Improve developer effectiveness: unify quality gates, add Ruff linting, and fast smoke tests#5262
Improve developer effectiveness: unify quality gates, add Ruff linting, and fast smoke tests#5262Manikantasai1724 wants to merge 1 commit intoMDAnalysis:developfrom
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Pull request overview
This PR standardizes and speeds up contributor/CI quality checks by adding pre-commit enforcement, introducing Ruff configuration, and adding a fast “smoke test” gate before running the full CI matrices.
Changes:
- Added pre-commit-driven quality gates (with caching) to Azure Pipelines and GitHub Actions.
- Introduced Ruff configuration and dedicated Ruff CI jobs.
- Added a fast Azure “smoke tests” job and made the full Azure test matrix depend on passing the quick gates.
Reviewed changes
Copilot reviewed 5 out of 5 changed files in this pull request and generated 5 comments.
Show a summary per file
| File | Description |
|---|---|
azure-pipelines.yml |
Adds pre-commit, Ruff, and smoke-test jobs; gates the main test matrix on these checks. |
.ruff.toml |
Introduces a Ruff configuration file (currently selecting fatal/syntax-level rules). |
.pre-commit-config.yaml |
Adds pre-commit hooks (YAML, whitespace, Ruff, Black) for local + CI enforcement. |
.github/workflows/linters.yaml |
Adds GitHub Actions jobs for pre-commit and Ruff lint checks. |
.github/CONTRIBUTING.md |
Documents running pre-commit locally before opening PRs. |
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| hooks: | ||
| - id: black | ||
| files: ^(package|testsuite)/ | ||
| args: [--line-length=88] |
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The pre-commit Black hook is configured with --line-length=88, but the repository’s canonical Black configuration in package/pyproject.toml and testsuite/pyproject.toml sets line-length = 79. This will cause inconsistent formatting (and likely CI failures against the existing GitHub Actions Black job). Align the pre-commit Black hook with the existing tool.black settings (or remove the explicit --line-length so Black reads from the pyproject config).
| args: [--line-length=88] |
| @@ -0,0 +1,5 @@ | |||
| line-length = 88 | |||
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.ruff.toml sets line-length = 88, but Black is configured for line-length = 79 in both package/pyproject.toml and testsuite/pyproject.toml. Even though the current Ruff rule selection is limited, keeping Ruff’s line-length consistent with Black avoids future drift when additional rules (or formatting) are enabled.
| line-length = 88 | |
| line-length = 79 |
| - job: Ruff_Lint | ||
| displayName: 'Ruff lint checks' | ||
| pool: | ||
| vmImage: 'ubuntu-latest' | ||
| steps: | ||
| - task: UsePythonVersion@0 | ||
| inputs: | ||
| versionSpec: '3.11' | ||
| addToPath: true | ||
| architecture: 'x64' | ||
| - script: python -m pip install --upgrade pip ruff | ||
| displayName: 'Install ruff' | ||
| - script: ruff check package testsuite | ||
| displayName: 'Run ruff checks' | ||
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Precommit_Lint already runs the Ruff hook from .pre-commit-config.yaml, but this pipeline adds a separate Ruff_Lint job that runs ruff check again. This duplicates work and makes it easier for the two jobs to drift in configuration over time; consider relying on pre-commit as the single source of truth (or remove Ruff from pre-commit and keep it standalone), but avoid running both.
