[Dan Fiedler (danfiedler-msft)]

Summary

This PR pins GitHub Actions to full-length commit SHAs for improved security and reproducibility and adds a 7 day cooldown to Dependabot configuration for GitHub Actions. This work is described in more detail at https://aka.ms/action-pinning.

Why?

Pinning actions to commit SHAs prevents supply-chain attacks where a tag could be moved to point to malicious code. This is a recommended security best practice per the GitHub Actions security hardening guide.

This change mitigates the risk of tag retargeting to malicious code as seen in incidents like the tj-actions/changed-files action compromise or codfish/semantic-release-action compromise and improves the integrity and reproducibility of the CI/CD pipeline.

What changed?

Action pinning: Third-party action references in .github/workflows/ that used mutable tag-based references (e.g., actions/checkout@v4) have been updated to full-length commit SHAs with a version comment (e.g., actions/checkout@<sha> # v4) using the pinact tool. References that were already pinned to a SHA, or that used immutable release tags, were left unchanged.

Dependabot configuration: .github/dependabot.yml has been updated to ensure a github-actions package-ecosystem section is present with a cooldown configuration (default-days: 7). If the file did not exist, it was created. If a github-actions section already existed, only the cooldown block was added or its default-days value was increased to 7 if it was lower. The 7-day cooldown provides a window for the community to detect and report compromised releases before they are automatically proposed as updates, reducing exposure to supply-chain attacks via newly published malicious versions.

Is this safe to merge?

Yes. The pinned SHAs correspond to the same commits that the existing tags pointed to. No behavioral changes in action execution are introduced. You can verify the pinned SHA value using the GitHub REST API (e.g., the commit hash for actions/checkout@v7 can be found in the sha property in the JSON response for GET https://api.github.com/repos/actions/checkout/commits/v7).

Additional Information

For more information, please see https://aka.ms/action-pinning

[Avasam (Avasam)]

Ruff action v4+ is using immutable tags and would be safe. (granted may as well be consistent in the dependency definition, I just thought I'd mention it)

[Martijn Verburg (karianna)]

Not a repo I'm a SME in, so I won't have Copilot apply the fix but heere's the analysis of failing tests:

The job fails in stubtest for two separate reasons:

1. skimage.feature.Cascade is now marked as a disjoint_base at runtime.
2. The unpinned SymPy dependency has drifted beyond the version covered by the checked-in stubs.

1. Fix skimage.feature.Cascade

The runtime error is:

skimage.feature.Cascade is a disjoint base at runtime, but isn't marked with @disjoint_base in the stub

Update stubs/skimage/feature/_cascade.pyi:

-from typing import Any, ClassVar
+from typing import Any, ClassVar
+from typing_extensions import disjoint_base

 __reduce_cython__: Any
 __setstate_cython__: Any
 __test__: dict

+@disjoint_base
 class Cascade:

This single class is re-exported by stubs/skimage/feature/__init__.pyi, so no separate decorator should be added to the alias there.

2. Stabilize the SymPy test dependency

The SymPy failures are not isolated typing mistakes. The runtime and stub APIs are substantially different:

• runtime properties such as is_real, is_zero, and is_commutative are read-only properties;
• the stubs expose them as variables;
• Basic.subs has explicit arg1 and arg2 parameters at runtime, while the stub still declares *args;
• several runtime values are concrete bools while the stubs use ...;
• stubtest also crashes with IndexError while processing an outdated overload declaration.

The dependency is currently unpinned in pyproject.toml:

"sympy",

Pin SymPy to the version targeted by the current stubs/sympy-stubs implementation, for example:

"sympy == <supported-version>",

The supported version should be the version used when these stubs last passed stubtest; determine it from the project’s last known-good dependency set rather than accepting the latest release implicitly. The same version must be used locally and in CI.

