivalent_curie_column!r} — skipping ResolvesWith")
+            else:
+                add("ResolvesWith", [curie, equiv], row_idx)
+
+        if emit_resolves:
+            add("Resolves", [curie], row_idx)
+
+    return dict(blocks), warnings
+
+
+def emit_yaml(
+    blocks: dict[str, list[BlockEntry]],
+    *,
+    fence: bool = True,
+    header: str | None = None,
+) -> str:
+    """Render a ``{assertion_name: [BlockEntry, ...]}`` map as a YAML block.
+
+    Each param_set is emitted as an inline flow list so the output reads like
+    the existing examples in ``assertions/nodenorm.py``::
+
+        babel_tests:
+          HasLabel:
+          - [CHEBI:15365, aspirin]
+
+    A round-trip self-check via ``yaml.safe_load`` ensures we never emit
+    something the GitHub-issue parser would reject.
+    """
+    # Match the convention used in src/babel_validation/assertions/nodenorm.py:
+    # single-element param_sets are emitted as bare strings ("- CHEBI:15365"),
+    # multi-element ones as inline flow lists ("- [CHEBI:15365, aspirin]").
+    # Both parse to the same param_set via the GitHub issue loader.
+    data = {
+        "babel_tests": {
+            assertion: [
+                e.param_set[0] if len(e.param_set) == 1 else _FlowList(e.param_set)
+                for e in entries
+            ]
+            for assertion, entries in blocks.items()
+        }
+    }
+    body = yaml.safe_dump(
+        data,
+        sort_keys=False,
+        default_flow_style=False,
+        allow_unicode=True,
+        width=10_000,
+    )
+
+    # Round-trip self-check; raises if our output isn't loadable.
+    yaml.safe_load(body)
+
+    parts: list[str] = []
+    if header:
+        parts.append(f"# {header}")
+    if fence:
+        parts.append("```yaml")
+    parts.append(body.rstrip())
+    if fence:
+        parts.append("```")
+    return "\n".join(parts) + "\n"
+
+
+# --- Validation ------------------------------------------------------------
+
+def validate_blocks(
+    blocks: dict[str, list[BlockEntry]],
+    nodenorm: CachedNodeNorm,
+) -> list[ValidationResult]:
+    """Run each (assertion, param_set) through the matching ASSERTION_HANDLER.
+
+    Param_sets are evaluated one at a time so each ``TestResult`` can be
+    attributed back to its source CSV row. ``CachedNodeNorm`` deduplicates
+    network calls per CURIE, so the per-row loop is no slower than batching.
+    """
+    # Pre-warm the cache with every CURIE we'll need across all blocks.
+    all_curies: set[str] = set()
+    for assertion, entries in blocks.items():
+        handler = ASSERTION_HANDLERS[assertion.lower()]
+        for entry in entries:
+            all_curies.update(handler.curie_params(entry.param_set))
+    if all_curies:
+        nodenorm.normalize_curies(list(all_curies))
+
+    results: list[ValidationResult] = []
+    for assertion, entries in blocks.items():
+        handler = ASSERTION_HANDLERS[assertion.lower()]
+        for entry in entries:
+            test_results = list(
+                handler.test_with_nodenorm(
+                    [entry.param_set], nodenorm,
+                    label=f"row {entry.row_idx}",
+                )
+            )
+            if test_results and all(r.status == TestStatus.Passed for r in test_results):
+                status = TestStatus.Passed
+                messages: list[str] = []
+            else:
+                status = TestStatus.Failed
+                messages = [r.message for r in test_results
+                            if r.status != TestStatus.Passed] or ["no result"]
+            results.append(ValidationResult(
+                assertion=assertion,
+                row_idx=entry.row_idx,
+                param_set=entry.param_set,
+                status=status,
+                messages=messages,
+            ))
+    return results
+
+
+def format_report(
+    results: list[ValidationResult],
+    target_name: str,
+    nodenorm_url: str,
+) -> str:
+    """Human-readable validation summary, suitable for stderr."""
+    by_assertion: dict[str, list[ValidationResult]] = defaultdict(list)
+    for r in results:
+        by_assertion[r.assertion].append(r)
+
+    lines = [f"Validation against target {target_name!r} ({nodenorm_url}):"]
+    for assertion, rows in by_assertion.items():
+        passed = sum(1 for r in rows if r.status == TestStatus.Passed)
+        failed = sum(1 for r in rows if r.status == TestStatus.Failed)
+        lines.append(f"  {assertion}: {passed} passed, {failed} failed.")
+        for r in rows:
+            if r.status == TestStatus.Failed:
+                params_str = ", ".join(r.param_set)
+                lines.append(
+                    f"    FAIL  row {r.row_idx}  [{params_str}]  →  {r.messages[0]}"
+                )
+    return "\n".join(lines) + "\n"
+
+
+# --- targets.ini -----------------------------------------------------------
+
+def _default_targets_ini() -> Path:
+    """Locate tests/targets.ini relative to this file's repo."""
+    # src/babel_validation/tools/csv_to_babeltests.py → ../../../tests/targets.ini
+    return Path(__file__).resolve().parents[3] / "tests" / "targets.ini"
+
+
+def load_nodenorm_url(target_name: str, targets_ini_path: Path) -> str:
+    """Look up ``NodeNormURL`` for ``target_name`` in ``targets_ini_path``."""
+    if not targets_ini_path.is_file():
+        raise click.ClickException(f"targets.ini not found at {targets_ini_path}")
+    cp = configparser.ConfigParser()
+    cp.read(targets_ini_path, encoding="utf-8")
+    if target_name not in cp:
+        raise click.ClickException(
+            f"target {target_name!r} not found in {targets_ini_path}; "
+            f"available: {', '.join(cp.sections())}"
+        )
+    section = cp[target_name]
+    if "NodeNormURL" not in section:
+        raise click.ClickException(
+            f"target {target_name!r} in {targets_ini_path} has no NodeNormURL"
+        )
+    return section["NodeNormURL"]
+
+
+# --- CLI -------------------------------------------------------------------
+
+@click.command(context_settings={"help_option_names": ["-h", "--help"]})
+@click.argument(
+    "input_csv",
+    type=click.Path(exists=True, dir_okay=False, allow_dash=True, path_type=Path),
+)
+@click.option(
+    "--curie-column", required=True,
+    help="Column name containing the primary CURIE.",
+)
+@click.option(
+    "--label-column", default=None,
+    help="Column with the expected label → emits a HasLabel block.",
+)
+@click.option(
+    "--type-column", default=None,
+    help="Column with a Biolink type (e.g. 'biolink:SmallMolecule') → emits a ResolvesWithType block.",
+)
+@click.option(
+    "--equivalent-curie-column", default=None,
+    help="Column with a CURIE that should merge to the same canonical id → emits a ResolvesWith block.",
+)
+@click.option(
+    "--resolves/--no-resolves", "emit_resolves_flag", default=None,
+    help=("Force-emit (or suppress) a Resolves block. Default: emit a Resolves "
+          "block only when no other assertion column was given."),
+)
+@click.option("--dedupe", is_flag=True, default=False,
+              help="Drop duplicate param_sets within each assertion block.")
+@click.option("--skip-empty/--no-skip-empty", default=True,
+              help="Skip rows where the assertion column is blank (with a stderr warning).")
+@click.option("--delimiter", default=None,
+              help="CSV delimiter (default: auto-detect via csv.Sniffer; falls back to comma).")
+@click.option("--target", default=None,
+              help="Target name from targets.ini to validate against (e.g. dev, prod, ci).")
+@click.option(
+    "--targets-ini",
+    type=click.Path(exists=False, dir_okay=False, path_type=Path),
+    default=None,
+    help="Override path to targets.ini (default: tests/targets.ini in the repo).",
+)
+@click.option("--fence/--no-fence", default=True,
+              help="Wrap output in ```yaml … ``` Markdown fences (default: on).")
+@click.option("--header", default=None,
+              help="Optional comment line emitted above the YAML block "
+                   "(useful for recording provenance).")
+def main(
+    input_csv: Path,
+    curie_column: str,
+    label_column: str | None,
+    type_column: str | None,
+    equivalent_curie_column: str | None,
+    emit_resolves_flag: bool | None,
+    dedupe: bool,
+    skip_empty: bool,
+    delimiter: str | None,
+    target: str | None,
+    targets_ini: Path | None,
+    fence: bool,
+    header: str | None,
+) -> None:
+    """Convert INPUT_CSV into a BabelTests YAML block on stdout."""
+
+    # Default behavior for --resolves: emit Resolves only when the user
+    # didn't ask for any of the other assertion blocks.
+    if emit_resolves_flag is None:
+        emit_resolves = not (label_column or type_column or equivalent_curie_column)
+    else:
+        emit_resolves = emit_resolves_flag
+
+    rows = read_csv(input_csv, delimiter=delimiter)
+    if rows and curie_column not in rows[0]:
+        raise click.ClickException(
+            f"--curie-column {curie_column!r} not found in CSV header. "
+            f"Available columns: {list(rows[0].keys())}"
+        )
+    for col_name, col_label in [
+        (label_column, "--label-column"),
+        (type_column, "--type-column"),
+        (equivalent_curie_column, "--equivalent-curie-column"),
+    ]:
+        if col_name and rows and col_name not in rows[0]:
+            raise click.ClickException(
+                f"{col_label} {col_name!r} not found in CSV header. "
+                f"Available columns: {list(rows[0].keys())}"
+            )
+
+    blocks, warnings = build_blocks(
+        rows,
+        curie_column=curie_column,
+        label_column=label_column,
+        type_column=type_column,
+        equivalent_curie_column=equivalent_curie_column,
+        emit_resolves=emit_resolves,
+        dedupe=dedupe,
+        skip_empty=skip_empty,
+    )
+
+    if not blocks:
+        raise click.ClickException(
+            "No assertions to emit — every row was skipped or no assertion "
+            "columns were given. Pass --label-column / --type-column / "
+            "--equivalent-curie-column, or use --resolves to force a Resolves "
+            "block on the CURIE column."
+        )
+
+    for w in warnings:
+        click.echo(w, err=True)
+
+    yaml_text = emit_yaml(blocks, fence=fence, header=header)
+    sys.stdout.write(yaml_text)
+
+    if target:
+        ini_path = targets_ini or _default_targets_ini()
+        nodenorm_url = load_nodenorm_url(target, ini_path)
+        nodenorm = CachedNodeNorm.from_url(nodenorm_url)
+        results = validate_blocks(blocks, nodenorm)
+        click.echo(format_report(results, target, nodenorm_url), err=True)
+
+
+if __name__ == "__main__":  # pragma: no cover
+    main()
diff --git a/tests/tools/test_csv_to_babeltests.py b/tests/tools/test_csv_to_babeltests.py
new file mode 100644
index 00000000..2f585ad8
--- /dev/null
+++ b/tests/tools/test_csv_to_babeltests.py
@@ -0,0 +1,227 @@
+"""Unit tests for the csv-to-babeltests CLI helpers.
+
+These exercise the pure-function parts of the tool — CSV parsing, block
+construction, YAML emission, and round-trip parsing through the same regex
++ yaml.safe_load that the GitHub-issue test discovery uses. No network.
+"""
+
+import io
+import re
+from pathlib import Path
+
+import pytest
+import yaml
+
+from src.babel_validation.tools.csv_to_babeltests import (
+    BlockEntry,
+    build_blocks,
+    emit_yaml,
+    read_csv,
+)
+
+
+pytestmark = pytest.mark.unit
+
+
+# Same regex as src/babel_validation/sources/github/github_issues_test_cases.py
+GITHUB_YAML_PATTERN = re.compile(r"```yaml\s+babel_tests:\s+.*?\s+```", re.DOTALL)
+
+
+def _parse_emitted(yaml_text: str) -> dict:
+    """Run emit_yaml() output through the GitHub-issue parser path."""
+    match = GITHUB_YAML_PATTERN.search(yaml_text)
+    assert match is not None, f"emitted YAML didn't match the issue regex:\n{yaml_text}"
+    return yaml.safe_load(
+        match.group(0).removeprefix("```yaml").removesuffix("```")
+    )
+
+
+# --- read_csv --------------------------------------------------------------
+
+def test_read_csv_basic(tmp_path: Path):
+    p = tmp_path / "in.csv"
+    p.write_text("CURIE,Label\nCHEBI:15365,aspirin\nMONDO:1,asthma\n", encoding="utf-8")
+    rows = read_csv(p)
+    assert rows == [
+        {"CURIE": "CHEBI:15365", "Label": "aspirin"},
+        {"CURIE": "MONDO:1", "Label": "asthma"},
+    ]
+
+
+def test_read_csv_strips_bom(tmp_path: Path):
+    p = tmp_path / "in.csv"
+    p.write_bytes("CURIE,Label\nCHEBI:1,foo\n".encode("utf-8"))
+    rows = read_csv(p)
+    assert rows[0]["CURIE"] == "CHEBI:1"
+
+
+def test_read_csv_handles_quoted_field_with_comma(tmp_path: Path):
+    p = tmp_path / "in.csv"
+    p.write_text(
+        'CURIE,"Long, Name"\nCHEBI:1,"foo, bar"\n', encoding="utf-8"
+    )
+    rows = read_csv(p)
+    assert rows[0] == {"CURIE": "CHEBI:1", "Long, Name": "foo, bar"}
+
+
+# --- build_blocks ----------------------------------------------------------
+
+ROWS = [
+    {"OutputID": "CHEBI:15365", "Label": "aspirin",   "Type": "biolink:SmallMolecule", "Equiv": "PUBCHEM.COMPOUND:1"},
+    {"OutputID": "MONDO:0005015", "Label": "diabetes", "Type": "biolink:Disease",       "Equiv": ""},
+    {"OutputID": "",              "Label": "missing",  "Type": "",                       "Equiv": ""},
+    {"OutputID": "CHEBI:15365", "Label": "aspirin",   "Type": "biolink:SmallMolecule", "Equiv": "PUBCHEM.COMPOUND:1"},  # dup
+]
+
+
+def test_build_blocks_haslabel_only():
+    blocks, warnings = build_blocks(
+        ROWS,
+        curie_column="OutputID", label_column="Label",
+        type_column=None, equivalent_curie_column=None,
+        emit_resolves=False, dedupe=False, skip_empty=True,
+    )
+    assert set(blocks) == {"HasLabel"}
+    assert [e.param_set for e in blocks["HasLabel"]] == [
+        ["CHEBI:15365", "aspirin"],
+        ["MONDO:0005015", "diabetes"],
+        ["CHEBI:15365", "aspirin"],   # dup kept (dedupe=False)
+    ]
+    # row 4 (offset 2 → row index 4) was empty CURIE.
+    assert any("row 4" in w and "OutputID" in w for w in warnings)
+
+
+def test_build_blocks_dedupe_drops_duplicate_param_sets():
+    blocks, _ = build_blocks(
+        ROWS,
+        curie_column="OutputID", label_column="Label",
+        type_column=None, equivalent_curie_column=None,
+        emit_resolves=False, dedupe=True, skip_empty=True,
+    )
+    assert [e.param_set for e in blocks["HasLabel"]] == [
+        ["CHEBI:15365", "aspirin"],
+        ["MONDO:0005015", "diabetes"],
+    ]
+
+
+def test_build_blocks_multiple_assertions():
+    blocks, _ = build_blocks(
+        ROWS,
+        curie_column="OutputID", label_column="Label",
+        type_column="Type", equivalent_curie_column="Equiv",
+        emit_resolves=True, dedupe=True, skip_empty=True,
+    )
+    # All four assertion blocks should be present.
+    assert set(blocks) == {"HasLabel", "ResolvesWithType", "ResolvesWith", "Resolves"}
+    # ResolvesWithType places the Biolink type first.
+    rwt = [e.param_set for e in blocks["ResolvesWithType"]]
+    assert rwt == [
+        ["biolink:SmallMolecule", "CHEBI:15365"],
+        ["biolink:Disease", "MONDO:0005015"],
+    ]
+    # ResolvesWith only fires when Equiv is non-empty.
+    rw = [e.param_set for e in blocks["ResolvesWith"]]
+    assert rw == [["CHEBI:15365", "PUBCHEM.COMPOUND:1"]]
+
+
+def test_build_blocks_row_indices_match_spreadsheet_rows():
+    """row_idx should be 1-based with the header at row 1 — matches spreadsheet UIs."""
+    blocks, _ = build_blocks(
+        ROWS,
+        curie_column="OutputID", label_column="Label",
+        type_column=None, equivalent_curie_column=None,
+        emit_resolves=False, dedupe=False, skip_empty=True,
+    )
+    indices = [e.row_idx for e in blocks["HasLabel"]]
+    # ROWS[0] → row 2, ROWS[1] → row 3, ROWS[3] → row 5 (ROWS[2] was empty).
+    assert indices == [2, 3, 5]
+
+
+# --- emit_yaml -------------------------------------------------------------
+
+def test_emit_yaml_round_trips_through_github_parser():
+    blocks = {
+        "HasLabel": [
+            BlockEntry(2, ["CHEBI:15365", "aspirin"]),
+            BlockEntry(3, ["MONDO:0005015", "type 2 diabetes mellitus"]),
+        ],
+        "ResolvesWithType": [
+            BlockEntry(2, ["biolink:SmallMolecule", "CHEBI:15365"]),
+        ],
+    }
+    out = emit_yaml(blocks, fence=True, header=None)
+    parsed = _parse_emitted(out)
+    assert list(parsed["babel_tests"].keys()) == ["HasLabel", "ResolvesWithType"]
+    assert parsed["babel_tests"]["HasLabel"] == [
+        ["CHEBI:15365", "aspirin"],
+        ["MONDO:0005015", "type 2 diabetes mellitus"],
+    ]
+    assert parsed["babel_tests"]["ResolvesWithType"] == [
+        ["biolink:SmallMolecule", "CHEBI:15365"],
+    ]
+
+
+def test_emit_yaml_with_special_characters():
+    """Labels with apostrophes, commas, brackets must round-trip."""
+    blocks = {
+        "HasLabel": [
+            BlockEntry(2, ["DRUGBANK:DB00001", "Adenosine 5'-phosphosulfate"]),
+            BlockEntry(3, ["CHEBI:1", "foo, bar [baz]"]),
+            BlockEntry(4, ["CHEBI:2", ""]),  # empty label edge case
+        ],
+    }
+    out = emit_yaml(blocks)
+    parsed = _parse_emitted(out)
+    assert parsed["babel_tests"]["HasLabel"] == [
+        ["DRUGBANK:DB00001", "Adenosine 5'-phosphosulfate"],
+        ["CHEBI:1", "foo, bar [baz]"],
+        ["CHEBI:2", ""],
+    ]
+
+
+def test_emit_yaml_no_fence():
+    blocks = {"Resolves": [BlockEntry(2, ["CHEBI:15365"])]}
+    out = emit_yaml(blocks, fence=False)
+    assert "```" not in out
+    assert "babel_tests:" in out
+    # Without the fence the GitHub parser regex shouldn't find a match.
+    assert GITHUB_YAML_PATTERN.search(out) is None
+
+
+def test_emit_yaml_with_header_comment():
+    blocks = {"Resolves": [BlockEntry(2, ["CHEBI:15365"])]}
+    out = emit_yaml(blocks, header="from data/test-assets.csv")
+    assert out.startswith("# from data/test-assets.csv\n")
+    # Header doesn't break the round-trip.
+    parsed = _parse_emitted(out)
+    # Single-element param_sets are emitted as bare strings (matching the
+    # convention in assertions/nodenorm.py); the GitHub parser later wraps
+    # them back into [["CHEBI:15365"]].
+    assert parsed["babel_tests"]["Resolves"] == ["CHEBI:15365"]
+
+
+def test_emit_yaml_single_element_param_sets_emit_as_bare_strings():
+    """Single-element param_sets should match the existing YAML examples in
+    assertions/nodenorm.py — bare strings, not single-item flow lists."""
+    blocks = {"Resolves": [BlockEntry(2, ["CHEBI:15365"]), BlockEntry(3, ["MONDO:1"])]}
+    out = emit_yaml(blocks, fence=False)
+    # Bare-string form, not single-element flow lists.
+    assert "- CHEBI:15365" in out
+    assert "- [CHEBI:15365]" not in out
+
+
+# --- assertion-name compatibility with ASSERTION_HANDLERS ------------------
+
+def test_emitted_assertion_names_match_handler_registry():
+    """The names build_blocks emits must each resolve in ASSERTION_HANDLERS."""
+    from src.babel_validation.assertions import ASSERTION_HANDLERS
+    blocks, _ = build_blocks(
+        ROWS,
+        curie_column="OutputID", label_column="Label",
+        type_column="Type", equivalent_curie_column="Equiv",
+        emit_resolves=True, dedupe=True, skip_empty=True,
+    )
+    for assertion in blocks:
+        assert assertion.lower() in ASSERTION_HANDLERS, (
+            f"build_blocks emitted unknown assertion name {assertion!r}"
+        )
diff --git a/uv.lock b/uv.lock
index 3559d52f..6d3c2f62 100644
--- a/uv.lock
+++ b/uv.lock
@@ -23,9 +23,10 @@ wheels = [
 [[package]]
 name = "babel-validation"
 version = "0.1.0"
-source = { virtual = "." }
+source = { editable = "." }
 dependencies = [
     { name = "black" },
+    { name = "click" },
     { name = "deepdiff" },
     { name = "filelock" },
     { name = "openapi-spec-validator" },
@@ -34,6 +35,7 @@ dependencies = [
     { name = "pytest-timeout" },
     { name = "pytest-xdist", extra = ["psutil"] },
     { name = "python-dotenv" },
+    { name = "pyyaml" },
     { name = "requests" },
     { name = "tqdm" },
 ]
@@ -41,6 +43,7 @@ dependencies = [
 [package.metadata]
 requires-dist = [
     { name = "black", specifier = ">=25.9.0" },
+    { name = "click", specifier = ">=8.1" },
     { name = "deepdiff", specifier = ">=8.6.1" },
     { name = "filelock" },
     { name = "openapi-spec-validator", specifier = ">=0.7.2" },
@@ -49,6 +52,7 @@ requires-dist = [
     { name = "pytest-timeout", specifier = ">=2.4.0" },
     { name = "pytest-xdist", extras = ["psutil"] },
     { name = "python-dotenv", specifier = ">=0.9.9" },
+    { name = "pyyaml", specifier = ">=6.0" },
     { name = "requests", specifier = ">=2.32.5" },
     { name = "tqdm", specifier = ">=4.67.1" },
 ]

