Investigate intermittent regression test failures in GitHub Actions CI

.github/workflows/pr.yaml

@@ -7,6 +7,13 @@ concurrency:
   group: pr-${{ github.ref }}
   cancel-in-progress: true
 
+env:
+  OMP_NUM_THREADS: 1
+  MKL_NUM_THREADS: 1
+  OPENBLAS_NUM_THREADS: 1
+  NUMEXPR_NUM_THREADS: 1
+  PYTHONHASHSEED: 0
+
 jobs:
   unit:
     name: Unit
@@ -34,7 +41,7 @@ jobs:
           python -m pip install -e .[testing]
 
       - name: Pytest (unit) • ${{ matrix.os }}, ${{ matrix.python-version }}
-        run: python -m pytest tests/unit
+        run: python -m pytest tests/unit --cache-clear
 
   discover-systems:
     name: Discover regression systems
@@ -81,29 +88,30 @@ jobs:
       - name: Set up Python 3.14
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
         with:
-          python-version: "3.14"
+          python-version: "3.13"
           cache: pip
 
-      - name: Cache testdata
-        uses: actions/cache@v4
-        with:
-          path: .testdata
-          key: codeentropy-testdata-${{ runner.os }}-py314
-
       - name: Install testing dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install -e .[testing]
 
+      - name: Clean local test caches
+        shell: bash
+        run: |
+          rm -rf .pytest_cache
+          find . -type d -name "__pycache__" -prune -exec rm -rf {} +
+
       - name: Run fast regression tests (per system)
         run: |
           python -m pytest tests/regression \
             -m "not slow" \
-            -n auto \
-            --dist=loadscope \
-            -k "${{ matrix.system }}" \
+            --cache-clear \
+            -n 1 \
+            --system "${{ matrix.system }}" \
             -vv \
-            --durations=20
+            --durations=20 \
+            --codeentropy-debug
 
       - name: Upload artifacts (failure)
         if: failure()
@@ -200,6 +208,7 @@ jobs:
       - name: Run coverage
         run: |
           pytest tests/unit \
+            --cache-clear \
             --cov CodeEntropy \
             --cov-report term-missing \
             --cov-report xml \

tests/regression/conftest.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import os
 import random
 
 import numpy as np
@@ -48,8 +47,6 @@ def pytest_configure(config: pytest.Config) -> None:
     random.seed(seed)
     np.random.seed(seed)
 
-    os.environ["PYTHONHASHSEED"] = "0"
-
 
 def pytest_collection_modifyitems(
     config: pytest.Config, items: list[pytest.Item]

tests/regression/prepare_testdata.py

@@ -0,0 +1,64 @@
+from __future__ import annotations
+
+import argparse
+from pathlib import Path
+from typing import Any
+
+import yaml
+
+from tests.regression.cases import discover_cases
+from tests.regression.helpers import (
+    _abspathify_config_paths,
+    ensure_testdata_for_system,
+)
+
+
+def unwrap_case(case_or_param: Any) -> Any:
+    if hasattr(case_or_param, "values"):
+        values = case_or_param.values
+        if values:
+            return values[0]
+    return case_or_param
+
+
+def required_paths_for_case(case: Any) -> list[Path]:
+    raw = yaml.safe_load(case.config_path.read_text())
+    cooked = _abspathify_config_paths(raw, base_dir=case.config_path.parent)
+
+    required: list[Path] = []
+    run1 = cooked.get("run1")
+
+    if isinstance(run1, dict):
+        ff = run1.get("force_file")
+        if isinstance(ff, str) and ff:
+            required.append(Path(ff))
+
+        for p in run1.get("top_traj_file") or []:
+            if isinstance(p, str) and p:
+                required.append(Path(p))
+
+    return required
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--system", action="append", default=None)
+    args = parser.parse_args()
+
+    selected = set(args.system or [])
+
+    for case_or_param in discover_cases():
+        case = unwrap_case(case_or_param)
+
+        if selected and case.system not in selected:
+            continue
+
+        required = required_paths_for_case(case)
+        if required:
+            ensure_testdata_for_system(case.system, required_paths=required)
+
+    print("Regression test data prepared.")
+
+
+if __name__ == "__main__":
+    main()