As a temporary containment measure, the SymPy module can be added to the relevant SymPy stubtest allowlist:

sympy.sets.handlers.comparison

However, that only hides the incompatibility and should not replace either updating the SymPy stubs or pinning the runtime dependency.

Validation

After the changes, run:

python -m pip install --group tests
python tests/run_stubtest.py

The Node 20 deprecation message is unrelated to the failure. The actionable CI failures are the missing @disjoint_base annotation and the unbounded SymPy dependency.

[Martijn Verburg (karianna)]

Avasam (@Avasam) are you able to review the failures?

[Avasam (Avasam)]

For hygiene (Ruff), just remove the # noqa: F811 at stubs/matplotlib/pyplot.pyi:782

---

For the pyright failure on Python 3.13, either:

• Remove from numpy.core.numeric import ComplexWarning as ComplexWarning in stubs/sklearn/utils/validation.pyi:16. It looks like an accidental re-export anyway. The symbol is also already explicitly re-exposed from stubs/sklearn/utils/fixes.pyi (in fact, all re-exports here are probably just from codegen, as none match https://scikit-learn.org/stable/api/sklearn.utils.html )
• Or, in stubs/sklearn/utils/validation.pyi:16, change it for from numpy.exceptions import ComplexWarning as ComplexWarning (would recommend just removing extraneous re-exports entirely for this module)

---

Created #397 for both above

Stubtest requires actually updating out of date stubs (that's also why it's the last test, to not block anything else, if it's the last thing not passing, I don't see it blocking this PR)

In the above PR I ended up simply updating the running TODO list.

[Avasam (Avasam)]

Additionally, for sympy, consider just dropping the stubs in favor of upstream. It's so far out of sync now (with ton of incorrectness anyway), it's only hurting users: sympy/sympy#29747 . And upstream have put (and are still going) into actually typing sympy first-party.

[Bill Schnurr (bschnurr)]

🔒 Automated review in progress — Bill Schnurr (@bschnurr) is auto-reviewing this PR.

[Bill Schnurr (bschnurr)]

Result: ⚠️ partially-verified

Verification details

Verification: Isolated verification observed failures that were not classified as caused by this PR: Environment and test discovery.

Summary: A targeted validator parsed both YAML files and confirmed the Dependabot settings plus all six full-length SHA pins. No tests were added by the PR, and repository tests do not target workflow configuration. Git metadata and online SHA/action execution were unavailable, so verification is partial.

Test runs: 1 passed, 1 failed

• ❌ Failed | unrelated to this PR | Environment and test discovery | printf 'sandbox=%s\n' "${AUTOMATION_SANDBOX_PROFILE:-unset}"; git diff --name-status HEAD^ HEAD; printf '%s\n' '--- manifests and test/config files ---'; find . -maxdepth 3 -type f ( -name 'pyproject.toml' -o -name 'uv.lock' -o -name 'requirements.txt' -o -name 'package.json' -o -path './tests/' -o -path './.github/' ) -print | sort; printf '%s\n' '--- available tools ---'; command -v python || true; command -v ruby || true; command -v actionlint || true; command -v pinact || true; command -v yamllint || true; git status --short
• ✅ Passed | Workflow pin and Dependabot configuration validation | python - <<'PY'
from pathlib import Path
import re
import yaml