| - job: Ruff_Lint | |
| displayName: 'Ruff lint checks' | |
| pool: | |
| vmImage: 'ubuntu-latest' | |
| steps: | |
| - task: UsePythonVersion@0 | |
| inputs: | |
| versionSpec: '3.11' | |
| addToPath: true | |
| architecture: 'x64' | |
| - script: python -m pip install --upgrade pip ruff | |
| displayName: 'Install ruff' | |
| - script: ruff check package testsuite | |
| displayName: 'Run ruff checks' |
| cython | ||
| h5py>=2.10 | ||
| matplotlib | ||
| numpy | ||
| packaging | ||
| pytest | ||
| tqdm | ||
| threadpoolctl | ||
| filelock |
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The smoke job installs a large set of unpinned runtime/test dependencies (e.g., numpy/matplotlib/pytest) directly from PyPI. Because this job is now a required quality gate for the full matrix, upstream releases can introduce flaky CI failures unrelated to the PR. Consider pinning these to a known-good constraints file (or to the same minimum/compatible versions used elsewhere in CI) to keep the smoke gate stable.
| cython | |
| h5py>=2.10 | |
| matplotlib | |
| numpy | |
| packaging | |
| pytest | |
| tqdm | |
| threadpoolctl | |
| filelock | |
| cython==3.0.8 | |
| h5py==3.10.0 | |
| matplotlib==3.8.2 | |
| numpy==1.26.4 | |
| packaging==23.2 | |
| pytest==7.4.4 | |
| tqdm==4.66.1 | |
| threadpoolctl==3.2.0 | |
| filelock==3.13.1 |
| precommit: | ||
| if: "github.repository == 'MDAnalysis/mdanalysis'" | ||
| runs-on: ubuntu-latest | ||
| timeout-minutes: 10 | ||
| env: | ||
| PRE_COMMIT_HOME: ~/.cache/pre-commit | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 0 | ||
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| - uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.11" | ||
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| - name: cache pre-commit | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: ~/.cache/pre-commit | ||
| key: pre-commit-${{ runner.os }}-${{ hashFiles('.pre-commit-config.yaml') }} | ||
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| - name: install pre-commit | ||
| run: | | ||
| python -m pip install --upgrade pip pre-commit | ||
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| - name: run pre-commit | ||
| run: | | ||
| pre-commit run --all-files | ||
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| ruff_check: | ||
| if: "github.repository == 'MDAnalysis/mdanalysis'" | ||
| runs-on: ubuntu-latest | ||
| timeout-minutes: 10 | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
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| - uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.11" | ||
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| - name: install ruff | ||
| run: | | ||
| python -m pip install --upgrade pip ruff | ||
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| - name: run ruff | ||
| run: | | ||
| ruff check package testsuite | ||
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The new precommit job runs the Ruff and Black hooks (per .pre-commit-config.yaml), but this workflow also runs Ruff again (ruff_check) and still has a dedicated black job. This triples the same checks and increases CI time; consider either (1) using pre-commit as the single quality gate and dropping the redundant Ruff/Black jobs, or (2) configuring pre-commit here to run only the non-duplicated hooks.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## develop #5262 +/- ##
===========================================
- Coverage 93.83% 93.82% -0.01%
===========================================
Files 180 180
Lines 22473 22473
Branches 3189 3189
===========================================
- Hits 21088 21086 -2
- Misses 923 924 +1
- Partials 462 463 +1 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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Summary:
This PR improves development workflow reliability and CI efficiency by standardizing quality checks across local development and both CI providers.
What changed:
Introduced pre-commit-based local/CI quality enforcement.
Added cache configuration to speed up repeated pre-commit runs.
Added Ruff lint configuration and CI jobs for static checks.
Added a smoke-test job to fail fast on critical issues.
Made full matrix tests depend on passing quick quality gates.
Updated contributor instructions for local quality-check workflow.
Why:
Reduce avoidable CI failures.
Provide faster feedback to contributors.
Lower CI resource usage by preventing expensive runs when basic checks fail.
Keep local and CI behavior consistent.
Validation performed:
Verified updated workflow/config files are syntactically valid.
Confirmed no editor-reported errors in modified CI and config files.
Impact/Risk:
CI may initially fail on newly surfaced lint issues, which is expected and improves code health.
No runtime/library behavior changes; impact is limited to workflow/tooling.
📚 Documentation preview 📚: https://mdanalysis--5262.org.readthedocs.build/en/5262/