ci: fix nightly E2E pointing at a non-existent test file

.github/workflows/nightly.yml

@@ -38,7 +38,7 @@ jobs:
         run: pip install -e ".[dev,improved]"
 
       - name: Run integration tests (excluding scale-marked)
-        run: pytest tests/integration/ tests/test_e2e_integration.py -m "not scale" -q --timeout=600
+        run: pytest tests/integration/ tests/test_plasmid_e2e.py tests/test_extension_reach_e2e_to_report.py -m "not scale" -q --timeout=600
 
       - name: Run plasmid example end-to-end
         run: |

tests/test_ci_workflow_paths.py

@@ -0,0 +1,61 @@
+"""Guard: every test path referenced in a CI workflow must exist.
+
+The nightly workflow once invoked `pytest tests/test_e2e_integration.py`, a file
+that never existed, so the job exited with pytest's usage error (code 4) every
+night. This test scans `.github/workflows/*.yml` for pytest path arguments and
+asserts each referenced file/directory is present, catching that typo class at
+PR time instead of at 04:00 UTC.
+"""
+
+import re
+from pathlib import Path
+
+import pytest
+
+_ROOT = Path(__file__).resolve().parent.parent
+_WORKFLOWS = sorted((_ROOT / ".github" / "workflows").glob("*.yml"))
+
+
+def _pytest_path_args(text):
+    """Yield path-like tokens passed to `pytest` invocations in a workflow."""
+    for line in text.splitlines():
+        if "pytest " not in line:
+            continue
+        # Tokens after 'pytest' up to a flag/pipe; keep ones that look like paths
+        # (contain '/' or end in .py) and are not flags or flag values.
+        after = line.split("pytest ", 1)[1]
+        tokens = after.replace("|", " ").split()
+        skip_next = False
+        for tok in tokens:
+            if skip_next:
+                skip_next = False
+                continue
+            if tok.startswith("-"):
+                # flags like -m take a following value (e.g. -m "not scale")
+                if tok in ("-m", "-k", "-p", "-o", "--timeout", "-n"):
+                    skip_next = True
+                continue
+            if tok.startswith('"') or tok.startswith("'"):
+                continue
+            if tok.endswith(".py") or "/" in tok:
+                yield tok
+
+
+@pytest.mark.skipif(not _WORKFLOWS, reason="no workflow files")
+@pytest.mark.parametrize("wf", _WORKFLOWS, ids=lambda p: p.name)
+def test_workflow_pytest_paths_exist(wf):
+    text = wf.read_text()
+    missing = [tok for tok in _pytest_path_args(text) if not (_ROOT / tok).exists()]
+    assert not missing, (
+        f"{wf.name} references test paths that do not exist: {missing}. "
+        f"Fix the path (pytest exits with code 4 on a missing file)."
+    )
+
+
+def test_guard_actually_inspects_a_pytest_line():
+    """Sanity: the parser finds the integration path in the nightly workflow."""
+    nightly = _ROOT / ".github" / "workflows" / "nightly.yml"
+    if not nightly.exists():
+        pytest.skip("no nightly workflow")
+    toks = list(_pytest_path_args(nightly.read_text()))
+    assert any("tests/integration" in t for t in toks), toks