Adding tests for yaml files in testcases

.github/workflows/ersem.yml

@@ -10,6 +10,18 @@ on:
   schedule:
     - cron: '0 9 * * 1'
 jobs:
+  check-testcase-yaml:
+    runs-on: ubuntu-latest
+    steps:
+        - uses: actions/checkout@v2
+        - name: Setup python
+          uses: actions/setup-python@v2
+          with:
+              python-version: '3.x'
+        - name: Check testcase YAML files
+          run: |
+              python -m pip install PyYAML
+              python testcases/check_yaml.py
   build-pyfabm-ersem-debian:
     runs-on: ubuntu-latest
     steps:

testcases/check_yaml.py

@@ -0,0 +1,115 @@
+#!/usr/bin/env python3
+"""Check that testcase YAML files can be parsed by PyYAML."""
+
+import argparse
+import sys
+from pathlib import Path
+
+try:
+    import yaml
+except ImportError:
+    sys.stderr.write(
+        "PyYAML is required. Install it with: python -m pip install PyYAML\n"
+    )
+    sys.exit(2)
+
+
+YAML_PATTERNS = ("*.yaml", "*.yml", "*.yaml.template", "*.yml.template")
+
+
+def iter_yaml_files(paths):
+    seen = set()
+
+    for path in paths:
+        path = path.resolve()
+        if path.is_dir():
+            candidates = (
+                candidate
+                for pattern in YAML_PATTERNS
+                for candidate in path.rglob(pattern)
+            )
+        elif path.is_file():
+            candidates = (path,)
+        else:
+            raise FileNotFoundError(path)
+
+        for candidate in candidates:
+            if candidate.is_file() and candidate not in seen:
+                seen.add(candidate)
+                yield candidate
+
+
+def format_yaml_error(path, error):
+    mark = getattr(error, "problem_mark", None)
+    if mark is not None:
+        location = f"{path}:{mark.line + 1}:{mark.column + 1}"
+    else:
+        location = str(path)
+
+    problem = getattr(error, "problem", None)
+    if problem:
+        return f"{location}: {problem}"
+    return f"{location}: {error}"
+
+
+def check_yaml(path):
+    try:
+        with path.open("r", encoding="utf-8") as stream:
+            yaml.safe_load(stream)
+    except yaml.YAMLError as error:
+        return format_yaml_error(path, error)
+    except OSError as error:
+        return f"{path}: {error}"
+    return None
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Check that testcase YAML files can be parsed by PyYAML."
+    )
+    parser.add_argument(
+        "paths",
+        nargs="*",
+        type=Path,
+        default=[Path(__file__).resolve().parent],
+        help="YAML files or directories to check; defaults to this script's directory.",
+    )
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        action="store_true",
+        help="Print each file as it is successfully parsed.",
+    )
+    args = parser.parse_args()
+
+    try:
+        paths = sorted(iter_yaml_files(args.paths))
+    except FileNotFoundError as error:
+        print(f"Path does not exist: {error}", file=sys.stderr)
+        return 2
+
+    if not paths:
+        print("No YAML files found.", file=sys.stderr)
+        return 2
+
+    failures = []
+    for path in paths:
+        error = check_yaml(path)
+        if error is None:
+            if args.verbose:
+                print(f"OK {path}")
+        else:
+            failures.append(error)
+            print(f"FAILED {error}", file=sys.stderr)
+
+    checked = len(paths)
+    if failures:
+        print(f"Checked {checked} YAML files: {len(failures)} failed.", file=sys.stderr)
+        return 1
+
+    print(f"Checked {checked} YAML files: all OK.")
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())

testcases/fabm-ersem-26.02-dvm-n2o.yaml

@@ -273,7 +273,7 @@ instances:
       q10: 2.0                                             # Q_10 temperature coefficient (-)
       srs: 0.04                                            # specific rest respiration at reference temperature (1/d)
       pu_ea: 0.05                                          # excreted fraction of primary production (-)
-      exulim: 0.3                     			   # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
+      exulim: 0.3                                      # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
       xqcpx: 1.3                                           # threshold for phosphorus limitation, relative to minimum ratio,default=2.0_rk
       xqcnx: 1.3                                           # threshold for nitrogen limitation, relative to minimum ratio, default=2.0_rk
       pu_ra: 0.2                                           # respired fraction of primary production (-)

testcases/fabm-ersem-26.02-dvm.yaml

@@ -263,7 +263,7 @@ instances:
       q10: 2.0                                             # Q_10 temperature coefficient (-)
       srs: 0.04                                            # specific rest respiration at reference temperature (1/d)
       pu_ea: 0.05                                          # excreted fraction of primary production (-)
-      exulim: 0.3                     			   # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
+      exulim: 0.3                                      # excreted fraction of primary production due to nutrient stress,maximum=1._rk-self%pu_ea
       xqcpx: 1.3                                           # threshold for phosphorus limitation, relative to minimum ratio,default=2.0_rk
       xqcnx: 1.3                                           # threshold for nitrogen limitation, relative to minimum ratio, default=2.0_rk
       pu_ra: 0.2                                           # respired fraction of primary production (-)