From 6d5d59363672dfe0ff5a90f2567023f472f0a258 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Tue, 5 May 2026 18:01:57 -0400
Subject: [PATCH 086/126] Add pytest-subtests dependency

test_github_issues.py uses the subtests fixture but pytest-subtests was
not listed as a dependency, causing fixture-not-found errors on a clean
install.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 pyproject.toml |  1 +
 uv.lock        | 15 +++++++++++++++
 2 files changed, 16 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 3cc1b9a8..7bfb475e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,6 +17,7 @@ dependencies = [
     "pytest>=9.0.2",
     "pytest-timeout>=2.4.0",
     "pytest-xdist[psutil]",
+    "pytest-subtests",
 ]
 
 [project.urls]
diff --git a/uv.lock b/uv.lock
index 3559d52f..4e105f7a 100644
--- a/uv.lock
+++ b/uv.lock
@@ -31,6 +31,7 @@ dependencies = [
     { name = "openapi-spec-validator" },
     { name = "pygithub" },
     { name = "pytest" },
+    { name = "pytest-subtests" },
     { name = "pytest-timeout" },
     { name = "pytest-xdist", extra = ["psutil"] },
     { name = "python-dotenv" },
@@ -46,6 +47,7 @@ requires-dist = [
     { name = "openapi-spec-validator", specifier = ">=0.7.2" },
     { name = "pygithub", specifier = ">=2.8.1" },
     { name = "pytest", specifier = ">=9.0.2" },
+    { name = "pytest-subtests" },
     { name = "pytest-timeout", specifier = ">=2.4.0" },
     { name = "pytest-xdist", extras = ["psutil"] },
     { name = "python-dotenv", specifier = ">=0.9.9" },
@@ -800,6 +802,19 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/3b/ab/b3226f0bd7cdcf710fbede2b3548584366da3b19b5021e74f5bde2a8fa3f/pytest-9.0.2-py3-none-any.whl", hash = "sha256:711ffd45bf766d5264d487b917733b453d917afd2b0ad65223959f59089f875b", size = 374801, upload-time = "2025-12-06T21:30:49.154Z" },
 ]
 
+[[package]]
+name = "pytest-subtests"
+version = "0.15.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "attrs" },
+    { name = "pytest" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/bb/d9/20097971a8d315e011e055d512fa120fd6be3bdb8f4b3aa3e3c6bf77bebc/pytest_subtests-0.15.0.tar.gz", hash = "sha256:cb495bde05551b784b8f0b8adfaa27edb4131469a27c339b80fd8d6ba33f887c", size = 18525, upload-time = "2025-10-20T16:26:18.358Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/23/64/bba465299b37448b4c1b84c7a04178399ac22d47b3dc5db1874fe55a2bd3/pytest_subtests-0.15.0-py3-none-any.whl", hash = "sha256:da2d0ce348e1f8d831d5a40d81e3aeac439fec50bd5251cbb7791402696a9493", size = 9185, upload-time = "2025-10-20T16:26:17.239Z" },
+]
+
 [[package]]
 name = "pytest-timeout"
 version = "2.4.0"

From b0a4dc03b4b82ffbd230419e1a4adb0a911f301c Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Tue, 5 May 2026 18:02:04 -0400
Subject: [PATCH 087/126] Add request timeouts and fix bulk_lookup error
 message

All requests.post calls in CachedNodeNorm and CachedNameRes now carry a
30-second timeout so a slow or hung endpoint cannot stall the test run
indefinitely. Also fixes a copy-paste error in CachedNameRes.bulk_lookup
where the ValueError message said "normalize_curies" instead of
"bulk_lookup".

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 src/babel_validation/services/nameres.py  | 6 +++---
 src/babel_validation/services/nodenorm.py | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/babel_validation/services/nameres.py b/src/babel_validation/services/nameres.py
index 251b0fcb..1300e17c 100644
--- a/src/babel_validation/services/nameres.py
+++ b/src/babel_validation/services/nameres.py
@@ -26,7 +26,7 @@ def bulk_lookup(self, queries: list[str], **params) -> dict[str, dict]:
         if not queries:
             raise ValueError(f"queries must not be empty when calling bulk_lookup({queries}, {params}) on {self}")
         if not isinstance(queries, list):
-            raise ValueError(f"queries must be a list when calling normalize_curies({queries}, {params}) on {self}")
+            raise ValueError(f"queries must be a list when calling bulk_lookup({queries}, {params}) on {self}")
 
         time_started = time.time_ns()
         queries_set = set(queries)
@@ -39,7 +39,7 @@ def bulk_lookup(self, queries: list[str], **params) -> dict[str, dict]:
             params['strings'] = list(queries_to_be_queried)
 
             self.logger.debug(f"Called NameRes {self} with params {params}")
-            response = requests.post(self.nameres_url + "bulk-lookup", json=params)
+            response = requests.post(self.nameres_url + "bulk-lookup", json=params, timeout=30)
             response.raise_for_status()
             result = response.json()
 
@@ -61,7 +61,7 @@ def lookup(self, query, **params):
         params['string'] = query
         self.logger.debug(f"Querying NameRes with params {params}")
 
-        response = requests.post(self.nameres_url + "lookup", params=params)
+        response = requests.post(self.nameres_url + "lookup", params=params, timeout=30)
         response.raise_for_status()
         result = response.json()
 
diff --git a/src/babel_validation/services/nodenorm.py b/src/babel_validation/services/nodenorm.py
index 88a3353d..452ea36c 100644
--- a/src/babel_validation/services/nodenorm.py
+++ b/src/babel_validation/services/nodenorm.py
@@ -38,7 +38,7 @@ def normalize_curies(self, curies: list[str], **params) -> dict[str, dict]:
             params['curies'] = list(curies_to_be_queried)
 
             self.logger.debug(f"Called NodeNorm {self} with params {params}")
-            response = requests.post(self.nodenorm_url + "get_normalized_nodes", json=params)
+            response = requests.post(self.nodenorm_url + "get_normalized_nodes", json=params, timeout=30)
             response.raise_for_status()
             result = response.json()
 

From 65236d6905f7b5a98666867260875a46cdfdfeaf Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Tue, 5 May 2026 18:02:11 -0400
Subject: [PATCH 088/126] Validate Google Sheet HTTP response before caching

Added raise_for_status() and a 30-second timeout to the Google Sheets
CSV download. Previously an HTTP error page could be silently written to
the cache file, causing misleading failures on subsequent runs.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .../sources/google_sheets/google_sheet_test_cases.py           | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py b/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py
index af076a7b..ab167fc6 100644
--- a/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py
+++ b/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py
@@ -42,7 +42,8 @@ def __init__(self, google_sheet_id="11zebx8Qs1Tc3ShQR9nh4HRW8QSoo8k65w_xIaftN0no
                 self.csv_content = cache_file.read_text(encoding="utf-8")
             else:
                 csv_url = f"https://docs.google.com/spreadsheets/d/{google_sheet_id}/gviz/tq?tqx=out:csv&sheet=Tests"
-                response = requests.get(csv_url)
+                response = requests.get(csv_url, timeout=30)
+                response.raise_for_status()
                 self.csv_content = response.text
                 cache_file.write_text(self.csv_content, encoding="utf-8")
 

From 5150703a3b93cc3a808553bf27acfa0a435dcf8b Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Tue, 5 May 2026 18:02:25 -0400
Subject: [PATCH 089/126] Fix wiki syntax parsing: allow assertion-name-only
 and warn on unresolved IDs

{{BabelTest|Needed}} (no extra params) previously raised ValueError at
parse time because the code required at least two pipe-separated fields.
The README documents it as valid wiki syntax, so this was a bug. The
check now only rejects an empty or missing assertion name; a single-field
wiki tag produces an empty param_set (consistent with how the Needed
handler works).

Also added a logger.warning when get_issues_by_ids() cannot resolve an
issue ID in any configured repository, replacing the previous silent
drop.

Updated test_system.py to document the new parsing behavior
(test_wiki_no_curie_params_parsed, test_wiki_needed_no_params).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .../github/github_issues_test_cases.py        | 19 +++++++++++++------
 tests/github_issues/test_system.py            | 17 ++++++++++++++---
 2 files changed, 27 insertions(+), 9 deletions(-)

diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index 73538b0b..79a0f67b 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -155,12 +155,12 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
                 # Figure out parameters.
                 test_string = match.removeprefix("{{BabelTest|").removesuffix("}}")
                 params = test_string.split("|")
-                if len(params) < 2:
-                    raise ValueError(f"Too few parameters found in BabelTest in issue {github_issue_id}: {match}")
-                else:
-                    # Wiki syntax: params[0] is the assertion name; params[1:] form a single
-                    # param_set, so param_sets is a one-element list: [params[1:]].
-                    testrows.append(GitHubIssueTest(github_issue_id, github_issue, params[0], [params[1:]]))
+                if not params or not params[0]:
+                    raise ValueError(f"Missing assertion name in BabelTest in issue {github_issue_id}: {match}")
+                # Wiki syntax: params[0] is the assertion name; params[1:] form a single
+                # param_set (may be empty for assertions like Needed), so param_sets is a
+                # one-element list: [params[1:]].
+                testrows.append(GitHubIssueTest(github_issue_id, github_issue, params[0], [params[1:]]))
 
         babeltest_yaml_matches = re.findall(self.babeltest_yaml_pattern, github_issue.body)
         if babeltest_yaml_matches:
@@ -202,16 +202,19 @@ def get_issues_by_ids(self, issue_ids: list[str]) -> list[Issue.Issue]:
         from github import GithubException
         issues = []
         for issue_id in issue_ids:
+            found = False
             if m := re.match(r'^([^/]+)/([^#]+)#(\d+)$', issue_id):
                 # org/repo#N
                 issue = self.github.get_repo(f"{m.group(1)}/{m.group(2)}").get_issue(int(m.group(3)))
                 issues.append(issue)
+                found = True
             elif m := re.match(r'^([^/#]+)#(\d+)$', issue_id):
                 # repo#N — find repo in configured list
                 repo_name, num = m.group(1), int(m.group(2))
                 for full_repo in self.github_repositories:
                     if full_repo.split('/')[1] == repo_name:
                         issues.append(self.github.get_repo(full_repo).get_issue(num))
+                        found = True
                         break
             elif m := re.match(r'^(\d+)$', issue_id):
                 # N — try all configured repos
@@ -219,8 +222,12 @@ def get_issues_by_ids(self, issue_ids: list[str]) -> list[Issue.Issue]:
                 for full_repo in self.github_repositories:
                     try:
                         issues.append(self.github.get_repo(full_repo).get_issue(num))
+                        found = True
                     except GithubException:
                         pass
+            if not found:
+                self.logger.warning("Could not resolve issue ID %r in configured repositories %s",
+                                    issue_id, self.github_repositories)
         return issues
 
     def get_issues_with_tests(self, github_repositories=None) -> Iterator[Issue.Issue]:
diff --git a/tests/github_issues/test_system.py b/tests/github_issues/test_system.py
index 008d613a..78705070 100644
--- a/tests/github_issues/test_system.py
+++ b/tests/github_issues/test_system.py
@@ -127,10 +127,21 @@ def test_whitespace_body_returns_empty(self, github_issues_test_cases):
 
     # --- wiki syntax: assertion name only, no curie params ---
 
-    def test_wiki_no_curie_params_raises(self, github_issues_test_cases):
+    def test_wiki_no_curie_params_parsed(self, github_issues_test_cases):
+        # {{BabelTest|Resolves}} with no params parses to an empty param_set, not a parse error.
         mock = _mock_issue("{{BabelTest|Resolves}}")
-        with pytest.raises(ValueError, match="Too few parameters"):
-            github_issues_test_cases.get_test_issues_from_issue(mock)
+        tests = github_issues_test_cases.get_test_issues_from_issue(mock)
+        assert len(tests) == 1
+        assert tests[0].assertion == "Resolves"
+        assert tests[0].param_sets == [[]]
+
+    def test_wiki_needed_no_params(self, github_issues_test_cases):
+        # {{BabelTest|Needed}} with no extra params is valid per the documented wiki syntax.
+        mock = _mock_issue("{{BabelTest|Needed}}")
+        tests = github_issues_test_cases.get_test_issues_from_issue(mock)
+        assert len(tests) == 1
+        assert tests[0].assertion == "Needed"
+        assert tests[0].param_sets == [[]]
 
     # --- YAML syntax: null / empty values ---
 

From da945773efe87460c7837ed6c9ab0982396a9f0c Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Tue, 5 May 2026 18:02:34 -0400
Subject: [PATCH 090/126] Clean up lock files on pytest startup and fix
 incomplete comment

pytest_configure now deletes the .lock files alongside the .csv cache
files (and the issues cache lock) so stale lock files do not accumulate
in tmpdir across runs. Also rewrote the truncated comment on the
selected_github_issues fixture to be a complete sentence.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 tests/conftest.py | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index cd923996..52c0df28 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -38,10 +38,16 @@ def pytest_configure(config):
                 os.unlink(f)
             except FileNotFoundError:
                 pass
-        try:
-            os.unlink(os.path.join(tempfile.gettempdir(), 'babel_validation_issues_cache.json'))
-        except FileNotFoundError:
-            pass
+            try:
+                os.unlink(f + '.lock')
+            except FileNotFoundError:
+                pass
+        tmpdir = tempfile.gettempdir()
+        for name in ('babel_validation_issues_cache.json', 'babel_validation_issues_cache.lock'):
+            try:
+                os.unlink(os.path.join(tmpdir, name))
+            except FileNotFoundError:
+                pass
 
 
 def pytest_addoption(parser):
@@ -148,7 +154,7 @@ def category_test(cat):
 
     return category_test
 
-# Issue is only used by the GitHub issue tests (tests/github_issues/*)
+# --issue is consumed by tests/github_issues/conftest.py; this fixture exposes it to any test that wants it.
 @pytest.fixture
 def selected_github_issues(pytestconfig):
     return pytestconfig.getoption('issue')

From 37d1da64f4399022b561f1baccacd91d45c778f4 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Tue, 5 May 2026 18:03:07 -0400
Subject: [PATCH 091/126] Fix CI unit-test workflow: restrict paths and inject
 GITHUB_TOKEN

Previously pytest -m unit collected every test file including
test_github_issues.py, which calls the GitHub search API during
collection regardless of the -m filter. The workflow now targets only
the unit test files (test_system.py and tests/test_environment) so
collection is network-free. GITHUB_TOKEN is passed from github.token so
the GitHubIssuesTestCases fixture can initialise without skipping.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .github/workflows/tests.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
index cca42051..793cc976 100644
--- a/.github/workflows/tests.yaml
+++ b/.github/workflows/tests.yaml
@@ -12,4 +12,6 @@ jobs:
       - uses: astral-sh/setup-uv@v6
 
       - name: Run unit tests
-        run: uv run pytest -m unit -v
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: uv run pytest tests/github_issues/test_system.py tests/test_environment -m unit -v

From f125cd587e6fb06965cc7b659a0d62401b58550a Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Tue, 5 May 2026 18:03:15 -0400
Subject: [PATCH 092/126] Move curie_params overrides after class attributes in
 assertion handlers

HasLabelHandler and ResolvesWithTypeHandler defined curie_params()
between the class docstring and the class-level attributes, which is
inconsistent with Python convention. Moved the method definitions to
after all class attributes.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 src/babel_validation/assertions/nodenorm.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/babel_validation/assertions/nodenorm.py b/src/babel_validation/assertions/nodenorm.py
index 23142780..cce9b347 100644
--- a/src/babel_validation/assertions/nodenorm.py
+++ b/src/babel_validation/assertions/nodenorm.py
@@ -148,9 +148,6 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
 class HasLabelHandler(NodeNormTest):
     """Test that a CURIE resolves to a specific primary label in NodeNorm."""
     NAME = "haslabel"
-
-    def curie_params(self, params: list[str]) -> list[str]:
-        return params[:1]
     DESCRIPTION = (
         "The CURIE must resolve in NodeNorm and its primary label (id.label) must "
         "match the expected label exactly (case-sensitive)."
@@ -159,6 +156,9 @@ def curie_params(self, params: list[str]) -> list[str]:
     WIKI_EXAMPLES = ["{{BabelTest|HasLabel|CHEBI:15365|aspirin}}"]
     YAML_PARAMS = "    - [CHEBI:15365, aspirin]"
 
+    def curie_params(self, params: list[str]) -> list[str]:
+        return params[:1]
+
     def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                        label: str = "") -> Iterator[TestResult]:
         # params[0] is the CURIE to resolve; params[1] is the expected label string.
@@ -206,9 +206,6 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
 class ResolvesWithTypeHandler(NodeNormTest):
     """Test that CURIEs resolve with a specific Biolink type in NodeNorm."""
     NAME = "resolveswithtype"
-
-    def curie_params(self, params: list[str]) -> list[str]:
-        return params[1:]
     DESCRIPTION = (
         "Each param_set must have at least two elements: the first is the expected Biolink type "
         "(e.g. 'biolink:Gene'), and the remainder are CURIEs that must resolve with that type."
@@ -220,6 +217,9 @@ def curie_params(self, params: list[str]) -> list[str]:
     WIKI_EXAMPLES = ["{{BabelTest|ResolvesWithType|biolink:Gene|NCBIGene:1}}"]
     YAML_PARAMS = "    - [biolink:Gene, NCBIGene:1, HGNC:5]"
 
+    def curie_params(self, params: list[str]) -> list[str]:
+        return params[1:]
+
     def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                        label: str = "") -> Iterator[TestResult]:
         # params[0] is the expected Biolink type (e.g. "biolink:Gene");

From 7eeafde3ee8bbe68bd3a05e7081e2785e35b384e Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Fri, 8 May 2026 01:32:41 -0400
Subject: [PATCH 093/126] Fix param-aware cache keys in CachedNodeNorm and
 CachedNameRes

Both services were keying their caches on the identifier string alone,
ignoring any extra **params passed by the caller. This caused stale cache
hits when the same CURIE/query was looked up with different parameters
(e.g. drug_chemical_conflate='true' vs default).

