fix: restore lineqlist2str, which CNApy imports at startup

.github/workflows/CI-test.yml

@@ -131,5 +131,8 @@ jobs:
         if: matrix.package-manager == 'conda'
         run: |
           micromamba install pytest pytest-timeout
+      # --downstream reads CNApy's source to check the names it imports from this
+      # package. It needs network and tracks a branch we do not control, so it is
+      # limited to the quarterly scheduled run rather than gating pull requests.
       - name: Test with pytest
-        run: pytest tests -v --medium --log-cli-level=INFO
+        run: pytest tests -v --medium ${{ github.event_name == 'schedule' && '--downstream' || '' }} --log-cli-level=INFO

conda-recipe/meta.yaml

@@ -2,7 +2,7 @@
 
 package:
   name: straindesign
-  version: {{ version }}
+  version: "{{ version }}"
 
 source:
   path: ..

straindesign/parse_constr.py

@@ -125,6 +125,28 @@ def lineq2list(equations, reaction_ids) -> List:
     return D
 
 
+def lineqlist2str(D):
+    """Translates a *linear* (in)equality from the list format [lhs,sign,rhs] to a string
+
+    E.g. input: D=[{"a":3.0,"b":-1.0,"c":2.0},"<=",2.0]] is translated to: out="3.0 a - 1.0 b + 2.0 c <= 2"
+
+    Args:
+        D (list):
+            (In)equality in list form, e.g.: D=[{"a":3.0,"b":-1.0,"c":2.0},"<=",2.0]]
+
+    Returns:
+        (str):
+        A list of (in)equalities in string form
+
+    """
+    if D[0]:
+        return linexprdict2str(D[0]) + " " + D[1] + " " + str(D[2])
+    elif D[1] and D[2]:
+        return D[1] + " " + str(D[2])
+    else:
+        return ""
+
+
 def lineqlist2mat(D, reaction_ids) -> Tuple[sparse.csr_matrix, Tuple, sparse.csr_matrix, Tuple]:
     """Translates *linear* (in)equalities presented in the list of lists format to matrices
 

tests/conftest.py

@@ -4,14 +4,16 @@
 from straindesign.names import *
 
 # ---------------------------------------------------------------------------
-# Custom CLI flags for test_performance.py tiered benchmarks
+# Custom CLI flags for opt-in tests: the tiered benchmarks in
+# test_09_performance.py and the downstream check in test_13_public_api.py
 # ---------------------------------------------------------------------------
 
 
 def pytest_addoption(parser):
     for name, help_text in [
         ("--medium", "Run iMLcore genome-scale benchmarks (~4 min total)."),
         ("--large", "Run iML1515 large-model benchmarks (several min/solver)."),
+        ("--downstream", "Check the names CNApy imports against this package (needs network)."),
     ]:
         try:
             parser.addoption(name, action="store_true", default=False, help=help_text)
@@ -23,6 +25,7 @@ def pytest_configure(config):
     for marker, desc in [
         ("medium", "genome-scale benchmark; enable with --medium"),
         ("large", "large-model benchmark; enable with --large"),
+        ("downstream", "downstream consumer check; enable with --downstream"),
     ]:
         config.addinivalue_line("markers", f"{marker}: {desc}")
     # Suppress known third-party warnings
@@ -31,9 +34,9 @@ def pytest_configure(config):
 
 
 def pytest_collection_modifyitems(config, items):
-    for flag, marker in [("--medium", "medium"), ("--large", "large")]:
+    for flag, marker in [("--medium", "medium"), ("--large", "large"), ("--downstream", "downstream")]:
         if not config.getoption(flag, default=False):
-            skip = pytest.mark.skip(reason=f"pass {flag} to enable this benchmark")
+            skip = pytest.mark.skip(reason=f"pass {flag} to enable this test")
             for item in items:
                 if marker in item.keywords:
                     item.add_marker(skip)