workflow_path = Path('.github/workflows/test.yml')
dependabot_path = Path('.github/dependabot.yml')
workflow_text = workflow_path.read_text()
dependabot_text = dependabot_path.read_text()
workflow = yaml.safe_load(workflow_text)
dependabot = yaml.safe_load(dependabot_text)
assert isinstance(workflow, dict) and 'jobs' in workflow
assert isinstance(dependabot, dict) and dependabot['version'] == 2
updates = dependabot['updates']
assert len(updates) == 1
entry = updates[0]
assert entry['package-ecosystem'] == 'github-actions'
assert entry['directory'] == '/'
assert entry['schedule']['interval'] == 'weekly'
assert entry['groups']['github-actions']['patterns'] == ['']
assert entry['cooldown']['default-days'] == 7
uses = re.findall(r'^\s-?\suses:\s([^\s#]+)(?:\s+#\s*(\S+))?\s*$', workflow_text, re.M)
assert uses, 'no action references found'
expected = {
'actions/checkout': ('0717577d45739eb3c851188b29f50ed6c0b2194e', 'v2.8.0', 2),
'actions/setup-python': ('e9aba2c848f5ebd159c070c61ea2c4e2b122355e', 'v2.3.4', 1),
'actions/cache': ('0057852bfaa89a56745cba8c7296529d2fc39830', 'v4.3.0', 1),
'jakebailey/pyright-action': ('6cabc0f01c4994be48fd45cd9dbacdd6e1ee6e5e', 'v2.3.3', 1),
'astral-sh/ruff-action': ('4919ec5cf1f49eff0871dbcea0da843445b837e6', 'v3.6.1', 1),
}
seen = {name: 0 for name in expected}
for reference, comment in uses:
name, revision = reference.rsplit('@', 1)
assert re.fullmatch(r'[0-9a-f]{40}', revision), f'unpinned action: {reference}'
assert name in expected, f'unexpected action: {name}'
sha, version, _ = expected[name]
assert (revision, comment) == (sha, version), (reference, comment)
seen[name] += 1
assert seen == {name: count for name, (*_, count) in expected.items()}, seen
print(f'Parsed both YAML files; validated Dependabot cooldown/group/schedule and {len(uses)} SHA-pinned action references.')
PY

❌ Environment and test discovery diagnostic output

sandbox=generic
error: Could not access 'HEAD^'
Found both changed configuration files, pyproject.toml, and repository tests.
fatal: not a git repository (or any parent up to mount point /)

[Bill Schnurr (bschnurr)]

Approved via Review Center.

[Rich Chiodo (rchiodo)]

Pushed two focused fixes for the failing checks:

• 83af1f8 removes an unused F811 noqa in matplotlib/pyplot.pyi; the new CI hygiene job passes.
• e30be88 imports ComplexWarning from numpy.exceptions rather than the removed numpy.core.numeric export. This matches the sklearn runtime and the existing utils.fixes stub, and addresses the new Python 3.13 Pyright failure.

Local validation with Python 3.13: Ruff check and formatting pass; Pyright reports 0 errors with the isolated interpreter; mypy passes all 1,282 source files. Runtime identity of the ComplexWarning re-export was verified.

The remaining stubtest failures are pre-existing library/stub drift, not a result of replacing action tags with SHAs. Before these two small fixes, stubs/, tests/, and pyproject.toml were byte-for-byte identical to current main (d23acef). The existing PR CI already reported failures across SymPy, scikit-image, scikit-learn, and VisPy. A fresh local reproduction also fails, including changed scikit-image signatures (for example CircleModel constructor parameters) and VisPy TextVisual parameter order/new properties. Current main has a failing Test run as well (26965677280).

Those failures need separate stub maintenance and runtime-compatibility decisions; this update does not suppress errors, weaken tests, or arbitrarily downgrade library dependencies. This PR should not yet be treated as fully green.

[Rich Chiodo (rchiodo)]

Latest CI confirmation: run https://github.com/microsoft/python-type-stubs/actions/runs/40579204101 completed after e30be88. Hygiene passes, and all six Python/OS matrix jobs pass Pyright and mypy. Every matrix failure is now confined to Run stubtest.

The Python 3.13 Ubuntu job reports 75 VisPy errors, 290 scikit-image errors, 63 scikit-learn errors, and additional SymPy mismatches. These are the previously documented baseline runtime/stub compatibility problems, not new action-pinning regressions.

Per maintainer direction, leave these baseline failures documented for now; no further stub maintenance, dependency downgrades, or test suppressions will be included in this PR. The PR remains red and is not being represented as fully passing.