Cache keys are now (identifier, frozenset(params.items())) tuples.
delete_query/clear_curie updated to clear all param variants for a key.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 src/babel_validation/services/nameres.py  | 21 +++++++++---------
 src/babel_validation/services/nodenorm.py | 26 ++++++++++++-----------
 2 files changed, 25 insertions(+), 22 deletions(-)

diff --git a/src/babel_validation/services/nameres.py b/src/babel_validation/services/nameres.py
index 1300e17c..5b377bc6 100644
--- a/src/babel_validation/services/nameres.py
+++ b/src/babel_validation/services/nameres.py
@@ -6,8 +6,6 @@
 cached_nameres_by_url = {}
 
 class CachedNameRes:
-    # Note: caching ignores extra **params (e.g. autocomplete, limit), so callers should use
-    # a consistent set of params or call delete_query() to invalidate before changing params.
     def __init__(self, nameres_url: str):
         self.nameres_url = nameres_url
         self.logger = logging.getLogger(str(self))
@@ -55,19 +53,22 @@ def bulk_lookup(self, queries: list[str], **params) -> dict[str, dict]:
         return result
 
     def lookup(self, query, **params):
-        if query in self.cache:
-            return self.cache[query]
+        cache_key = (query, frozenset(params.items()))
+        if cache_key in self.cache:
+            return self.cache[cache_key]
 
-        params['string'] = query
-        self.logger.debug(f"Querying NameRes with params {params}")
+        api_params = dict(params)
+        api_params['string'] = query
+        self.logger.debug(f"Querying NameRes with params {api_params}")
 
-        response = requests.post(self.nameres_url + "lookup", params=params, timeout=30)
+        response = requests.post(self.nameres_url + "lookup", params=api_params, timeout=30)
         response.raise_for_status()
         result = response.json()
 
-        self.cache[query] = result
+        self.cache[cache_key] = result
         return result
 
     def delete_query(self, query):
-        if query in self.cache:
-            del self.cache[query]
+        keys_to_delete = [k for k in self.cache if k[0] == query]
+        for k in keys_to_delete:
+            del self.cache[k]
diff --git a/src/babel_validation/services/nodenorm.py b/src/babel_validation/services/nodenorm.py
index 452ea36c..5104ba7f 100644
--- a/src/babel_validation/services/nodenorm.py
+++ b/src/babel_validation/services/nodenorm.py
@@ -21,32 +21,33 @@ def from_url(nodenorm_url: str) -> 'CachedNodeNorm':
         return cached_node_norms_by_url[nodenorm_url]
 
     def normalize_curies(self, curies: list[str], **params) -> dict[str, dict]:
-        # TODO: eventually we'll need some way to cache the parameters along with the curie.
         if not curies:
             raise ValueError(f"curies must not be empty when calling normalize_curies({curies}, {params}) on {self}")
         if not isinstance(curies, list):
             raise ValueError(f"curies must be a list when calling normalize_curies({curies}, {params}) on {self}")
 
         time_started = time.time_ns()
+        params_key = frozenset(params.items())
         curies_set = set(curies)
-        cached_curies = curies_set & self.cache.keys()
+        cached_curies = {c for c in curies_set if (c, params_key) in self.cache}
         curies_to_be_queried = curies_set - cached_curies
 
         # Make query.
         result = {}
         if curies_to_be_queried:
-            params['curies'] = list(curies_to_be_queried)
+            api_params = dict(params)
+            api_params['curies'] = list(curies_to_be_queried)
 
-            self.logger.debug(f"Called NodeNorm {self} with params {params}")
-            response = requests.post(self.nodenorm_url + "get_normalized_nodes", json=params, timeout=30)
+            self.logger.debug(f"Called NodeNorm {self} with params {api_params}")
+            response = requests.post(self.nodenorm_url + "get_normalized_nodes", json=api_params, timeout=30)
             response.raise_for_status()
             result = response.json()
 
             for curie in curies_to_be_queried:
-                self.cache[curie] = result.get(curie, None)
+                self.cache[(curie, params_key)] = result.get(curie, None)
 
         for curie in cached_curies:
-            result[curie] = self.cache[curie]
+            result[curie] = self.cache[(curie, params_key)]
 
         time_taken_sec = (time.time_ns() - time_started) / 1E9
         self.logger.info(f"Normalizing {len(curies_to_be_queried)} CURIEs {curies_to_be_queried} (with {len(cached_curies)} CURIEs cached) with params {params} on {self} in {time_taken_sec:.3f}s")
@@ -54,11 +55,12 @@ def normalize_curies(self, curies: list[str], **params) -> dict[str, dict]:
         return result
 
     def normalize_curie(self, curie, **params):
-        if curie in self.cache:
-            return self.cache[curie]
+        cache_key = (curie, frozenset(params.items()))
+        if cache_key in self.cache:
+            return self.cache[cache_key]
         return self.normalize_curies([curie], **params)[curie]
 
     def clear_curie(self, curie):
-        # This will be needed if you need to call a CURIE with different parameters.
-        if curie in self.cache:
-            del self.cache[curie]
+        keys_to_delete = [k for k in self.cache if k[0] == curie]
+        for k in keys_to_delete:
+            del self.cache[k]

From e8c4e6fc8464e6eed00a111ca02e20bd1bf9c047 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Fri, 8 May 2026 01:33:07 -0400
Subject: [PATCH 094/126] Improve robustness of GitHub issue parsing and
 fetching

- Narrow exception catch in get_issues_by_ids() from broad GithubException
  to UnknownObjectException (404 only), so auth failures and 500s are not
  silently swallowed when searching by bare issue number across repos.
- Replace yaml_dict['babel_tests'] with a .get() guard that raises
  ValueError with a clear message when a matched YAML block has no
  'babel_tests' top-level key, instead of a cryptic AttributeError/KeyError.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .../sources/github/github_issues_test_cases.py    | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index 79a0f67b..813f5fcd 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -170,7 +170,14 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
                 # Parse string as YAML.
                 yaml_dict = yaml.safe_load(match.removeprefix("```yaml").removesuffix("```"))
 
-                for assertion, original_param_sets in yaml_dict['babel_tests'].items():
+                babel_tests = yaml_dict.get('babel_tests') if isinstance(yaml_dict, dict) else None
+                if babel_tests is None:
+                    raise ValueError(
+                        f"YAML block in issue {github_issue_id} matched the detection pattern "
+                        f"but contains no 'babel_tests' top-level key: {match!r}"
+                    )
+
+                for assertion, original_param_sets in babel_tests.items():
                     # YAML syntax: each entry under an assertion key becomes one param_set.
                     # A bare string becomes a single-element param_set; a list is used as-is.
                     param_sets = []
@@ -199,7 +206,7 @@ def get_issues_by_ids(self, issue_ids: list[str]) -> list[Issue.Issue]:
         - 'repo#N'      → search self.github_repositories for matching repo name
         - 'N'           → fetch #N from all configured repositories
         """
-        from github import GithubException
+        from github import UnknownObjectException
         issues = []
         for issue_id in issue_ids:
             found = False
@@ -217,13 +224,13 @@ def get_issues_by_ids(self, issue_ids: list[str]) -> list[Issue.Issue]:
                         found = True
                         break
             elif m := re.match(r'^(\d+)$', issue_id):
-                # N — try all configured repos
+                # N — try all configured repos; skip repos that don't have this issue number.
                 num = int(m.group(1))
                 for full_repo in self.github_repositories:
                     try:
                         issues.append(self.github.get_repo(full_repo).get_issue(num))
                         found = True
-                    except GithubException:
+                    except UnknownObjectException:
                         pass
             if not found:
                 self.logger.warning("Could not resolve issue ID %r in configured repositories %s",

From f6088addc44c93d6b16a576f19a83b038f0fef73 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Fri, 8 May 2026 01:33:23 -0400
Subject: [PATCH 095/126] Fix GitHub issues test harness: lazy dotenv, xfail
 clarity, missing __init__

- Move dotenv.load_dotenv() inside _get_github_issues_test_cases() so the
  .env file is only loaded when GitHub tests are actually collected, not at
  module import time for every pytest run.
- Add tests/github_issues/__init__.py (was missing).
- Simplify open-issue xfail logic in test_github_issue: guard against zero
  subtests producing a ZeroDivisionError, remove the misleading assert True
  (the xfail marker handles XPASS when all subtests pass), and rename
  count_subtests_xfailed to count_subtests_failed for clarity.
- Update test_yaml_null_babel_tests_raises to expect the new ValueError
  (with message match) instead of the old AttributeError/TypeError.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 tests/github_issues/__init__.py           |  0
 tests/github_issues/conftest.py           |  8 +++++---
 tests/github_issues/test_github_issues.py | 24 ++++++++++++++---------
 tests/github_issues/test_system.py        |  4 ++--
 4 files changed, 22 insertions(+), 14 deletions(-)
 create mode 100644 tests/github_issues/__init__.py

diff --git a/tests/github_issues/__init__.py b/tests/github_issues/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/github_issues/conftest.py b/tests/github_issues/conftest.py
index 482f0828..05cdbe0f 100644
--- a/tests/github_issues/conftest.py
+++ b/tests/github_issues/conftest.py
@@ -11,8 +11,7 @@
 
 from src.babel_validation.sources.github.github_issues_test_cases import GitHubIssuesTestCases
 
-dotenv.load_dotenv()
-_github_token = os.getenv('GITHUB_TOKEN')
+_github_token = None
 
 _targets_config = configparser.ConfigParser()
 _targets_config.read(Path(__file__).parent.parent / 'targets.ini')
@@ -32,9 +31,12 @@
 
 def _get_github_issues_test_cases() -> GitHubIssuesTestCases:
     """Lazily construct GitHubIssuesTestCases, skipping tests if no token is available."""
-    global _github_issues_test_cases
+    global _github_issues_test_cases, _github_token
     if _github_issues_test_cases is not None:
         return _github_issues_test_cases
+    if _github_token is None:
+        dotenv.load_dotenv()
+        _github_token = os.getenv('GITHUB_TOKEN') or ''
     if not _github_token:
         pytest.skip(
             "GITHUB_TOKEN environment variable not set; skipping GitHub issues tests.",
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index a82dbd1f..5966ea1d 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -39,7 +39,7 @@ def test_github_issue(request, target_info, github_issue_id, github_issue, githu
         ))
 
     count_subtests = 0
-    count_subtests_xfailed = 0
+    count_subtests_failed = 0
     for test_issue in tests:
         results_nodenorm = test_issue.test_with_nodenorm(nodenorm)
         results_nameres = test_issue.test_with_nameres(nodenorm, nameres)
@@ -53,8 +53,8 @@ def test_github_issue(request, target_info, github_issue_id, github_issue, githu
                         assert True, f"{issue_id} ({github_issue.state}): {message}"
 
                     case TestResult(status=TestStatus.Failed, message=message):
+                        count_subtests_failed += 1
                         if is_open:
-                            count_subtests_xfailed += 1
                             pytest.xfail(message)
                         else:
                             assert False, f"{issue_id} ({github_issue.state}): {message}"
@@ -65,11 +65,17 @@ def test_github_issue(request, target_info, github_issue_id, github_issue, githu
                     case _:
                         assert False, f"Unknown result from {issue_id}: {result}"
 
-    # Always xfail open issues so the result stays in the xfail family.
-    # If all subtests pass the message signals the issue is ready to close;
-    # if some failed it reports the failure count.
+    # For open issues: xfail so the result stays in the xfail family.
+    # - Some subtests failed → xfail with a count summary (expected outcome).
+    # - All subtests passed  → the xfail marker added above makes this XPASS,
+    #   which (strict=True) reports as a failure and signals the issue is closeable.
+    # - No subtests ran      → xfail as a configuration error.
     if is_open:
-        if count_subtests_xfailed > 0:
-            pytest.xfail(f"Open issue {issue_id} has {count_subtests_xfailed:,} failing subtests out of {count_subtests:,} ({count_subtests_xfailed/count_subtests:.0%})")
-        else:
-            assert True, f"Open issue {issue_id} has all {count_subtests:,} subtests passing -- ready to close?"
+        if count_subtests == 0:
+            pytest.xfail(f"Open issue {issue_id} produced no test results — check assertion configuration")
+        elif count_subtests_failed > 0:
+            pct = count_subtests_failed / count_subtests
+            pytest.xfail(
+                f"Open issue {issue_id} has {count_subtests_failed:,} failing subtests "
+                f"out of {count_subtests:,} ({pct:.0%})"
+            )
diff --git a/tests/github_issues/test_system.py b/tests/github_issues/test_system.py
index 78705070..a4cf992b 100644
--- a/tests/github_issues/test_system.py
+++ b/tests/github_issues/test_system.py
@@ -146,9 +146,9 @@ def test_wiki_needed_no_params(self, github_issues_test_cases):
     # --- YAML syntax: null / empty values ---
 
     def test_yaml_null_babel_tests_raises(self, github_issues_test_cases):
-        # babel_tests: null → AttributeError calling .items() on None
+        # babel_tests: null → ValueError with a clear message (null yaml value has no .items())
         mock = _mock_issue("```yaml\nbabel_tests:\n\n```")
-        with pytest.raises((AttributeError, TypeError)):
+        with pytest.raises(ValueError, match="no 'babel_tests' top-level key"):
             github_issues_test_cases.get_test_issues_from_issue(mock)
 
     def test_yaml_null_assertion_params_raises(self, github_issues_test_cases):

From b7146b83fb74f4079896feda6eb0215340a69d98 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Fri, 8 May 2026 01:39:42 -0400
Subject: [PATCH 096/126] Fix two bugs surfaced by Copilot review

- Guard prewarm call in NodeNormTest.test_with_nodenorm against an empty
  CURIE set: when all param_sets yield no CURIEs (e.g. bare
  {{BabelTest|Resolves}} with no args), normalize_curies([]) raised
  ValueError before the per-param_set validation could yield a clean
  TestResult failure.
- Raise ValueError (with a clear message) in get_issues_by_ids() when an
  issue ID can't be resolved, instead of silently returning an empty list
  that would cause a confusing IndexError at the call site.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 src/babel_validation/assertions/__init__.py                | 7 +++++--
 .../sources/github/github_issues_test_cases.py             | 6 ++++--
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/src/babel_validation/assertions/__init__.py b/src/babel_validation/assertions/__init__.py
index 80ab1e5f..73e498b7 100644
--- a/src/babel_validation/assertions/__init__.py
+++ b/src/babel_validation/assertions/__init__.py
@@ -74,8 +74,11 @@ def test_with_nodenorm(self, param_sets: list[list[str]], nodenorm,
         if not param_sets:
             yield self.failed(f"No parameters provided in {label}")
             return
-        # warm the cache only for params that are CURIEs (deduplicated)
-        nodenorm.normalize_curies(list({p for params in param_sets for p in self.curie_params(params)}))
+        # warm the cache only for params that are CURIEs (deduplicated); skip if empty
+        # (normalize_curies raises ValueError on an empty list)
+        curies_to_warm = list({p for params in param_sets for p in self.curie_params(params)})
+        if curies_to_warm:
+            nodenorm.normalize_curies(curies_to_warm)
         found = False
         for index, params in enumerate(param_sets):
             if not params:
diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index 813f5fcd..01ecb844 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -233,8 +233,10 @@ def get_issues_by_ids(self, issue_ids: list[str]) -> list[Issue.Issue]:
                     except UnknownObjectException:
                         pass
             if not found:
-                self.logger.warning("Could not resolve issue ID %r in configured repositories %s",
-                                    issue_id, self.github_repositories)
+                raise ValueError(
+                    f"Could not resolve issue ID {issue_id!r} in configured repositories "
+                    f"{self.github_repositories}. Use 'org/repo#N', 'repo#N', or 'N'."
+                )
         return issues
 
     def get_issues_with_tests(self, github_repositories=None) -> Iterator[Issue.Issue]:

From 576fa0f1d7e99b9498a4201d84f2bd51ca2382c1 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Fri, 8 May 2026 01:48:45 -0400
Subject: [PATCH 097/126] Fix unbounded logger growth in GitHubIssueTest

logging.getLogger(str(self)) registered a unique logger per instance
because __str__ includes the issue ID and serialized param sets. The
logging module caches loggers by name, so this grew without bound and
made log filtering by logger name useless. Switch to __name__ (module
logger) and pass instance details in the log message instead.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .../sources/github/github_issues_test_cases.py                | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index 01ecb844..60e00fbd 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -61,8 +61,8 @@ def __init__(self, github_issue_id: str, github_issue: Issue.Issue, assertion: s
 
         self.github_issue_id = github_issue_id
 
-        self.logger = logging.getLogger(str(self))
-        self.logger.info(f"Creating GitHubIssueTest for {github_issue.html_url} {assertion}({param_sets})")
+        self.logger = logging.getLogger(__name__)
+        self.logger.info("Creating GitHubIssueTest for %s %s(%s)", github_issue.html_url, assertion, param_sets)
 
     def __str__(self):
         return f"{self.github_issue_id}: {self.assertion}({len(self.param_sets)} param sets: {json.dumps(self.param_sets)})"

From be3c09bcdb21e8b751fd7ffed656a601e5d5b4d4 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Fri, 8 May 2026 13:19:51 -0400
Subject: [PATCH 098/126] Fixed endpoint for NameRes blocklist.