tests/test_13_public_api.py

@@ -0,0 +1,104 @@
+"""Test that the public API downstream packages import stays importable.
+
+Being unused inside this repository is not evidence that a public name is unused:
+`lineqlist2str` had no caller here and was deleted as dead code, but CNApy imports
+it at startup in gui_elements/strain_design_dialog.py, so the removal broke the
+application. These names are re-checked here because grepping this repository
+cannot see that.
+"""
+import ast
+import importlib
+import io
+import tarfile
+import urllib.request
+import warnings
+
+import pytest
+
+CNAPY_TARBALL = "https://github.com/cnapy-org/CNApy/archive/refs/heads/master.tar.gz"
+
+# Imported by CNApy; see cnapy/gui_elements/strain_design_dialog.py and siblings.
+CNAPY_IMPORTS = {
+    "straindesign": [
+        "avail_solvers",
+        "compute_strain_designs",
+        "fba",
+        "lineq2list",
+        "lineqlist2str",
+        "linexpr2dict",
+        "linexprdict2str",
+        "plot_flux_space",
+        "SDModule",
+        "select_solver",
+        "yopt",
+    ],
+    "straindesign.parse_constr": ["lineq2list", "linexpr2dict", "linexprdict2str"],
+    "straindesign.names": ["CPLEX", "GLPK", "GUROBI", "SCIP"],
+    "straindesign.strainDesignSolutions": ["SDSolutions"],
+}
+
+
+@pytest.mark.parametrize("module,names", sorted(CNAPY_IMPORTS.items()))
+def test_public_names_are_importable(module, names):
+    """Names that downstream packages import must remain importable."""
+    mod = importlib.import_module(module)
+    missing = [n for n in names if not hasattr(mod, n)]
+    assert not missing, f"{module} no longer exports: {', '.join(missing)}"
+
+
+def _straindesign_names_imported_by(source):
+    """Yield (module, name) for every straindesign import in a source file."""
+    with warnings.catch_warnings():
+        # Parsing someone else's source can raise SyntaxWarning for things like
+        # invalid escape sequences. Those are CNApy's to fix, not signal here.
+        warnings.simplefilter("ignore", SyntaxWarning)
+        tree = ast.parse(source)
+    for node in ast.walk(tree):
+        if isinstance(node, ast.ImportFrom):
+            if node.level == 0 and node.module and node.module.split(".")[0] == "straindesign":
+                for alias in node.names:
+                    if alias.name != "*":
+                        yield node.module, alias.name
+
+
+@pytest.mark.downstream
+def test_cnapy_master_imports_still_exist():
+    """Every straindesign name CNApy imports must still be exported.
+
+    CNApy is read rather than installed: it depends on Qt, a JVM via jpype, and
+    CPLEX, none of which belong in this matrix. Reading the source catches names
+    CNApy has newly imported, which the hardcoded list above cannot.
+    """
+    try:
+        with urllib.request.urlopen(CNAPY_TARBALL, timeout=120) as response:
+            payload = response.read()
+    except Exception as exc:  # offline, rate-limited, or the branch moved
+        pytest.skip(f"could not fetch CNApy source: {exc}")
+
+    wanted = set()
+    with tarfile.open(fileobj=io.BytesIO(payload), mode="r:gz") as tar:
+        for member in tar.getmembers():
+            if not member.name.endswith(".py"):
+                continue
+            handle = tar.extractfile(member)
+            if handle is None:
+                continue
+            wanted.update(_straindesign_names_imported_by(handle.read().decode("utf-8", "replace")))
+
+    assert wanted, "found no straindesign imports in CNApy; the parser or the URL is wrong"
+
+    missing = []
+    for module, name in sorted(wanted):
+        mod = importlib.import_module(module)
+        if not hasattr(mod, name):
+            missing.append(f"{module}.{name}")
+    assert not missing, ("CNApy imports names this package no longer exports: " + ", ".join(missing))
+
+
+def test_lineqlist2str_formats_an_inequality():
+    """lineqlist2str renders [lhs, sign, rhs] as a string, as CNApy displays it."""
+    from straindesign import lineqlist2str
+
+    assert lineqlist2str([{"a": 3.0, "b": -1.0}, "<=", 2.0]) == "3.0 a - 1.0 b <= 2.0"
+    assert lineqlist2str([{}, "<=", 2.0]) == "<= 2.0"
+    assert lineqlist2str([{}, "", ""]) == ""