---
 tests/nameres/test_blocklist.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/nameres/test_blocklist.py b/tests/nameres/test_blocklist.py
index 3f3eb2e5..ab76b2f4 100644
--- a/tests/nameres/test_blocklist.py
+++ b/tests/nameres/test_blocklist.py
@@ -17,7 +17,7 @@ def test_check_blocklist_entry(target_info, blocklist_entry, categories_include)
     :param target_info: The test target information.
     """
     nameres_url = target_info['NameResURL']
-    nameres_url_reverse_lookup = nameres_url + 'reverse_lookup'
+    nameres_url_reverse_lookup = nameres_url + 'synonyms'
 
     # If there is any test category provided, this test is not relevant and we can skip it.
     if categories_include:

From 4250f15588369125ac2c3673c66431472dbf8996 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Mon, 11 May 2026 12:40:17 -0400
Subject: [PATCH 099/126] Fix four issues from Opus code review of PR #67

- conftest.py: fix lock-file cleanup deleting .csv.lock instead of .lock
- test_nameres_from_gsheet.py: reflow biolink_type dict literal to idiomatic form
- github_issues_test_cases.py: replace useless Github repr log with repo list;
  guard get_issues_by_ids against missing '/' in configured repo name
- test_assertions_docs.py: normalise CRLF before README comparison (Windows safety)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .../sources/github/github_issues_test_cases.py              | 5 +++--
 tests/conftest.py                                           | 2 +-
 tests/nameres/test_nameres_from_gsheet.py                   | 6 ++----
 tests/test_environment/test_assertions_docs.py              | 2 +-
 4 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index 60e00fbd..cd4a4b8b 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -105,11 +105,11 @@ def __init__(self, github_token: str, github_repositories):
 
         self.github = Github(auth=Auth.Token(self.github_token))
         self.logger = logging.getLogger(self.__class__.__name__)
-        self.logger.info(f"Set up GitHub object ({self.github})")
 
         if not github_repositories:
             raise ValueError("No GitHub repositories specified in `github_repositories`.")
         self.github_repositories = github_repositories
+        self.logger.info("Configured GitHub repositories: %s", self.github_repositories)
 
         # Prepare regular expressions.
         self.babeltest_pattern = re.compile(r'{{BabelTest\|.*?}}')
@@ -219,7 +219,8 @@ def get_issues_by_ids(self, issue_ids: list[str]) -> list[Issue.Issue]:
                 # repo#N — find repo in configured list
                 repo_name, num = m.group(1), int(m.group(2))
                 for full_repo in self.github_repositories:
-                    if full_repo.split('/')[1] == repo_name:
+                    parts = full_repo.split('/')
+                    if len(parts) >= 2 and parts[1] == repo_name:
                         issues.append(self.github.get_repo(full_repo).get_issue(num))
                         found = True
                         break
diff --git a/tests/conftest.py b/tests/conftest.py
index 52c0df28..3ac5a7c6 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -39,7 +39,7 @@ def pytest_configure(config):
             except FileNotFoundError:
                 pass
             try:
-                os.unlink(f + '.lock')
+                os.unlink(f.removesuffix('.csv') + '.lock')
             except FileNotFoundError:
                 pass
         tmpdir = tempfile.gettempdir()
diff --git a/tests/nameres/test_nameres_from_gsheet.py b/tests/nameres/test_nameres_from_gsheet.py
index 78118bf1..2e4979e8 100644
--- a/tests/nameres/test_nameres_from_gsheet.py
+++ b/tests/nameres/test_nameres_from_gsheet.py
@@ -56,10 +56,8 @@ def test_label(target_info, test_row, test_category):
             request = {
                 "string": label,
                 "autocomplete": autocomplete_flag,
-                "biolink_type": [
-                    # Turned it into a list to support multiple Biolink types.
-                    biolink_class,
-                ], "limit": limit
+                "biolink_type": [biolink_class],
+                "limit": limit,
             }
             if test_row.Prefixes:
                 only_prefixes = []
diff --git a/tests/test_environment/test_assertions_docs.py b/tests/test_environment/test_assertions_docs.py
index d1000c70..03e5b908 100644
--- a/tests/test_environment/test_assertions_docs.py
+++ b/tests/test_environment/test_assertions_docs.py
@@ -6,7 +6,7 @@
 @pytest.mark.unit
 def test_assertions_readme_is_up_to_date():
     expected = generate_readme()
-    actual = README_PATH.read_text(encoding="utf-8")
+    actual = README_PATH.read_text(encoding="utf-8").replace("\r\n", "\n")
     assert actual == expected, (
         "assertions/README.md is out of date.\n"
         "Regenerate it with:\n"

From e8089479d82b43d34a82343079983db5b220028f Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Tue, 12 May 2026 16:18:11 -0400
Subject: [PATCH 100/126] Catch expired GitHub token and fail only the GitHub
 issue tests

When a 401 GithubException is raised during test collection or fixture
hydration, surface a single failing test with a clear message (including
the URL to regenerate the token and instructions to delete the cache file)
rather than crashing collection and failing all tests.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 tests/github_issues/conftest.py | 40 +++++++++++++++++++++++++++++----
 1 file changed, 36 insertions(+), 4 deletions(-)

diff --git a/tests/github_issues/conftest.py b/tests/github_issues/conftest.py
index 05cdbe0f..1684d2a5 100644
--- a/tests/github_issues/conftest.py
+++ b/tests/github_issues/conftest.py
@@ -7,11 +7,21 @@
 import dotenv
 import pytest
 from filelock import FileLock
-from github import Issue
+from github import GithubException, Issue
 
 from src.babel_validation.sources.github.github_issues_test_cases import GitHubIssuesTestCases
 
 _github_token = None
+_github_auth_error: str | None = None
+
+_AUTH_ERROR_ID = "github-auth-error"
+_AUTH_HELP = (
+    "GitHub token is expired or invalid. Generate a new one at "
+    "https://github.com/settings/tokens and set it as the GITHUB_TOKEN "
+    "environment variable (or in a .env file), then delete the cache file "
+    f"at {Path(tempfile.gettempdir()) / 'babel_validation_issues_cache.json'} "
+    "if it exists."
+)
 
 _targets_config = configparser.ConfigParser()
 _targets_config.read(Path(__file__).parent.parent / 'targets.ini')
@@ -54,13 +64,20 @@ def _issue_id(issue: Issue.Issue) -> str:
 
 def _get_all_test_issue_ids() -> list[str]:
     """Return IDs of all issues that contain tests, using a file-based cache."""
+    global _github_auth_error
     with FileLock(_LOCK_FILE):
         if _CACHE_FILE.exists():
             try:
                 return json.loads(_CACHE_FILE.read_text())
             except (json.JSONDecodeError, OSError):
                 _CACHE_FILE.unlink(missing_ok=True)
-        issues = list(_get_github_issues_test_cases().get_issues_with_tests())
+        try:
+            issues = list(_get_github_issues_test_cases().get_issues_with_tests())
+        except GithubException as e:
+            if e.status == 401:
+                _github_auth_error = f"{_AUTH_HELP}\n\nOriginal error: {e}"
+                return [_AUTH_ERROR_ID]
+            raise
         ids = [_issue_id(i) for i in issues]
         for issue, id_ in zip(issues, ids):
             _fetched_issues_cache[id_] = issue
@@ -69,11 +86,19 @@ def _get_all_test_issue_ids() -> list[str]:
 
 
 def pytest_generate_tests(metafunc):
+    global _github_auth_error
     if "github_issue_id" not in metafunc.fixturenames:
         return
     issue_id_filter = metafunc.config.getoption("issue", default=[])
     if issue_id_filter:
-        issues = _get_github_issues_test_cases().get_issues_by_ids(issue_id_filter)
+        try:
+            issues = _get_github_issues_test_cases().get_issues_by_ids(issue_id_filter)
+        except GithubException as e:
+            if e.status == 401:
+                _github_auth_error = f"{_AUTH_HELP}\n\nOriginal error: {e}"
+                metafunc.parametrize("github_issue_id", [_AUTH_ERROR_ID], ids=[_AUTH_ERROR_ID])
+                return
+            raise
         ids = [_issue_id(i) for i in issues]
         for issue, id_ in zip(issues, ids):
             _fetched_issues_cache[id_] = issue
@@ -85,9 +110,16 @@ def pytest_generate_tests(metafunc):
 @pytest.fixture
 def github_issue(github_issue_id):
     """Hydrate a GitHub Issue object from its string ID."""
+    if github_issue_id == _AUTH_ERROR_ID:
+        pytest.fail(_github_auth_error or _AUTH_HELP)
     if github_issue_id in _fetched_issues_cache:
         return _fetched_issues_cache[github_issue_id]
-    return _get_github_issues_test_cases().get_issues_by_ids([github_issue_id])[0]
+    try:
+        return _get_github_issues_test_cases().get_issues_by_ids([github_issue_id])[0]
+    except GithubException as e:
+        if e.status == 401:
+            pytest.fail(f"{_AUTH_HELP}\n\nOriginal error: {e}")
+        raise
 
 
 @pytest.fixture(scope="session")

From 39e4e0edaa1c45d51caf2e038207da0f2597cd9a Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 17 May 2026 15:13:04 -0400
Subject: [PATCH 101/126] Fix bugs and clean up code quality from simplify
 review

- Fix CachedNameRes.bulk_lookup: cache key now includes params (was
  ignoring them, causing stale hits when called with different params);
  use api_params copy instead of mutating the kwargs dict in-place
- Fix CachedNameRes.delete_query: both lookup and bulk_lookup now use
  (query, params_key) tuple keys, so eviction works for both
- Fix NeededHandler: was yielding failures from both test_with_nodenorm
  and test_with_nameres, doubling the failure count per issue
- Extract GitHubIssueTest._get_handler() to eliminate duplicated
  lookup+raise and the diverging error messages
- Unify HasLabelHandler and SearchByNameHandler param-count checks into
  a single len(params) != 2 branch
- Promote GitHubIssuesTestCases regex patterns to class-level constants
- Remove per-instance self.logger from GitHubIssueTest; use module-level
- Fix dead isinstance check in GitHubIssueTest.__init__ (ran after the
  None default was applied, so was always True)
- SearchByNameHandler: request exactly pass_if_found_in_top results
  instead of 2x; remove now-unreachable else branch
- Remove redundant issue_id alias in test_github_issues.py
- Remove "what" comments in handler methods
- Convert f-strings in logging calls to lazy %s format

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 src/babel_validation/assertions/common.py     |  3 --
 src/babel_validation/assertions/nameres.py    | 25 +++------
 src/babel_validation/assertions/nodenorm.py   | 11 +---
 src/babel_validation/services/nameres.py      | 20 +++----
 .../github/github_issues_test_cases.py        | 54 +++++++++----------
 tests/github_issues/test_github_issues.py     | 17 +++---
 6 files changed, 54 insertions(+), 76 deletions(-)

diff --git a/src/babel_validation/assertions/common.py b/src/babel_validation/assertions/common.py
index ac12daca..68c5db22 100644
--- a/src/babel_validation/assertions/common.py
+++ b/src/babel_validation/assertions/common.py
@@ -11,6 +11,3 @@ class NeededHandler(AssertionHandler):
 
     def test_with_nodenorm(self, param_sets, nodenorm, label=""):
         yield self.failed("Test needed for issue")
-
-    def test_with_nameres(self, param_sets, nodenorm, nameres, pass_if_found_in_top=5, label=""):
-        yield self.failed("Test needed for issue")
diff --git a/src/babel_validation/assertions/nameres.py b/src/babel_validation/assertions/nameres.py
index acf05c6f..da4cb390 100644
--- a/src/babel_validation/assertions/nameres.py
+++ b/src/babel_validation/assertions/nameres.py
@@ -26,11 +26,7 @@ class SearchByNameHandler(NameResTest):
     def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                        nameres: CachedNameRes, pass_if_found_in_top: int = 5,
                        label: str = "") -> Iterator[TestResult]:
-        # params[0] is the search query string; params[1] is the expected CURIE.
-        if len(params) < 2:
-            yield self.failed(f"Two parameters expected for SearchByName in {label}, but params = {params}")
-            return
-        elif len(params) > 2:
+        if len(params) != 2:
             yield self.failed(
                 f"SearchByName requires exactly two parameters (search query, expected CURIE) in {label}, "
                 f"but got {len(params)}: {params}"
@@ -47,24 +43,19 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
         expected_curie_label = expected_curie_result['id']['label']
         expected_curie_string = f"Expected CURIE {expected_curie_from_test}, normalized to {expected_curie} '{expected_curie_label}'"
 
-        # Search for the expected CURIE in the first {pass_if_found_in_top} results.
-        results = nameres.lookup(search_query, autocomplete='false', limit=(2 * pass_if_found_in_top))
+        results = nameres.lookup(search_query, autocomplete='false', limit=pass_if_found_in_top)
         if not results:
             yield self.failed(f"No results found for '{search_query}' on NameRes {nameres} ({expected_curie_string})")
             return
 
         curies = [result['curie'] for result in results]
-        try:
-            found_index = curies.index(expected_curie)
-        except ValueError:
+        if expected_curie not in curies:
             logging.getLogger(__name__).debug(
-                "%s not found when searching for '%s' in NameRes %s: %s",
-                expected_curie_string, search_query, nameres, json.dumps(results, indent=2, sort_keys=True)
+                "%s not found in top %d results for '%s' in NameRes %s: %s",
+                expected_curie_string, pass_if_found_in_top, search_query, nameres,
+                json.dumps(results, indent=2, sort_keys=True)
             )
-            yield self.failed(f"{expected_curie_string} not found when searching for '{search_query}' in NameRes {nameres}")
+            yield self.failed(f"{expected_curie_string} not found in top {pass_if_found_in_top} results for '{search_query}' in NameRes {nameres}")
             return
 
-        if found_index < pass_if_found_in_top:
-            yield self.passed(f"{expected_curie_string} found at index {found_index + 1} on NameRes {nameres}")
-        else:
-            yield self.failed(f"{expected_curie_string} found at index {found_index + 1} which is greater than {pass_if_found_in_top} on NameRes {nameres}")
+        yield self.passed(f"{expected_curie_string} found at index {curies.index(expected_curie) + 1} on NameRes {nameres}")
diff --git a/src/babel_validation/assertions/nodenorm.py b/src/babel_validation/assertions/nodenorm.py
index cce9b347..3e999999 100644
--- a/src/babel_validation/assertions/nodenorm.py
+++ b/src/babel_validation/assertions/nodenorm.py
@@ -161,14 +161,7 @@ def curie_params(self, params: list[str]) -> list[str]:
 
     def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                        label: str = "") -> Iterator[TestResult]:
-        # params[0] is the CURIE to resolve; params[1] is the expected label string.
-        if len(params) < 2:
-            yield self.failed(
-                f"HasLabel requires two parameters (CURIE, expected label) in {label}, "
-                f"but got: {params}"
-            )
-            return
-        elif len(params) > 2:
+        if len(params) != 2:
             yield self.failed(
                 f"HasLabel requires exactly two parameters (CURIE, expected label) in {label}, "
                 f"but got {len(params)}: {params}"
@@ -222,8 +215,6 @@ def curie_params(self, params: list[str]) -> list[str]:
 
     def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                        label: str = "") -> Iterator[TestResult]:
-        # params[0] is the expected Biolink type (e.g. "biolink:Gene");
-        # params[1:] are the CURIEs that must resolve with that type.
         if len(params) < 2:
             yield self.failed(f"Too few parameters provided in param_set in {label}: {params}")
             return
diff --git a/src/babel_validation/services/nameres.py b/src/babel_validation/services/nameres.py
index 5b377bc6..01d36bb1 100644
--- a/src/babel_validation/services/nameres.py
+++ b/src/babel_validation/services/nameres.py
@@ -27,28 +27,30 @@ def bulk_lookup(self, queries: list[str], **params) -> dict[str, dict]:
             raise ValueError(f"queries must be a list when calling bulk_lookup({queries}, {params}) on {self}")
 
         time_started = time.time_ns()
+        params_key = frozenset(params.items())
         queries_set = set(queries)
-        cached_queries = queries_set & self.cache.keys()
+        cached_queries = {q for q in queries_set if (q, params_key) in self.cache}
         queries_to_be_queried = queries_set - cached_queries
 
-        # Make query.
         result = {}
         if queries_to_be_queried:
-            params['strings'] = list(queries_to_be_queried)
+            api_params = dict(params)
+            api_params['strings'] = list(queries_to_be_queried)
 
-            self.logger.debug(f"Called NameRes {self} with params {params}")
-            response = requests.post(self.nameres_url + "bulk-lookup", json=params, timeout=30)
+            self.logger.debug("Called NameRes %s with params %s", self, api_params)
+            response = requests.post(self.nameres_url + "bulk-lookup", json=api_params, timeout=30)
             response.raise_for_status()
             result = response.json()
 
             for query in queries_to_be_queried:
-                self.cache[query] = result.get(query, None)
+                self.cache[(query, params_key)] = result.get(query, None)
 
         for query in cached_queries:
-            result[query] = self.cache[query]
+            result[query] = self.cache[(query, params_key)]
 
         time_taken_sec = (time.time_ns() - time_started) / 1E9
-        self.logger.info(f"Looked up {len(queries_to_be_queried)} queries {queries_to_be_queried} (with {len(cached_queries)} queries cached) with params {params} on {self} in {time_taken_sec:.3f}s")
+        self.logger.info("Looked up %d queries (with %d cached) with params %s on %s in %.3fs",
+                         len(queries_to_be_queried), len(cached_queries), params, self, time_taken_sec)
 
         return result
 
@@ -59,7 +61,7 @@ def lookup(self, query, **params):
 
         api_params = dict(params)
         api_params['string'] = query
-        self.logger.debug(f"Querying NameRes with params {api_params}")
+        self.logger.debug("Querying NameRes with params %s", api_params)
 
         response = requests.post(self.nameres_url + "lookup", params=api_params, timeout=30)
         response.raise_for_status()
diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index cd4a4b8b..c677e1af 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -38,6 +38,8 @@
 from src.babel_validation.services.nameres import CachedNameRes
 from src.babel_validation.services.nodenorm import CachedNodeNorm
 
+_logger = logging.getLogger(__name__)
+
 
 class GitHubIssueTest:
     """Represents one assertion extracted from a GitHub issue body — an assertion name paired with a list of param_sets to evaluate."""
@@ -51,33 +53,29 @@ def __init__(self, github_issue_id: str, github_issue: Issue.Issue, assertion: s
         :param param_sets: A list of param_sets (list[list[str]]) to evaluate for this assertion.
                            Each inner list is one param_set — see module docstring for details.
         """
+        if not isinstance(param_sets, list) and param_sets is not None:
+            raise ValueError(f"param_sets must be a list when creating a GitHubIssueTest({github_issue}, {assertion}, {param_sets})")
         self.github_issue = github_issue
         self.assertion = assertion
-        if param_sets is None:
-            param_sets = []
-        self.param_sets = param_sets
-        if not isinstance(self.param_sets, list):
-            raise ValueError(f"param_sets must be a list when creating a GitHubIssueTest({self.github_issue}, {self.assertion}, {self.param_sets})")
-
+        self.param_sets = param_sets if param_sets is not None else []
         self.github_issue_id = github_issue_id
 
-        self.logger = logging.getLogger(__name__)
-        self.logger.info("Creating GitHubIssueTest for %s %s(%s)", github_issue.html_url, assertion, param_sets)
+        _logger.info("Creating GitHubIssueTest for %s %s(%s)", github_issue.html_url, assertion, param_sets)
 
     def __str__(self):
         return f"{self.github_issue_id}: {self.assertion}({len(self.param_sets)} param sets: {json.dumps(self.param_sets)})"
 
-    def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
+    def _get_handler(self):
         handler = ASSERTION_HANDLERS.get(self.assertion.lower())
         if handler is None:
             raise ValueError(f"Unknown assertion type for {self}: {self.assertion}")
-        return handler.test_with_nodenorm(self.param_sets, nodenorm, label=str(self))
+        return handler
+
+    def test_with_nodenorm(self, nodenorm: CachedNodeNorm) -> Iterator[TestResult]:
+        return self._get_handler().test_with_nodenorm(self.param_sets, nodenorm, label=str(self))
 
     def test_with_nameres(self, nodenorm: CachedNodeNorm, nameres: CachedNameRes, pass_if_found_in_top=5) -> Iterator[TestResult]:
-        handler = ASSERTION_HANDLERS.get(self.assertion.lower())
-        if handler is None:
-            raise ValueError(f"Unknown assertion type: {self.assertion}")
-        return handler.test_with_nameres(self.param_sets, nodenorm, nameres, pass_if_found_in_top, label=str(self))
+        return self._get_handler().test_with_nameres(self.param_sets, nodenorm, nameres, pass_if_found_in_top, label=str(self))
 
 
 class GitHubIssuesTestCases:
@@ -88,6 +86,9 @@ class GitHubIssuesTestCases:
     - A closed issue has test cases that are now failing (and so should be reopened).
     """
 
+    _BABELTEST_RE = re.compile(r'{{BabelTest\|.*?}}')
+    _BABELTEST_YAML_RE = re.compile(r'```yaml\s+babel_tests:\s+.*?\s+```', re.DOTALL)
+
     def __init__(self, github_token: str, github_repositories):
         """
         Create a GitHubIssuesTestCase object.
@@ -111,10 +112,6 @@ def __init__(self, github_token: str, github_repositories):
         self.github_repositories = github_repositories
         self.logger.info("Configured GitHub repositories: %s", self.github_repositories)
 
-        # Prepare regular expressions.
-        self.babeltest_pattern = re.compile(r'{{BabelTest\|.*?}}')
-        self.babeltest_yaml_pattern = re.compile(r'```yaml\s+babel_tests:\s+.*?\s+```', re.DOTALL)
-
     def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIssueTest]:
         """
         Extract test rows from a single GitHub issue.
@@ -138,7 +135,8 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
         """
 
         github_issue_id = f"{github_issue.repository.full_name}#{github_issue.number}"
-        self.logger.debug(f"Looking for tests in issue {github_issue_id}: {github_issue.title} ({str(github_issue.state)}, {github_issue.html_url})")
+        self.logger.debug("Looking for tests in issue %s: %s (%s, %s)",
+                          github_issue_id, github_issue.title, github_issue.state, github_issue.html_url)
 
         # Is there an issue body at all?
         if not github_issue.body or github_issue.body.strip() == '':
@@ -147,10 +145,10 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
         # Look for BabelTest syntax.
         testrows = []
 
-        babeltest_matches = re.findall(self.babeltest_pattern, github_issue.body)
+        babeltest_matches = re.findall(self._BABELTEST_RE, github_issue.body)
         if babeltest_matches:
             for match in babeltest_matches:
-                self.logger.info(f"Found BabelTest in issue {github_issue_id}: {match}")
+                self.logger.info("Found BabelTest in issue %s: %s", github_issue_id, match)
 
                 # Figure out parameters.
                 test_string = match.removeprefix("{{BabelTest|").removesuffix("}}")
@@ -162,10 +160,10 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
                 # one-element list: [params[1:]].
                 testrows.append(GitHubIssueTest(github_issue_id, github_issue, params[0], [params[1:]]))
 
-        babeltest_yaml_matches = re.findall(self.babeltest_yaml_pattern, github_issue.body)
+        babeltest_yaml_matches = re.findall(self._BABELTEST_YAML_RE, github_issue.body)
         if babeltest_yaml_matches:
             for match in babeltest_yaml_matches:
-                self.logger.info(f"Found BabelTest YAML in issue {github_issue_id}: {match}")
+                self.logger.info("Found BabelTest YAML in issue %s: %s", github_issue_id, match)
 
                 # Parse string as YAML.
                 yaml_dict = yaml.safe_load(match.removeprefix("```yaml").removesuffix("```"))
@@ -196,8 +194,8 @@ def issue_has_tests(self, issue: Issue.Issue) -> bool:
         """Quick regex check to see if an issue body contains any BabelTest syntax."""
         if not issue.body or issue.body.strip() == '':
             return False
-        return bool(self.babeltest_pattern.search(issue.body) or
-                    self.babeltest_yaml_pattern.search(issue.body))
+        return bool(self._BABELTEST_RE.search(issue.body) or
+                    self._BABELTEST_YAML_RE.search(issue.body))
 
     def get_issues_by_ids(self, issue_ids: list[str]) -> list[Issue.Issue]:
         """
@@ -257,7 +255,7 @@ def get_issues_with_tests(self, github_repositories=None) -> Iterator[Issue.Issu
             seen_numbers = set()
             for keyword in ['{{BabelTest', 'babel_tests:']:
                 query = f'"{keyword}" is:issue in:body repo:{repo_id}'
-                self.logger.info(f"Searching GitHub issues with query: {query}")
+                self.logger.info("Searching GitHub issues with query: %s", query)
                 for issue in self.github.search_issues(query):
                     if issue.number not in seen_numbers:
                         seen_numbers.add(issue.number)
@@ -276,7 +274,7 @@ def get_all_issues(self, github_repositories=None) -> Iterator[Issue.Issue]:
             github_repositories = self.github_repositories
 
         for repo_id in github_repositories:
-            self.logger.info(f"Looking up issues in GitHub repository {repo_id}")
+            self.logger.info("Looking up issues in GitHub repository %s", repo_id)
             repo = self.github.get_repo(repo_id, lazy=True)
 
             issue_count = 0
@@ -284,4 +282,4 @@ def get_all_issues(self, github_repositories=None) -> Iterator[Issue.Issue]:
                 issue_count += 1
                 yield issue
 
-            self.logger.info(f"Found {issue_count} issues in GitHub repository {repo_id}")
+            self.logger.info("Found %d issues in GitHub repository %s", issue_count, repo_id)
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 5966ea1d..610ef99c 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -17,7 +17,6 @@ def test_github_issue(request, target_info, github_issue_id, github_issue, githu
         pytest.skip(f"No tests found in issue {github_issue}")
         return
 
-    issue_id = github_issue_id
     is_open = github_issue.state == "open"
 
     # Unknown assertion types must fail hard, not XFAIL.
@@ -25,7 +24,7 @@ def test_github_issue(request, target_info, github_issue_id, github_issue, githu
                if t.assertion.lower() not in ASSERTION_HANDLERS]
     if unknown:
         pytest.fail(
-            f"Issue {issue_id} uses unknown assertion type(s): "
+            f"Issue {github_issue_id} uses unknown assertion type(s): "
             f"{', '.join(unknown)} with param sets {json.dumps([t.param_sets for t in tests])}. "
             f"Valid types (case-insensitive): {sorted(ASSERTION_HANDLERS.keys())}"
         )
@@ -47,23 +46,23 @@ def test_github_issue(request, target_info, github_issue_id, github_issue, githu
         for result in itertools.chain(results_nodenorm, results_nameres):
             count_subtests += 1
 
-            with subtests.test(msg=issue_id):
+            with subtests.test(msg=github_issue_id):
                 match result:
                     case TestResult(status=TestStatus.Passed, message=message):
-                        assert True, f"{issue_id} ({github_issue.state}): {message}"
+                        assert True, f"{github_issue_id} ({github_issue.state}): {message}"
 
                     case TestResult(status=TestStatus.Failed, message=message):
                         count_subtests_failed += 1
                         if is_open:
                             pytest.xfail(message)
                         else:
-                            assert False, f"{issue_id} ({github_issue.state}): {message}"
+                            assert False, f"{github_issue_id} ({github_issue.state}): {message}"
 
                     case TestResult(status=TestStatus.Skipped, message=message):
-                        pytest.skip(f"{issue_id} ({github_issue.state}): {message}")
+                        pytest.skip(f"{github_issue_id} ({github_issue.state}): {message}")
 
                     case _:
-                        assert False, f"Unknown result from {issue_id}: {result}"
+                        assert False, f"Unknown result from {github_issue_id}: {result}"
 
     # For open issues: xfail so the result stays in the xfail family.
     # - Some subtests failed → xfail with a count summary (expected outcome).
@@ -72,10 +71,10 @@ def test_github_issue(request, target_info, github_issue_id, github_issue, githu
     # - No subtests ran      → xfail as a configuration error.
     if is_open:
         if count_subtests == 0:
-            pytest.xfail(f"Open issue {issue_id} produced no test results — check assertion configuration")
+            pytest.xfail(f"Open issue {github_issue_id} produced no test results — check assertion configuration")
         elif count_subtests_failed > 0:
             pct = count_subtests_failed / count_subtests
             pytest.xfail(
-                f"Open issue {issue_id} has {count_subtests_failed:,} failing subtests "
+                f"Open issue {github_issue_id} has {count_subtests_failed:,} failing subtests "
                 f"out of {count_subtests:,} ({pct:.0%})"
             )

From 692418a6fc810df50f2b7695ceac26e3c96d3288 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 17 May 2026 17:28:43 -0400
Subject: [PATCH 102/126] Fix three bugs identified in PR #67 review

- Replace pytest.xfail() inside subtests.test() context with assert False:
  XFailed raised inside a pytest-subtests context may be caught by the
  subtest handler rather than propagating as xfail. The outer xfail marker
  and the pytest.xfail() at the end of the function already handle the
  open-issue XFAIL outcome correctly.

- Convert null YAML assertion param list from TypeError to ValueError:
  When a YAML block contains 'Assertion: null', iterating None raised an
  opaque TypeError. Now raises ValueError with a clear actionable message.
  Updated the corresponding test to assert ValueError with "null param list".

- Fix eager f-string evaluation in CachedNodeNorm logging calls:
  logger.debug/info with f-strings evaluate the message even when the log
  level suppresses output. Switched to %s/%d format strings to match the
  lazy-evaluation style already used in CachedNameRes.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 src/babel_validation/services/nodenorm.py                    | 5 +++--
 .../sources/github/github_issues_test_cases.py               | 5 +++++
 tests/github_issues/test_github_issues.py                    | 5 +----
 tests/github_issues/test_system.py                           | 4 ++--
 4 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/src/babel_validation/services/nodenorm.py b/src/babel_validation/services/nodenorm.py
index 5104ba7f..742ed848 100644
--- a/src/babel_validation/services/nodenorm.py
+++ b/src/babel_validation/services/nodenorm.py
@@ -38,7 +38,7 @@ def normalize_curies(self, curies: list[str], **params) -> dict[str, dict]:
             api_params = dict(params)
             api_params['curies'] = list(curies_to_be_queried)
 
-            self.logger.debug(f"Called NodeNorm {self} with params {api_params}")
+            self.logger.debug("Called NodeNorm %s with params %s", self, api_params)
             response = requests.post(self.nodenorm_url + "get_normalized_nodes", json=api_params, timeout=30)
             response.raise_for_status()
             result = response.json()
@@ -50,7 +50,8 @@ def normalize_curies(self, curies: list[str], **params) -> dict[str, dict]:
             result[curie] = self.cache[(curie, params_key)]
 
         time_taken_sec = (time.time_ns() - time_started) / 1E9
-        self.logger.info(f"Normalizing {len(curies_to_be_queried)} CURIEs {curies_to_be_queried} (with {len(cached_curies)} CURIEs cached) with params {params} on {self} in {time_taken_sec:.3f}s")
+        self.logger.info("Normalizing %d CURIEs %s (with %d CURIEs cached) with params %s on %s in %.3fs",
+                         len(curies_to_be_queried), curies_to_be_queried, len(cached_curies), params, self, time_taken_sec)
 
         return result
 
diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index c677e1af..64e2b6e7 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -178,6 +178,11 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
                 for assertion, original_param_sets in babel_tests.items():
                     # YAML syntax: each entry under an assertion key becomes one param_set.
                     # A bare string becomes a single-element param_set; a list is used as-is.
+                    if original_param_sets is None:
+                        raise ValueError(
+                            f"YAML block in issue {github_issue_id}: assertion '{assertion}' has a null "
+                            f"param list — use an empty list [] or remove the entry"
+                        )
                     param_sets = []
                     for param_set in original_param_sets:
                         if isinstance(param_set, str):
diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 610ef99c..a7820035 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -53,10 +53,7 @@ def test_github_issue(request, target_info, github_issue_id, github_issue, githu
 
                     case TestResult(status=TestStatus.Failed, message=message):
                         count_subtests_failed += 1
-                        if is_open:
-                            pytest.xfail(message)
-                        else:
-                            assert False, f"{github_issue_id} ({github_issue.state}): {message}"
+                        assert False, f"{github_issue_id} ({github_issue.state}): {message}"
 
                     case TestResult(status=TestStatus.Skipped, message=message):
                         pytest.skip(f"{github_issue_id} ({github_issue.state}): {message}")
diff --git a/tests/github_issues/test_system.py b/tests/github_issues/test_system.py
index a4cf992b..886dfc5f 100644
--- a/tests/github_issues/test_system.py
+++ b/tests/github_issues/test_system.py
@@ -152,9 +152,9 @@ def test_yaml_null_babel_tests_raises(self, github_issues_test_cases):
             github_issues_test_cases.get_test_issues_from_issue(mock)
 
     def test_yaml_null_assertion_params_raises(self, github_issues_test_cases):
-        # Resolves: null → TypeError iterating over None
+        # Resolves: null → ValueError with a clear message (null param list is a config error)
         mock = _mock_issue("```yaml\nbabel_tests:\n  Resolves:\n```")
-        with pytest.raises(TypeError):
+        with pytest.raises(ValueError, match="null param list"):
             github_issues_test_cases.get_test_issues_from_issue(mock)
 
     def test_yaml_empty_assertion_params(self, github_issues_test_cases):

From 09f9a84bb560aebffbf6550512762089405f0e9e Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Sun, 17 May 2026 23:21:42 -0400
Subject: [PATCH 103/126] Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
---
 .github/workflows/tests.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
index 793cc976..22fd8eef 100644
--- a/.github/workflows/tests.yaml
+++ b/.github/workflows/tests.yaml
@@ -14,4 +14,4 @@ jobs:
       - name: Run unit tests
         env:
           GITHUB_TOKEN: ${{ github.token }}
-        run: uv run pytest tests/github_issues/test_system.py tests/test_environment -m unit -v
+        run: uv run pytest -m unit -v

From d873d4a6e10c3ca6ad05ff63216095bea74fbeee Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 17 May 2026 23:29:57 -0400
Subject: [PATCH 104/126] Removed unused import.

---
 tests/nameres/test_blocklist.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/nameres/test_blocklist.py b/tests/nameres/test_blocklist.py
index ab76b2f4..2fc9acbf 100644
--- a/tests/nameres/test_blocklist.py
+++ b/tests/nameres/test_blocklist.py
@@ -3,7 +3,7 @@
 import requests
 import pytest
 
-from src.babel_validation.sources.google_sheets.blocklist import BlocklistEntry, load_blocklist_from_gsheet
+from src.babel_validation.sources.google_sheets.blocklist import load_blocklist_from_gsheet
 
 # Parameterize blocklist entries.
 blocklist_entries = load_blocklist_from_gsheet()

From bbba0d946b2a6b1284a77e5c999b111358c00334 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 17 May 2026 23:30:48 -0400
Subject: [PATCH 105/126] Removed unused import.

---
 tests/tools/test_csv_to_babeltests.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/tools/test_csv_to_babeltests.py b/tests/tools/test_csv_to_babeltests.py
index 2f585ad8..32aad267 100644
--- a/tests/tools/test_csv_to_babeltests.py
+++ b/tests/tools/test_csv_to_babeltests.py
@@ -5,7 +5,6 @@
 + yaml.safe_load that the GitHub-issue test discovery uses. No network.
 """
 
-import io
 import re
 from pathlib import Path
 

From 27e45ecbcf051fb01dca61d8ad41382350d42ec3 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Sun, 17 May 2026 23:31:27 -0400
Subject: [PATCH 106/126] Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
---
 .../sources/github/github_issues_test_cases.py   | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index 64e2b6e7..0e0decc5 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -183,14 +183,26 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
                             f"YAML block in issue {github_issue_id}: assertion '{assertion}' has a null "
                             f"param list — use an empty list [] or remove the entry"
                         )
+                    if isinstance(original_param_sets, str):
+                        normalized_param_sets = [original_param_sets]
+                    elif isinstance(original_param_sets, list):
+                        normalized_param_sets = original_param_sets
+                    else:
+                        raise ValueError(
+                            f"YAML block in issue {github_issue_id}: assertion '{assertion}' must be a "
+                            f"string or list, got {type(original_param_sets).__name__}"
+                        )
                     param_sets = []
-                    for param_set in original_param_sets:
+                    for param_set in normalized_param_sets:
                         if isinstance(param_set, str):
                             param_sets.append([param_set])
                         elif isinstance(param_set, list):
                             param_sets.append(param_set)
                         else:
-                            raise RuntimeError(f"Unknown parameter set type {param_set} in issue {github_issue_id}")
+                            raise ValueError(
+                                f"YAML block in issue {github_issue_id}: assertion '{assertion}' contains "
+                                f"an unsupported parameter set type {type(param_set).__name__}"
+                            )
                     testrows.append(GitHubIssueTest(github_issue_id, github_issue, assertion, param_sets))
 
         return testrows

From a329eb0ba4ce5b247a61df372db4f21793f8ad21 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Sun, 17 May 2026 23:48:50 -0400
Subject: [PATCH 107/126] Add test documenting YAML scalar assertion param
 handling

A bare YAML scalar (e.g. 'Resolves: CHEBI:15365') is now wrapped as a
single one-element param_set rather than iterating its characters. This
test documents that behaviour and guards against regression.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 tests/github_issues/test_system.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/tests/github_issues/test_system.py b/tests/github_issues/test_system.py
index 886dfc5f..d51c850f 100644
--- a/tests/github_issues/test_system.py
+++ b/tests/github_issues/test_system.py
@@ -164,6 +164,13 @@ def test_yaml_empty_assertion_params(self, github_issues_test_cases):
         assert len(tests) == 1
         assert tests[0].param_sets == []
 
+    def test_yaml_scalar_assertion_params_treated_as_single_param_set(self, github_issues_test_cases):
+        # Resolves: CHEBI:15365 (bare scalar) → wrapped as a single one-element param_set
+        mock = _mock_issue("```yaml\nbabel_tests:\n  Resolves: CHEBI:15365\n```")
+        tests = github_issues_test_cases.get_test_issues_from_issue(mock)
+        assert len(tests) == 1
+        assert tests[0].param_sets == [["CHEBI:15365"]]
+
 
 @pytest.mark.unit
 class TestIssueHasTests:

From 063975d6bc600e1c03b25a1324c66992d72bfd87 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 10 Jun 2026 11:50:28 -0400
Subject: [PATCH 108/126] Simplify assertion loop logic and YAML param
 normalization

Replace `found`-flag tracking in NodeNormTest/NameResTest with a
results-list approach. Extract `_to_list()` helper in
github_issues_test_cases to collapse the two-level str/list
type-dispatch into a single reusable function.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 src/babel_validation/assertions/__init__.py   | 31 +++++++---------
 .../github/github_issues_test_cases.py        | 37 +++++++++----------
 2 files changed, 31 insertions(+), 37 deletions(-)

diff --git a/src/babel_validation/assertions/__init__.py b/src/babel_validation/assertions/__init__.py
index 73e498b7..ccb4d83e 100644
--- a/src/babel_validation/assertions/__init__.py
+++ b/src/babel_validation/assertions/__init__.py
@@ -79,25 +79,23 @@ def test_with_nodenorm(self, param_sets: list[list[str]], nodenorm,
         curies_to_warm = list({p for params in param_sets for p in self.curie_params(params)})
         if curies_to_warm:
             nodenorm.normalize_curies(curies_to_warm)
-        found = False
+        results = []
         for index, params in enumerate(param_sets):
             if not params:
-                yield self.failed(f"No parameters in param_set {index} in {label}")
-                found = True
+                results.append(self.failed(f"No parameters in param_set {index} in {label}"))
                 continue
             invalid = [c for c in self.curie_params(params) if not self._CURIE_RE.match(c)]
             if invalid:
-                yield self.failed(
+                results.append(self.failed(
                     f"Malformed CURIE(s) {invalid} in param_set {index} in {label}: "
                     f"expected format PREFIX:LOCAL_ID (e.g. CHEBI:15365)"
-                )
-                found = True
+                ))
                 continue
-            for result in self.test_param_set(params, nodenorm, label):
-                found = True
-                yield result
-        if not found:
+            results.extend(self.test_param_set(params, nodenorm, label))
+        if not results:
             yield self.failed(f"No test results returned in {label}")
+            return
+        yield from results
 
     def test_param_set(self, params: list[str], nodenorm, label: str = "") -> Iterator[TestResult]:
         """Override this to implement the assertion. Called once per param_set.
@@ -126,17 +124,16 @@ def test_with_nameres(self, param_sets: list[list[str]], nodenorm, nameres,
         if not param_sets:
             yield self.failed(f"No parameters provided in {label}")
             return
-        found = False
+        results = []
         for index, params in enumerate(param_sets):
             if not params:
-                yield self.failed(f"No parameters in param_set {index} in {label}")
-                found = True
+                results.append(self.failed(f"No parameters in param_set {index} in {label}"))
                 continue
-            for result in self.test_param_set(params, nodenorm, nameres, pass_if_found_in_top, label):
-                found = True
-                yield result
-        if not found:
+            results.extend(self.test_param_set(params, nodenorm, nameres, pass_if_found_in_top, label))
+        if not results:
             yield self.failed(f"No test results returned in {label}")
+            return
+        yield from results
 
     def test_param_set(self, params: list[str], nodenorm, nameres,
                        pass_if_found_in_top: int, label: str = "") -> Iterator[TestResult]:
diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index 0e0decc5..33734d9d 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -41,6 +41,15 @@
 _logger = logging.getLogger(__name__)
 
 
+def _to_list(value, context: str) -> list:
+    """Normalize a YAML value that may be a bare string or a list; raise on anything else."""
+    if isinstance(value, str):
+        return [value]
+    if isinstance(value, list):
+        return value
+    raise ValueError(f"{context}: expected str or list, got {type(value).__name__}")
+
+
 class GitHubIssueTest:
     """Represents one assertion extracted from a GitHub issue body — an assertion name paired with a list of param_sets to evaluate."""
 
@@ -183,26 +192,14 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
                             f"YAML block in issue {github_issue_id}: assertion '{assertion}' has a null "
                             f"param list — use an empty list [] or remove the entry"
                         )
-                    if isinstance(original_param_sets, str):
-                        normalized_param_sets = [original_param_sets]
-                    elif isinstance(original_param_sets, list):
-                        normalized_param_sets = original_param_sets
-                    else:
-                        raise ValueError(
-                            f"YAML block in issue {github_issue_id}: assertion '{assertion}' must be a "
-                            f"string or list, got {type(original_param_sets).__name__}"
-                        )
-                    param_sets = []
-                    for param_set in normalized_param_sets:
-                        if isinstance(param_set, str):
-                            param_sets.append([param_set])
-                        elif isinstance(param_set, list):
-                            param_sets.append(param_set)
-                        else:
-                            raise ValueError(
-                                f"YAML block in issue {github_issue_id}: assertion '{assertion}' contains "
-                                f"an unsupported parameter set type {type(param_set).__name__}"
-                            )
+                    normalized = _to_list(
+                        original_param_sets,
+                        f"YAML block in issue {github_issue_id}: assertion '{assertion}'"
+                    )
+                    param_sets = [
+                        _to_list(ps, f"YAML block in issue {github_issue_id}: assertion '{assertion}' param_set")
+                        for ps in normalized
+                    ]
                     testrows.append(GitHubIssueTest(github_issue_id, github_issue, assertion, param_sets))
 
         return testrows

From e36334f6a014b3583776ce53e040b51b4d1e6a9a Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 10 Jun 2026 11:50:37 -0400
Subject: [PATCH 109/126] Simplify test config cleanup and GitHub issue caching

Extract _silent_unlink() in tests/conftest.py to replace three
copy-paste try/unlink/except blocks. In github_issues/conftest.py:
fix _issue_id() to use issue.repository.full_name instead of parsing
html_url, extract _record_auth_error() to deduplicate 401 handling,
and add _cached_ids sentinel to avoid repeated JSON file reads during
collection.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 tests/conftest.py               | 22 ++++++++++------------
 tests/github_issues/conftest.py | 27 +++++++++++++++++++--------
 2 files changed, 29 insertions(+), 20 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 3ac5a7c6..58d9925d 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -28,26 +28,24 @@ def get_targets_ini_path(config):
     return config_path
 
 
+def _silent_unlink(path: str) -> None:
+    try:
+        os.unlink(path)
+    except FileNotFoundError:
+        pass
+
+
 def pytest_configure(config):
     # Delete the Google Sheet CSV cache at the start of each run so tests always
     # use a fresh download. Only the controller does this — xdist workers skip it
     # so they can share the cache file written by the controller.
     if not os.environ.get('PYTEST_XDIST_WORKER'):
         for f in glob.glob(os.path.join(tempfile.gettempdir(), 'babel_validation_gsheet_*.csv')):
-            try:
-                os.unlink(f)
-            except FileNotFoundError:
-                pass
-            try:
-                os.unlink(f.removesuffix('.csv') + '.lock')
-            except FileNotFoundError:
-                pass
+            _silent_unlink(f)
+            _silent_unlink(f.removesuffix('.csv') + '.lock')
         tmpdir = tempfile.gettempdir()
         for name in ('babel_validation_issues_cache.json', 'babel_validation_issues_cache.lock'):
-            try:
-                os.unlink(os.path.join(tmpdir, name))
-            except FileNotFoundError:
-                pass
+            _silent_unlink(os.path.join(tmpdir, name))
 
 
 def pytest_addoption(parser):
diff --git a/tests/github_issues/conftest.py b/tests/github_issues/conftest.py
index 1684d2a5..83ceb330 100644
--- a/tests/github_issues/conftest.py
+++ b/tests/github_issues/conftest.py
@@ -58,35 +58,46 @@ def _get_github_issues_test_cases() -> GitHubIssuesTestCases:
 
 def _issue_id(issue: Issue.Issue) -> str:
     """Derive a test ID from an issue without making extra API calls."""
-    parts = issue.html_url.split('/')
-    return f"{parts[3]}/{parts[4]}#{issue.number}"
+    return f"{issue.repository.full_name}#{issue.number}"
+
+
+def _record_auth_error(e: GithubException) -> None:
+    global _github_auth_error
+    _github_auth_error = f"{_AUTH_HELP}\n\nOriginal error: {e}"
+
+
+_cached_ids: list[str] | None = None
 
 
 def _get_all_test_issue_ids() -> list[str]:
     """Return IDs of all issues that contain tests, using a file-based cache."""
-    global _github_auth_error
+    global _cached_ids
+    if _cached_ids is not None:
+        return _cached_ids
     with FileLock(_LOCK_FILE):
         if _CACHE_FILE.exists():
             try:
-                return json.loads(_CACHE_FILE.read_text())
+                _cached_ids = json.loads(_CACHE_FILE.read_text())
+                return _cached_ids
             except (json.JSONDecodeError, OSError):
                 _CACHE_FILE.unlink(missing_ok=True)
         try:
             issues = list(_get_github_issues_test_cases().get_issues_with_tests())
         except GithubException as e:
             if e.status == 401:
-                _github_auth_error = f"{_AUTH_HELP}\n\nOriginal error: {e}"
-                return [_AUTH_ERROR_ID]
+                _record_auth_error(e)
+                _cached_ids = [_AUTH_ERROR_ID]
+                return _cached_ids
             raise
         ids = [_issue_id(i) for i in issues]
         for issue, id_ in zip(issues, ids):
             _fetched_issues_cache[id_] = issue
         _CACHE_FILE.write_text(json.dumps(ids))
+        _cached_ids = ids
         return ids
 
 
 def pytest_generate_tests(metafunc):
-    global _github_auth_error
     if "github_issue_id" not in metafunc.fixturenames:
         return
     issue_id_filter = metafunc.config.getoption("issue", default=[])
@@ -95,7 +106,7 @@ def pytest_generate_tests(metafunc):
             issues = _get_github_issues_test_cases().get_issues_by_ids(issue_id_filter)
         except GithubException as e:
             if e.status == 401:
-                _github_auth_error = f"{_AUTH_HELP}\n\nOriginal error: {e}"
+                _record_auth_error(e)
                 metafunc.parametrize("github_issue_id", [_AUTH_ERROR_ID], ids=[_AUTH_ERROR_ID])
                 return
             raise

From e1ee783359a29545fca56583cfe089c49aae3771 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 10 Jun 2026 12:36:18 -0400
Subject: [PATCH 110/126] Keep open-issue assertion failures inside the xfail
 family

pytest-subtests failures do not respect the xfail marker on the parent
test, so an open issue with failing assertions was reported as real
SUBFAILED failures (failing the whole run) even though the outer test
xfailed. For open issues, collect failing assertion messages instead of
asserting inside subtests, and xfail with a summary that includes the
first few failure messages. Closed issues keep granular subtest
reporting, and a fully-passing open issue still surfaces as a strict
XPASS failure signalling the issue may be closeable.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---
 tests/github_issues/test_github_issues.py | 28 +++++++++++++++--------
 1 file changed, 19 insertions(+), 9 deletions(-)

diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index a7820035..9ff44aec 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -38,7 +38,7 @@ def test_github_issue(request, target_info, github_issue_id, github_issue, githu
         ))
 
     count_subtests = 0
-    count_subtests_failed = 0
+    failed_messages = []
     for test_issue in tests:
         results_nodenorm = test_issue.test_with_nodenorm(nodenorm)
         results_nameres = test_issue.test_with_nameres(nodenorm, nameres)
@@ -46,13 +46,20 @@ def test_github_issue(request, target_info, github_issue_id, github_issue, githu
         for result in itertools.chain(results_nodenorm, results_nameres):
             count_subtests += 1
 
+            if is_open:
+                # Don't assert inside subtests for open issues: subtest failures
+                # don't respect the xfail marker on the parent test, so they would
+                # be reported as real failures. Collect them and xfail below instead.
+                if result.status == TestStatus.Failed:
+                    failed_messages.append(f"{github_issue_id} ({github_issue.state}): {result.message}")
+                continue
+
             with subtests.test(msg=github_issue_id):
                 match result:
                     case TestResult(status=TestStatus.Passed, message=message):
                         assert True, f"{github_issue_id} ({github_issue.state}): {message}"
 
                     case TestResult(status=TestStatus.Failed, message=message):
-                        count_subtests_failed += 1
                         assert False, f"{github_issue_id} ({github_issue.state}): {message}"
 
                     case TestResult(status=TestStatus.Skipped, message=message):
@@ -62,16 +69,19 @@ def test_github_issue(request, target_info, github_issue_id, github_issue, githu
                         assert False, f"Unknown result from {github_issue_id}: {result}"
 
     # For open issues: xfail so the result stays in the xfail family.
-    # - Some subtests failed → xfail with a count summary (expected outcome).
-    # - All subtests passed  → the xfail marker added above makes this XPASS,
+    # - Some assertions failed → xfail with a count summary (expected outcome).
+    # - All assertions passed  → the xfail marker added above makes this XPASS,
     #   which (strict=True) reports as a failure and signals the issue is closeable.
-    # - No subtests ran      → xfail as a configuration error.
+    # - No assertions ran      → xfail as a configuration error.
     if is_open:
         if count_subtests == 0:
             pytest.xfail(f"Open issue {github_issue_id} produced no test results — check assertion configuration")
-        elif count_subtests_failed > 0:
-            pct = count_subtests_failed / count_subtests
+        elif failed_messages:
+            pct = len(failed_messages) / count_subtests
+            details = "\n".join(failed_messages[:5])
+            if len(failed_messages) > 5:
+                details += f"\n... and {len(failed_messages) - 5} more"
             pytest.xfail(
-                f"Open issue {github_issue_id} has {count_subtests_failed:,} failing subtests "
-                f"out of {count_subtests:,} ({pct:.0%})"
+                f"Open issue {github_issue_id} has {len(failed_messages):,} failing assertions "
+                f"out of {count_subtests:,} ({pct:.0%}):\n{details}"
             )

From adb7829d4351ad13e17642dd94d52e8ae9a6711a Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 10 Jun 2026 12:47:25 -0400
Subject: [PATCH 111/126] Make the {{BabelTest|...}} wiki marker
 case-insensitive

Assertion names were already case-insensitive, but the wiki marker
regex matched '{{BabelTest' exactly, so '{{babeltest|...}}' was
silently ignored. Match the marker case-insensitively, document it,
and add unit tests.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---
 src/babel_validation/assertions/README.md     |  2 +-
 src/babel_validation/assertions/gen_docs.py   |  2 +-
 .../github/github_issues_test_cases.py        | 31 ++++++++++---------
 tests/github_issues/test_system.py            | 18 +++++++++++
 4 files changed, 36 insertions(+), 17 deletions(-)

diff --git a/src/babel_validation/assertions/README.md b/src/babel_validation/assertions/README.md
index 813394bb..9cc4ef7d 100644
--- a/src/babel_validation/assertions/README.md
+++ b/src/babel_validation/assertions/README.md
@@ -24,7 +24,7 @@ babel_tests:
 ```
 ````
 
-Assertion names are case-insensitive.
+Assertion names are case-insensitive, as is the `{{BabelTest|...}}` marker itself.
 
 ## Param Sets
 
diff --git a/src/babel_validation/assertions/gen_docs.py b/src/babel_validation/assertions/gen_docs.py
index b6e90270..c5a77a43 100644
--- a/src/babel_validation/assertions/gen_docs.py
+++ b/src/babel_validation/assertions/gen_docs.py
@@ -39,7 +39,7 @@
 ```
 ````
 
-Assertion names are case-insensitive.
+Assertion names are case-insensitive, as is the `{{BabelTest|...}}` marker itself.
 
 ## Param Sets
 
diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index 33734d9d..190f94db 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -95,7 +95,9 @@ class GitHubIssuesTestCases:
     - A closed issue has test cases that are now failing (and so should be reopened).
     """
 
-    _BABELTEST_RE = re.compile(r'{{BabelTest\|.*?}}')
+    # Case-insensitive, matching the case-insensitivity of assertion names.
+    # Group 1 captures everything between '{{BabelTest|' and '}}'.
+    _BABELTEST_RE = re.compile(r'{{BabelTest\|(.*?)}}', re.IGNORECASE)
     _BABELTEST_YAML_RE = re.compile(r'```yaml\s+babel_tests:\s+.*?\s+```', re.DOTALL)
 
     def __init__(self, github_token: str, github_repositories):
@@ -154,20 +156,19 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
         # Look for BabelTest syntax.
         testrows = []
 
-        babeltest_matches = re.findall(self._BABELTEST_RE, github_issue.body)
-        if babeltest_matches:
-            for match in babeltest_matches:
-                self.logger.info("Found BabelTest in issue %s: %s", github_issue_id, match)
-
-                # Figure out parameters.
-                test_string = match.removeprefix("{{BabelTest|").removesuffix("}}")
-                params = test_string.split("|")
-                if not params or not params[0]:
-                    raise ValueError(f"Missing assertion name in BabelTest in issue {github_issue_id}: {match}")
-                # Wiki syntax: params[0] is the assertion name; params[1:] form a single
-                # param_set (may be empty for assertions like Needed), so param_sets is a
-                # one-element list: [params[1:]].
-                testrows.append(GitHubIssueTest(github_issue_id, github_issue, params[0], [params[1:]]))
+        for babeltest_match in self._BABELTEST_RE.finditer(github_issue.body):
+            match = babeltest_match.group(0)
+            self.logger.info("Found BabelTest in issue %s: %s", github_issue_id, match)
+
+            # Figure out parameters.
+            test_string = babeltest_match.group(1)
+            params = test_string.split("|")
+            if not params or not params[0]:
+                raise ValueError(f"Missing assertion name in BabelTest in issue {github_issue_id}: {match}")
+            # Wiki syntax: params[0] is the assertion name; params[1:] form a single
+            # param_set (may be empty for assertions like Needed), so param_sets is a
+            # one-element list: [params[1:]].
+            testrows.append(GitHubIssueTest(github_issue_id, github_issue, params[0], [params[1:]]))
 
         babeltest_yaml_matches = re.findall(self._BABELTEST_YAML_RE, github_issue.body)
         if babeltest_yaml_matches:
diff --git a/tests/github_issues/test_system.py b/tests/github_issues/test_system.py
index d51c850f..202eafa8 100644
--- a/tests/github_issues/test_system.py
+++ b/tests/github_issues/test_system.py
@@ -172,6 +172,24 @@ def test_yaml_scalar_assertion_params_treated_as_single_param_set(self, github_i
         assert tests[0].param_sets == [["CHEBI:15365"]]
 
 
+@pytest.mark.unit
+class TestWikiMarkerCaseInsensitivity:
+    """The {{BabelTest|...}} marker is case-insensitive, like assertion names."""
+
+    @pytest.mark.parametrize("marker", ["BabelTest", "babeltest", "BABELTEST", "Babeltest"])
+    def test_wiki_marker_any_case_parsed(self, github_issues_test_cases, marker):
+        mock = _mock_issue(f"{{{{{marker}|Resolves|CHEBI:15365}}}}")
+        tests = github_issues_test_cases.get_test_issues_from_issue(mock)
+        assert len(tests) == 1
+        assert tests[0].assertion == "Resolves"
+        assert tests[0].param_sets == [["CHEBI:15365"]]
+
+    def test_wiki_marker_any_case_detected(self, github_issues_test_cases):
+        assert github_issues_test_cases.issue_has_tests(
+            _mock_issue("{{babeltest|Resolves|CHEBI:12345}}")
+        ) is True
+
+
 @pytest.mark.unit
 class TestIssueHasTests:
     """Documents issue_has_tests() behaviour for various body contents."""

From 03e0c6b7158883bec758defcc25acd2ab5c669a0 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 10 Jun 2026 13:30:51 -0400
Subject: [PATCH 112/126] Run GitHub-issue unit tests without a GITHUB_TOKEN

The system tests in test_system.py only parse mocked issue bodies and
never call the GitHub API, but the shared github_issues_test_cases
fixture skipped them when GITHUB_TOKEN was unset. Override the fixture
locally with a dummy token so 'pytest -m unit' works anywhere.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---
 tests/github_issues/test_system.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/tests/github_issues/test_system.py b/tests/github_issues/test_system.py
index 202eafa8..16c42ab9 100644
--- a/tests/github_issues/test_system.py
+++ b/tests/github_issues/test_system.py
@@ -5,12 +5,20 @@
 import yaml
 
 from src.babel_validation.core.testrow import TestStatus
+from src.babel_validation.sources.github.github_issues_test_cases import GitHubIssuesTestCases
 
 pytestmark = pytest.mark.unit
 
 INVALID_NAME = "NotARealAssertion"
 
 
+@pytest.fixture
+def github_issues_test_cases():
+    """Override the conftest fixture: these unit tests never hit the GitHub API,
+    so build the parser with a dummy token rather than requiring GITHUB_TOKEN."""
+    return GitHubIssuesTestCases("unit-test-dummy-token", ["test-org/test-repo"])
+
+
 def _mock_issue(body: str, number: int = 999) -> MagicMock:
     """Minimal mock GitHub Issue for get_test_issues_from_issue()."""
     issue = MagicMock()

From e3220407442d40b5bb49dd878bfe03c5bb739c8b Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 10 Jun 2026 13:32:12 -0400
Subject: [PATCH 113/126] Validate CURIEs before warming the NodeNorm cache

Malformed CURIEs were rejected per-param_set, but only after the
cache-warming normalize_curies() call had already sent them to the
NodeNorm API. Validate all param_sets first and exclude invalid ones
from the warm-up request.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---
 src/babel_validation/assertions/__init__.py | 29 ++++++++++++++-------
 1 file changed, 20 insertions(+), 9 deletions(-)

diff --git a/src/babel_validation/assertions/__init__.py b/src/babel_validation/assertions/__init__.py
index ccb4d83e..cce1d851 100644
--- a/src/babel_validation/assertions/__init__.py
+++ b/src/babel_validation/assertions/__init__.py
@@ -74,22 +74,33 @@ def test_with_nodenorm(self, param_sets: list[list[str]], nodenorm,
         if not param_sets:
             yield self.failed(f"No parameters provided in {label}")
             return
-        # warm the cache only for params that are CURIEs (deduplicated); skip if empty
-        # (normalize_curies raises ValueError on an empty list)
-        curies_to_warm = list({p for params in param_sets for p in self.curie_params(params)})
-        if curies_to_warm:
-            nodenorm.normalize_curies(curies_to_warm)
-        results = []
+        # Validate each param_set up front so malformed CURIEs are never sent to
+        # NodeNorm — not even in the cache-warming call below.
+        failures: dict[int, TestResult] = {}
         for index, params in enumerate(param_sets):
             if not params:
-                results.append(self.failed(f"No parameters in param_set {index} in {label}"))
+                failures[index] = self.failed(f"No parameters in param_set {index} in {label}")
                 continue
             invalid = [c for c in self.curie_params(params) if not self._CURIE_RE.match(c)]
             if invalid:
-                results.append(self.failed(
+                failures[index] = self.failed(
                     f"Malformed CURIE(s) {invalid} in param_set {index} in {label}: "
                     f"expected format PREFIX:LOCAL_ID (e.g. CHEBI:15365)"
-                ))
+                )
+        # warm the cache only for params that are CURIEs (deduplicated); skip if empty
+        # (normalize_curies raises ValueError on an empty list)
+        curies_to_warm = list({
+            p
+            for index, params in enumerate(param_sets)
+            if index not in failures
+            for p in self.curie_params(params)
+        })
+        if curies_to_warm:
+            nodenorm.normalize_curies(curies_to_warm)
+        results = []
+        for index, params in enumerate(param_sets):
+            if index in failures:
+                results.append(failures[index])
                 continue
             results.extend(self.test_param_set(params, nodenorm, label))
         if not results:

From a9ec8e472ce49ef13c8c636e8f3bb22180ba5c53 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 10 Jun 2026 14:32:42 -0400
Subject: [PATCH 114/126] Expire the Google Sheet CSV cache after an hour

pytest deletes the tempdir cache at the start of each run, but other
consumers (csv-to-babeltests, library users) would read a stale cache
indefinitely. Treat cached downloads older than CACHE_TTL_SECONDS
(1 hour) as expired and re-download.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---
 .../sources/google_sheets/google_sheet_test_cases.py      | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py b/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py
index ab167fc6..935b019e 100644
--- a/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py
+++ b/src/babel_validation/sources/google_sheets/google_sheet_test_cases.py
@@ -6,6 +6,7 @@
 import hashlib
 import io
 import tempfile
+import time
 from collections import Counter
 from pathlib import Path
 
@@ -25,6 +26,11 @@ class GoogleSheetTestCases:
     def __str__(self):
         return f"Google Sheet Test Cases ({len(self.rows)} test cases from {self.google_sheet_id})"
 
+    # How long a cached download stays valid. pytest deletes the cache at the
+    # start of every run (see tests/conftest.py), so this TTL mainly protects
+    # other consumers (e.g. csv-to-babeltests) from reading stale data forever.
+    CACHE_TTL_SECONDS = 3600
+
     def __init__(self, google_sheet_id="11zebx8Qs1Tc3ShQR9nh4HRW8QSoo8k65w_xIaftN0no"):
         """ Create a Google Sheet test case.
 
@@ -38,7 +44,7 @@ def __init__(self, google_sheet_id="11zebx8Qs1Tc3ShQR9nh4HRW8QSoo8k65w_xIaftN0no
         lock_file = cache_file.with_suffix(".lock")
 
         with FileLock(lock_file):
-            if cache_file.exists():
+            if cache_file.exists() and time.time() - cache_file.stat().st_mtime < self.CACHE_TTL_SECONDS:
                 self.csv_content = cache_file.read_text(encoding="utf-8")
             else:
                 csv_url = f"https://docs.google.com/spreadsheets/d/{google_sheet_id}/gviz/tq?tqx=out:csv&sheet=Tests"

From 7e58ba78dc7a2e3df9838ad6a53a1d8de5b541cb Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 10 Jun 2026 14:33:16 -0400
Subject: [PATCH 115/126] Limit bare pytest collection to the tests directory

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---
 pyproject.toml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 3b5bacb4..0d8c88a8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,6 +38,9 @@ build-backend = "hatchling.build"
 packages = ["src"]
 
 [tool.pytest.ini_options]
+# Without testpaths, a bare `pytest` would also scan the website directories
+# (including node_modules) during collection.
+testpaths = ["tests"]
 timeout = 300
 markers = [
     "unit: unit tests that do not require network access",

From af19a1efd8517dc78e6e603f6dbdee3cb1bb18f5 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 10 Jun 2026 14:33:47 -0400
Subject: [PATCH 116/126] Correct Repositories comment in targets.ini

The GitHub issue tests always read Repositories from [DEFAULT];
per-environment overrides are not implemented.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---
 tests/targets.ini | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/targets.ini b/tests/targets.ini
index be12baf3..1484ce09 100644
--- a/tests/targets.ini
+++ b/tests/targets.ini
@@ -15,7 +15,8 @@
 NameResLimit = 20
 NameResXFailIfInTop = 5
 # GitHub repositories to scan for embedded BabelTest assertions.
-# One "org/repo" per line. Can be overridden per-environment section if needed.
+# One "org/repo" per line. Read from this DEFAULT section only — the GitHub
+# issue tests do not support per-environment overrides.
 Repositories =
     NCATSTranslator/Babel
     NCATSTranslator/NodeNormalization

From 0a202879e017fa370be765011deaa525c31c1f6e Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 10 Jun 2026 17:14:32 -0400
Subject: [PATCH 117/126] Skip GitHub issue fetch when -m deselects the test

pytest_generate_tests for test_github_issue fetches issues from GitHub at
collection time. pytest applies -m marker deselection only *after* generation,
so running 'pytest -m unit' (as CI does) would still hit the GitHub search API
across every configured repo before deselecting the test.

Evaluate the marker expression ourselves against the test's own markers and,
when it would deselect this test, parametrize an empty set instead of fetching.
This keeps unit-only runs offline.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 tests/github_issues/conftest.py | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/tests/github_issues/conftest.py b/tests/github_issues/conftest.py
index 83ceb330..ccfd8035 100644
--- a/tests/github_issues/conftest.py
+++ b/tests/github_issues/conftest.py
@@ -97,9 +97,38 @@ def _get_all_test_issue_ids() -> list[str]:
         return ids
 
 
+def _deselected_by_markexpr(metafunc) -> bool:
+    """True if a -m marker expression is active that would deselect this test.
+
+    Parametrizing ``test_github_issue`` fetches issues from GitHub at collection
+    time. When the user runs e.g. ``pytest -m unit`` that test is deselected
+    anyway (it carries no ``unit`` marker), so we must avoid the network round
+    trip. pytest only applies ``-m`` deselection *after* generation, so we
+    evaluate the expression ourselves against the markers on the test.
+    """
+    markexpr = metafunc.config.getoption("markexpr")
+    if not markexpr:
+        return False
+    try:
+        from _pytest.mark.expression import Expression
+    except ImportError:
+        # Internal API moved; fall back to the (network-using) default.
+        return False
+    own_markers = {m.name for m in metafunc.definition.iter_markers()}
+    try:
+        return not Expression.compile(markexpr).evaluate(lambda name: name in own_markers)
+    except Exception:
+        # Unparseable expression — let pytest handle it; don't suppress tests.
+        return False
+
+
 def pytest_generate_tests(metafunc):
     if "github_issue_id" not in metafunc.fixturenames:
         return
+    if _deselected_by_markexpr(metafunc):
+        # Skip the GitHub fetch entirely; this test won't run under this -m filter.
+        metafunc.parametrize("github_issue_id", [], ids=[])
+        return
     issue_id_filter = metafunc.config.getoption("issue", default=[])
     if issue_id_filter:
         try:

From 2a3085a0725c9cb167c343a00608f5e027ebaf78 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 10 Jun 2026 17:14:41 -0400
Subject: [PATCH 118/126] Enforce 2+ CURIE arity in
 ResolvesWith/DoesNotResolveWith
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Both assertions document 'Two or more CURIEs per param_set' but never checked.
A single-CURIE ResolvesWith passed vacuously (canonical id == itself) while a
single-CURIE DoesNotResolveWith always failed (one canonical id) — both silent
authoring traps. Fail loudly with a clear message instead, matching HasLabel
and SearchByName. Adds unit coverage for the too-few-params case.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 src/babel_validation/assertions/nodenorm.py | 14 +++++++++++
 tests/github_issues/test_system.py          | 28 +++++++++++++++++++++
 2 files changed, 42 insertions(+)

diff --git a/src/babel_validation/assertions/nodenorm.py b/src/babel_validation/assertions/nodenorm.py
index 3e999999..58038bdf 100644
--- a/src/babel_validation/assertions/nodenorm.py
+++ b/src/babel_validation/assertions/nodenorm.py
@@ -73,6 +73,13 @@ class ResolvesWithHandler(NodeNormTest):
 
     def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                        label: str = "") -> Iterator[TestResult]:
+        if len(params) < 2:
+            yield self.failed(
+                f"ResolvesWith requires at least two CURIEs per param_set in {label}, "
+                f"but got {len(params)}: {params}"
+            )
+            return
+
         first_good, results = _compare_resolutions(params, nodenorm)
 
         if first_good is None:
@@ -112,6 +119,13 @@ class DoesNotResolveWithHandler(NodeNormTest):
 
     def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
                        label: str = "") -> Iterator[TestResult]:
+        if len(params) < 2:
+            yield self.failed(
+                f"DoesNotResolveWith requires at least two CURIEs per param_set in {label}, "
+                f"but got {len(params)}: {params}"
+            )
+            return
+
         first_good, results = _compare_resolutions(params, nodenorm)
 
         # Every CURIE must resolve — an unresolved CURIE is a configuration error.
diff --git a/tests/github_issues/test_system.py b/tests/github_issues/test_system.py
index 16c42ab9..935d5ff8 100644
--- a/tests/github_issues/test_system.py
+++ b/tests/github_issues/test_system.py
@@ -107,6 +107,34 @@ def test_searchbyname_too_many_params(self, github_issues_test_cases):
         assert "exactly two" in results[0].message
 
 
+@pytest.mark.unit
+class TestTooFewParams:
+    """Comparison assertions require 2+ CURIEs; a single CURIE must fail loudly,
+    not pass (ResolvesWith) or fail (DoesNotResolveWith) vacuously."""
+
+    def _results(self, fixture, wiki_syntax):
+        mock = _mock_issue(wiki_syntax)
+        tests = fixture.get_test_issues_from_issue(mock)
+        assert len(tests) == 1
+        return list(tests[0].test_with_nodenorm(MagicMock()))
+
+    def test_resolveswith_single_curie_fails(self, github_issues_test_cases):
+        results = self._results(
+            github_issues_test_cases, "{{BabelTest|ResolvesWith|CHEBI:15365}}"
+        )
+        assert len(results) == 1
+        assert results[0].status == TestStatus.Failed
+        assert "at least two" in results[0].message
+
+    def test_doesnotresolvewith_single_curie_fails(self, github_issues_test_cases):
+        results = self._results(
+            github_issues_test_cases, "{{BabelTest|DoesNotResolveWith|CHEBI:15365}}"
+        )
+        assert len(results) == 1
+        assert results[0].status == TestStatus.Failed
+        assert "at least two" in results[0].message
+
+
 @pytest.mark.unit
 class TestMalformedYaml:
     """A YAML block that matches the detection regex but is not valid YAML raises yaml.YAMLError."""

From f0c6cb80bee6a169eadf0c4f469bbc1dd29231bd Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 10 Jun 2026 17:14:52 -0400
Subject: [PATCH 119/126] Avoid KeyError in normalize_curie if NodeNorm omits a
 CURIE

normalize_curie indexed the result dict directly while every other code path
uses .get(). NodeNorm normally echoes every requested CURIE (null when
unresolvable), but switch to .get() so an omitted key returns None rather than
raising.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 src/babel_validation/services/nodenorm.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/babel_validation/services/nodenorm.py b/src/babel_validation/services/nodenorm.py
index 742ed848..633f7a4b 100644
--- a/src/babel_validation/services/nodenorm.py
+++ b/src/babel_validation/services/nodenorm.py
@@ -59,7 +59,9 @@ def normalize_curie(self, curie, **params):
         cache_key = (curie, frozenset(params.items()))
         if cache_key in self.cache:
             return self.cache[cache_key]
-        return self.normalize_curies([curie], **params)[curie]
+        # Use .get(): NodeNorm normally echoes every requested CURIE (null when
+        # unresolvable), but don't crash if it ever omits one.
+        return self.normalize_curies([curie], **params).get(curie)
 
     def clear_curie(self, curie):
         keys_to_delete = [k for k in self.cache if k[0] == curie]

From c7b9da94ea97e4348aeee80c89f3d0f471872daa Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 10 Jun 2026 17:14:52 -0400
Subject: [PATCH 120/126] Wire SearchByName top-N from targets.ini
 NameResXFailIfInTop

The NameRes 'found in top N' threshold was hardcoded to the handler default of
5, ignoring NameResXFailIfInTop in targets.ini. Read it from target_info so the
threshold is configurable per environment.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 tests/github_issues/test_github_issues.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/github_issues/test_github_issues.py b/tests/github_issues/test_github_issues.py
index 9ff44aec..32aa5790 100644
--- a/tests/github_issues/test_github_issues.py
+++ b/tests/github_issues/test_github_issues.py
@@ -12,6 +12,9 @@
 def test_github_issue(request, target_info, github_issue_id, github_issue, github_issues_test_cases, subtests):
     nodenorm = CachedNodeNorm.from_url(target_info['NodeNormURL'])
     nameres = CachedNameRes.from_url(target_info['NameResURL'])
+    # NameRes assertions pass if the expected CURIE is in the top N results; N
+    # comes from targets.ini (NameResXFailIfInTop) rather than being hardcoded.
+    pass_if_found_in_top = int(target_info.get('NameResXFailIfInTop', 5))
     tests = github_issues_test_cases.get_test_issues_from_issue(github_issue)
     if not tests:
         pytest.skip(f"No tests found in issue {github_issue}")
@@ -41,7 +44,7 @@ def test_github_issue(request, target_info, github_issue_id, github_issue, githu
     failed_messages = []
     for test_issue in tests:
         results_nodenorm = test_issue.test_with_nodenorm(nodenorm)
-        results_nameres = test_issue.test_with_nameres(nodenorm, nameres)
+        results_nameres = test_issue.test_with_nameres(nodenorm, nameres, pass_if_found_in_top)
 
         for result in itertools.chain(results_nodenorm, results_nameres):
             count_subtests += 1

From 24ed4f454cc823201583a259c3b627d129214346 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 10 Jun 2026 17:57:43 -0400
Subject: [PATCH 121/126] Extract deselected_by_markexpr into a shared helper

Move the marker-expression check out of the github_issues conftest into
tests/_pytest_helpers.py so the Google Sheet test modules can reuse it to defer
their own network-backed parametrization.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 tests/_pytest_helpers.py        | 31 +++++++++++++++++++++++++++++++
 tests/github_issues/conftest.py | 32 +++++---------------------------
 2 files changed, 36 insertions(+), 27 deletions(-)
 create mode 100644 tests/_pytest_helpers.py

diff --git a/tests/_pytest_helpers.py b/tests/_pytest_helpers.py
new file mode 100644
index 00000000..fa84dca4
--- /dev/null
+++ b/tests/_pytest_helpers.py
@@ -0,0 +1,31 @@
+"""Shared pytest helpers for deferring network-backed parametrization.
+
+Several test modules build their parametrization from network sources (the
+Google Sheet, GitHub issues) at collection time. pytest only applies ``-m``
+marker deselection *after* test generation, so a run like ``pytest -m unit``
+would still pay for those fetches before discarding the tests. Evaluating the
+marker expression ourselves lets us skip the fetch when the test won't run.
+"""
+
+
+def deselected_by_markexpr(metafunc) -> bool:
+    """True if an active ``-m`` marker expression would deselect this test.
+
+    Returns False (i.e. "keep it") whenever there is no ``-m`` filter, the
+    internal expression API is unavailable, or the expression can't be parsed —
+    so this never suppresses a test that pytest would otherwise run.
+    """
+    markexpr = metafunc.config.getoption("markexpr")
+    if not markexpr:
+        return False
+    try:
+        from _pytest.mark.expression import Expression
+    except ImportError:
+        # Internal API moved; fall back to the (network-using) default.
+        return False
+    own_markers = {m.name for m in metafunc.definition.iter_markers()}
+    try:
+        return not Expression.compile(markexpr).evaluate(lambda name: name in own_markers)
+    except Exception:
+        # Unparseable expression — let pytest handle it; don't suppress tests.
+        return False
diff --git a/tests/github_issues/conftest.py b/tests/github_issues/conftest.py
index ccfd8035..ec1bdb21 100644
--- a/tests/github_issues/conftest.py
+++ b/tests/github_issues/conftest.py
@@ -10,6 +10,7 @@
 from github import GithubException, Issue
 
 from src.babel_validation.sources.github.github_issues_test_cases import GitHubIssuesTestCases
+from tests._pytest_helpers import deselected_by_markexpr
 
 _github_token = None
 _github_auth_error: str | None = None
@@ -97,36 +98,13 @@ def _get_all_test_issue_ids() -> list[str]:
         return ids
 
 
-def _deselected_by_markexpr(metafunc) -> bool:
-    """True if a -m marker expression is active that would deselect this test.
-
-    Parametrizing ``test_github_issue`` fetches issues from GitHub at collection
-    time. When the user runs e.g. ``pytest -m unit`` that test is deselected
-    anyway (it carries no ``unit`` marker), so we must avoid the network round
-    trip. pytest only applies ``-m`` deselection *after* generation, so we
-    evaluate the expression ourselves against the markers on the test.
-    """
-    markexpr = metafunc.config.getoption("markexpr")
-    if not markexpr:
-        return False
-    try:
-        from _pytest.mark.expression import Expression
-    except ImportError:
-        # Internal API moved; fall back to the (network-using) default.
-        return False
-    own_markers = {m.name for m in metafunc.definition.iter_markers()}
-    try:
-        return not Expression.compile(markexpr).evaluate(lambda name: name in own_markers)
-    except Exception:
-        # Unparseable expression — let pytest handle it; don't suppress tests.
-        return False
-
-
 def pytest_generate_tests(metafunc):
     if "github_issue_id" not in metafunc.fixturenames:
         return
-    if _deselected_by_markexpr(metafunc):
-        # Skip the GitHub fetch entirely; this test won't run under this -m filter.
+    if deselected_by_markexpr(metafunc):
+        # Parametrizing fetches issues from GitHub at collection time. Skip the
+        # network round trip when a -m filter (e.g. `pytest -m unit`) would
+        # deselect this test anyway.
         metafunc.parametrize("github_issue_id", [], ids=[])
         return
     issue_id_filter = metafunc.config.getoption("issue", default=[])

From e9830201d607d9574e33d36458d0bf9a9095497b Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 10 Jun 2026 17:57:45 -0400
Subject: [PATCH 122/126] Defer Google Sheet downloads so -m unit stays offline
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The gsheet and blocklist test modules instantiated GoogleSheetTestCases /
load_blocklist_from_gsheet at import time and parametrized via a module-level
@pytest.mark.parametrize, so every collection — including 'pytest -m unit' —
downloaded the sheets even though those tests aren't unit tests.

Move parametrization into pytest_generate_tests with a lazy, cached fetch, and
skip the fetch entirely when a -m filter would deselect the test. Row IDs
(row=N) and xfail marks are unchanged, so -k 'row=42' still works.

With this, 'pytest -m unit' runs fully offline: ~0.3s and no network, versus
~2.5s and a GitHub + Google Sheet round trip before.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 tests/nameres/test_blocklist.py             | 24 +++++++++++++++---
 tests/nameres/test_nameres_from_gsheet.py   | 28 ++++++++++++++++++---
 tests/nodenorm/test_nodenorm_from_gsheet.py | 28 ++++++++++++++++++---
 3 files changed, 71 insertions(+), 9 deletions(-)

diff --git a/tests/nameres/test_blocklist.py b/tests/nameres/test_blocklist.py
index 7206547d..c1d803d2 100644
--- a/tests/nameres/test_blocklist.py
+++ b/tests/nameres/test_blocklist.py
@@ -4,12 +4,30 @@
 import pytest
 
 from src.babel_validation.sources.google_sheets.blocklist import load_blocklist_from_gsheet
+from tests._pytest_helpers import deselected_by_markexpr
 
-# Parameterize blocklist entries.
-blocklist_entries = load_blocklist_from_gsheet()
+# The blocklist Google Sheet is downloaded lazily in pytest_generate_tests so
+# that runs which deselect these tests (e.g. `pytest -m unit`) never hit the
+# network.
+_blocklist_entries = None
+
+
+def _get_blocklist_entries():
+    global _blocklist_entries
+    if _blocklist_entries is None:
+        _blocklist_entries = load_blocklist_from_gsheet()
+    return _blocklist_entries
+
+
+def pytest_generate_tests(metafunc):
+    if "blocklist_entry" not in metafunc.fixturenames:
+        return
+    if deselected_by_markexpr(metafunc):
+        metafunc.parametrize("blocklist_entry", [])
+        return
+    metafunc.parametrize("blocklist_entry", _get_blocklist_entries())
 
 
-@pytest.mark.parametrize("blocklist_entry", blocklist_entries)
 def test_check_blocklist_entry(target_info, blocklist_entry, categories_include):
     """
     Test whether a NameRes instance has blocked every item from a blocklist.
diff --git a/tests/nameres/test_nameres_from_gsheet.py b/tests/nameres/test_nameres_from_gsheet.py
index 2e4979e8..1b9403f6 100644
--- a/tests/nameres/test_nameres_from_gsheet.py
+++ b/tests/nameres/test_nameres_from_gsheet.py
@@ -2,15 +2,37 @@
 import requests
 import pytest
 from src.babel_validation.sources.google_sheets.google_sheet_test_cases import GoogleSheetTestCases
+from tests._pytest_helpers import deselected_by_markexpr
 
 # Configuration options
 NAMERES_TIMEOUT = 10 # If we don't get a response in 10 seconds, that's a fail.
 
-# We generate a set of tests from the GoogleSheetTestCases.
-gsheet = GoogleSheetTestCases()
+# The Google Sheet is downloaded lazily in pytest_generate_tests so that runs
+# which deselect these tests (e.g. `pytest -m unit`) never hit the network.
+_gsheet = None
+
+
+def _get_gsheet() -> GoogleSheetTestCases:
+    global _gsheet
+    if _gsheet is None:
+        _gsheet = GoogleSheetTestCases()
+    return _gsheet
+
+
+def pytest_generate_tests(metafunc):
+    if "test_row" not in metafunc.fixturenames:
+        return
+    if deselected_by_markexpr(metafunc):
+        metafunc.parametrize("test_row", [])
+        return
+    metafunc.parametrize(
+        "test_row",
+        _get_gsheet().test_rows(
+            'test_nameres_from_gsheet.test_label', test_nodenorm=False, test_nameres=True
+        ),
+    )
 
 
-@pytest.mark.parametrize("test_row", gsheet.test_rows('test_nameres_from_gsheet.test_label', test_nodenorm=False, test_nameres=True))
 def test_label(target_info, test_row, test_category):
     nameres_url = target_info['NameResURL']
     limit = target_info['NameResLimit']
diff --git a/tests/nodenorm/test_nodenorm_from_gsheet.py b/tests/nodenorm/test_nodenorm_from_gsheet.py
index ebf4dfee..057e8a7a 100644
--- a/tests/nodenorm/test_nodenorm_from_gsheet.py
+++ b/tests/nodenorm/test_nodenorm_from_gsheet.py
@@ -2,12 +2,34 @@
 import requests
 import pytest
 from src.babel_validation.sources.google_sheets.google_sheet_test_cases import GoogleSheetTestCases
+from tests._pytest_helpers import deselected_by_markexpr
 
-# We generate a set of tests from the GoogleSheetTestCases.
-gsheet = GoogleSheetTestCases()
+# The Google Sheet is downloaded lazily in pytest_generate_tests so that runs
+# which deselect these tests (e.g. `pytest -m unit`) never hit the network.
+_gsheet = None
+
+
+def _get_gsheet() -> GoogleSheetTestCases:
+    global _gsheet
+    if _gsheet is None:
+        _gsheet = GoogleSheetTestCases()
+    return _gsheet
+
+
+def pytest_generate_tests(metafunc):
+    if "test_row" not in metafunc.fixturenames:
+        return
+    if deselected_by_markexpr(metafunc):
+        metafunc.parametrize("test_row", [])
+        return
+    metafunc.parametrize(
+        "test_row",
+        _get_gsheet().test_rows(
+            'test_nodenorm_from_gsheet.test_row', test_nodenorm=True, test_nameres=False
+        ),
+    )
 
 
-@pytest.mark.parametrize("test_row", gsheet.test_rows('test_nodenorm_from_gsheet.test_row', test_nodenorm=True, test_nameres=False))
 def test_normalization(target_info, test_row, test_category):
     nodenorm_url = target_info['NodeNormURL']
 

From d71ae23025142381ec18f68fd0ae4b78fd0ef151 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 24 Jun 2026 10:44:31 -0400
Subject: [PATCH 123/126] Validate babel_tests YAML shape with clear errors

A `babel_tests:` value that is a list/scalar (not a mapping) previously
crashed with an opaque AttributeError on `.items()`, and a non-string
assertion key (e.g. `123:`) blew up later when `.lower()` was called.
Both now raise a clear ValueError up front, with unit coverage.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 .../sources/github/github_issues_test_cases.py      | 10 ++++++++++
 tests/github_issues/test_system.py                  | 13 +++++++++++++
 2 files changed, 23 insertions(+)

diff --git a/src/babel_validation/sources/github/github_issues_test_cases.py b/src/babel_validation/sources/github/github_issues_test_cases.py
index 190f94db..fa33dab2 100644
--- a/src/babel_validation/sources/github/github_issues_test_cases.py
+++ b/src/babel_validation/sources/github/github_issues_test_cases.py
@@ -184,10 +184,20 @@ def get_test_issues_from_issue(self, github_issue: Issue.Issue) -> list[GitHubIs
                         f"YAML block in issue {github_issue_id} matched the detection pattern "
                         f"but contains no 'babel_tests' top-level key: {match!r}"
                     )
+                if not isinstance(babel_tests, dict):
+                    raise ValueError(
+                        f"YAML block in issue {github_issue_id}: 'babel_tests' must be a mapping of "
+                        f"assertion name to param sets, but got {type(babel_tests).__name__}: {babel_tests!r}"
+                    )
 
                 for assertion, original_param_sets in babel_tests.items():
                     # YAML syntax: each entry under an assertion key becomes one param_set.
                     # A bare string becomes a single-element param_set; a list is used as-is.
+                    if not isinstance(assertion, str):
+                        raise ValueError(
+                            f"YAML block in issue {github_issue_id}: assertion name must be a string, "
+                            f"but got {type(assertion).__name__}: {assertion!r}"
+                        )
                     if original_param_sets is None:
                         raise ValueError(
                             f"YAML block in issue {github_issue_id}: assertion '{assertion}' has a null "
diff --git a/tests/github_issues/test_system.py b/tests/github_issues/test_system.py
index 935d5ff8..dafc93ed 100644
--- a/tests/github_issues/test_system.py
+++ b/tests/github_issues/test_system.py
@@ -207,6 +207,19 @@ def test_yaml_scalar_assertion_params_treated_as_single_param_set(self, github_i
         assert len(tests) == 1
         assert tests[0].param_sets == [["CHEBI:15365"]]
 
+    def test_yaml_babel_tests_as_list_raises(self, github_issues_test_cases):
+        # babel_tests as a list (not a mapping) → clear ValueError, not an AttributeError on .items().
+        mock = _mock_issue("```yaml\nbabel_tests:\n  - Resolves\n```")
+        with pytest.raises(ValueError, match="must be a mapping"):
+            github_issues_test_cases.get_test_issues_from_issue(mock)
+
+    def test_yaml_non_string_assertion_name_raises(self, github_issues_test_cases):
+        # A non-string assertion key (e.g. an integer) → clear ValueError, not a later
+        # AttributeError when .lower() is called on the assertion name.
+        mock = _mock_issue("```yaml\nbabel_tests:\n  123:\n  - CHEBI:15365\n```")
+        with pytest.raises(ValueError, match="assertion name must be a string"):
+            github_issues_test_cases.get_test_issues_from_issue(mock)
+
 
 @pytest.mark.unit
 class TestWikiMarkerCaseInsensitivity:

From add08485e4f3a2d1626ce5523f9888ca7d1e826d Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 24 Jun 2026 10:44:40 -0400
Subject: [PATCH 124/126] Guard against empty NodeNorm type list in assertion
 messages

Resolved-node message formatting indexed result['type'][0] in five
places, which would raise IndexError if NodeNorm ever returned a node
with an empty type list. Route all sites through a NodeNormTest.first_type()
helper and use .get('label', '') for the same robustness.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 src/babel_validation/assertions/__init__.py | 11 ++++++++++-
 src/babel_validation/assertions/nodenorm.py |  8 ++++----
 2 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/src/babel_validation/assertions/__init__.py b/src/babel_validation/assertions/__init__.py
index cce1d851..4ac70edc 100644
--- a/src/babel_validation/assertions/__init__.py
+++ b/src/babel_validation/assertions/__init__.py
@@ -116,10 +116,19 @@ def test_param_set(self, params: list[str], nodenorm, label: str = "") -> Iterat
         """
         raise NotImplementedError
 
+    @staticmethod
+    def first_type(result: dict) -> str:
+        """First Biolink type of a resolved node, or a placeholder if the node has none.
+
+        NodeNorm normally returns a non-empty `type` list, but guard against an empty
+        (or missing) one so message formatting never raises IndexError/KeyError."""
+        types = result.get('type') or []
+        return types[0] if types else 'unknown type'
+
     def resolved_message(self, curie: str, result: dict, nodenorm) -> str:
         """Standard pass-message when a CURIE resolves."""
         return (f"Resolved {curie} to {result['id']['identifier']} "
-                f"({result['type'][0]}, \"{result['id']['label']}\") "
+                f"({self.first_type(result)}, \"{result['id'].get('label', '')}\") "
                 f"with NodeNormalization service {nodenorm}")
 
 
diff --git a/src/babel_validation/assertions/nodenorm.py b/src/babel_validation/assertions/nodenorm.py
index 58038bdf..bcd010a3 100644
--- a/src/babel_validation/assertions/nodenorm.py
+++ b/src/babel_validation/assertions/nodenorm.py
@@ -44,7 +44,7 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
             if not result:
                 yield self.passed(f"Could not resolve {curie} with NodeNormalization service {nodenorm} as expected")
             else:
-                yield self.failed(f"Resolved {curie} to {result['id']['identifier']} ({result['type'][0]}, \"{result['id']['label']}\") with NodeNormalization service {nodenorm}, but expected not to resolve")
+                yield self.failed(f"Resolved {curie} to {result['id']['identifier']} ({self.first_type(result)}, \"{result['id'].get('label', '')}\") with NodeNormalization service {nodenorm}, but expected not to resolve")
 
 
 def _compare_resolutions(
@@ -100,9 +100,9 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
             else:
                 yield self.failed(
                     f"Resolved {curie} to {result['id']['identifier']} "
-                    f"({result['type'][0]}, \"{result['id'].get('label', '')}\"), but expected "
+                    f"({self.first_type(result)}, \"{result['id'].get('label', '')}\"), but expected "
                     f"{canonical_id} "
-                    f"({first_good['type'][0]}, \"{first_good['id']['label']}\") on {nodenorm}"
+                    f"({self.first_type(first_good)}, \"{first_good['id'].get('label', '')}\") on {nodenorm}"
                 )
 
 
@@ -146,7 +146,7 @@ def test_param_set(self, params: list[str], nodenorm: CachedNodeNorm,
             yield self.failed(
                 f"All CURIEs {params} resolved to the same result "
                 f"{shared['id']['identifier']} "
-                f"({shared['type'][0]}, \"{shared['id']['label']}\") on {nodenorm}, "
+                f"({self.first_type(shared)}, \"{shared['id'].get('label', '')}\") on {nodenorm}, "
                 f"but expected them to resolve differently"
             )
         else:

From c0ddd7b3d7d4010a118ef48140be64271e551f51 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Wed, 24 Jun 2026 10:44:40 -0400
Subject: [PATCH 125/126] Use a module-local YAML dumper in csv_to_babeltests

Importing the tool registered the _FlowList representer on the global
yaml.SafeDumper, changing YAML output process-wide. Move it onto a local
_BabelTestDumper subclass; emitter output is unchanged.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 src/babel_validation/tools/csv_to_babeltests.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/src/babel_validation/tools/csv_to_babeltests.py b/src/babel_validation/tools/csv_to_babeltests.py
index 668456d3..565f23f0 100644
--- a/src/babel_validation/tools/csv_to_babeltests.py
+++ b/src/babel_validation/tools/csv_to_babeltests.py
@@ -36,7 +36,7 @@
 # --- YAML emission ---------------------------------------------------------
 
 class _FlowList(list):
-    """List subclass that yaml.safe_dump emits in inline flow style."""
+    """List subclass that _BabelTestDumper emits in inline flow style."""
 
 
 def _represent_flow_list(dumper, data):
@@ -45,7 +45,12 @@ def _represent_flow_list(dumper, data):
     )
 
 
-yaml.SafeDumper.add_representer(_FlowList, _represent_flow_list)
+class _BabelTestDumper(yaml.SafeDumper):
+    """Module-local dumper so the _FlowList representer doesn't mutate the global
+    yaml.SafeDumper (which would change YAML output process-wide for other code)."""
+
+
+_BabelTestDumper.add_representer(_FlowList, _represent_flow_list)
 
 
 # --- Data structures -------------------------------------------------------
@@ -182,8 +187,9 @@ def emit_yaml(
             for assertion, entries in blocks.items()
         }
     }
-    body = yaml.safe_dump(
+    body = yaml.dump(
         data,
+        Dumper=_BabelTestDumper,
         sort_keys=False,
         default_flow_style=False,
         allow_unicode=True,

From 1adf1941ace32c4cebf8a3cb076e584a64ce0b9b Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@ggvaidya.com>
Date: Fri, 26 Jun 2026 01:09:28 -0400
Subject: [PATCH 126/126] Document testing/repo gotchas in CLAUDE.md

Record the non-obvious things: `-m unit` is the offline CI suite and
network-backed modules defer fetches via deselected_by_markexpr; src/ is
importable thanks to the hatch wheel packaging; black isn't strictly
enforced; and commits sign through 1Password's SSH agent. Also fix the
`-k "row=42"` example, which pytest's expression parser rejects.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 CLAUDE.md | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/CLAUDE.md b/CLAUDE.md
index c911bbbb..c9f814bc 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -20,7 +20,14 @@ pytest --target all                    # Run against all targets in targets.ini
 pytest --category "Unit Tests"         # Filter by Google Sheet category
 pytest --category-exclude "Slow"       # Exclude a category
 pytest tests/nodenorm/test_nodenorm_from_gsheet.py  # Run a specific test file
-pytest tests/nodenorm/test_nodenorm_from_gsheet.py -k "row=42"  # Run a specific test row
+pytest -m unit                         # Offline unit suite (no network/token) — what CI runs on PRs
+```
+
+To run a single Google Sheet row, pass its full node ID (NOT `-k "row=42"` — pytest's
+`-k` expression parser rejects the `=`):
+
+```bash
+pytest "tests/nodenorm/test_nodenorm_from_gsheet.py::test_normalization[dev-gsheet:row=42]"
 ```
 
 ### Code Formatting
@@ -92,3 +99,19 @@ When writing new tests:
 - Hand-written per-issue regression tests go in `tests/nodenorm/by_issue/`
 - GitHub-issue-driven tests are picked up automatically by `tests/github_issues/test_github_issues.py` via `GitHubIssuesTestCases`
 - Import shared classes from `src.babel_validation.*` (e.g. `from src.babel_validation.services.nodenorm import CachedNodeNorm`)
+
+## Gotchas (learned the hard way)
+
+- **Offline vs. networked tests.** `pytest -m unit` is the offline suite CI runs on PRs (no
+  network, no `GITHUB_TOKEN`). Network-backed modules (Google Sheet, GitHub issues) defer all
+  fetching to `pytest_generate_tests` and call `tests/_pytest_helpers.deselected_by_markexpr`
+  so a marker-deselected run never hits the network. If you add a module that fetches at
+  import/collection time, replicate that pattern or you'll break `-m unit`.
+- **`src/babel_validation` is importable only because** `[tool.hatch.build.targets.wheel]` in
+  `pyproject.toml` packages `src/`. Imports use the full `src.babel_validation.*` path.
+- **Black is not strictly enforced** — `black --check` flags much of the existing tree. Match
+  the surrounding style of the file you're editing; don't mass-reformat (it creates huge,
+  review-hostile diffs).
+- **Commits are signed via 1Password's SSH agent** (`op-ssh-sign`). It can lock mid-session;
+  a `failed to fill whole buffer` / `failed to write commit object` error means 1Password
+  needs unlocking, not a git problem.