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Improve developer effectiveness: unify quality gates, add Ruff linting, and fast smoke tests #5262

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Improve developer effectiveness: unify quality gates, add Ruff linting, and fast smoke tests #5262

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12 changes: 12 additions & 0 deletions .github/CONTRIBUTING.md
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Expand Up @@ -16,3 +16,15 @@ If you're contributing code, please check out [How to contribute](https://www.md

MDAnalysis devs are most easily reached through the [development list](https://groups.google.com/forum/#!forum/mdnalysis-devel).

#### Local quality checks

Before opening a pull request, please run the same style checks locally using pre-commit:

```bash
python -m pip install pre-commit
pre-commit install
pre-commit run --all-files
```

Running these checks before pushing helps keep pull requests focused and reduces CI turnaround time.

48 changes: 48 additions & 0 deletions .github/workflows/linters.yaml
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Expand Up @@ -16,6 +16,54 @@ defaults:
shell: bash -l {0}

jobs:
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

- uses: actions/setup-python@v5
with:
python-version: "3.11"

- name: cache pre-commit
uses: actions/cache@v4
with:
path: ~/.cache/pre-commit
key: pre-commit-${{ runner.os }}-${{ hashFiles('.pre-commit-config.yaml') }}

- name: install pre-commit
run: |
python -m pip install --upgrade pip pre-commit

- name: run pre-commit
run: |
pre-commit run --all-files

ruff_check:
if: "github.repository == 'MDAnalysis/mdanalysis'"
runs-on: ubuntu-latest
timeout-minutes: 10
steps:
- uses: actions/checkout@v4

- uses: actions/setup-python@v5
with:
python-version: "3.11"

- name: install ruff
run: |
python -m pip install --upgrade pip ruff

- name: run ruff
run: |
ruff check package testsuite

Comment on lines +19 to +66
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Copilot AI Feb 28, 2026

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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.

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black:
if: "github.repository == 'MDAnalysis/mdanalysis'"
runs-on: ubuntu-latest
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21 changes: 21 additions & 0 deletions .pre-commit-config.yaml
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@@ -0,0 +1,21 @@
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v5.0.0
hooks:
- id: check-ast
- id: check-yaml
- id: end-of-file-fixer
- id: trailing-whitespace

- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.9.10
hooks:
- id: ruff
files: ^(package|testsuite)/

- repo: https://github.com/psf/black
rev: 24.10.0
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).

Suggested change
args: [--line-length=88]

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5 changes: 5 additions & 0 deletions .ruff.toml
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@@ -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.

Suggested change
line-length = 88
line-length = 79

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target-version = "py311"

[lint]
select = ["E9", "F63", "F7", "F82"]
77 changes: 77 additions & 0 deletions azure-pipelines.yml
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Expand Up @@ -15,7 +15,84 @@ pr:


jobs:
- job: Precommit_Lint
displayName: 'Pre-commit checks'
pool:
vmImage: 'ubuntu-latest'
variables:
PRE_COMMIT_HOME: '$(Pipeline.Workspace)/.pre-commit-cache'
steps:
- task: UsePythonVersion@0
inputs:
versionSpec: '3.11'
addToPath: true
architecture: 'x64'
- task: Cache@2
inputs:
key: 'pre-commit | "$(Agent.OS)" | .pre-commit-config.yaml'
path: '$(PRE_COMMIT_HOME)'
restoreKeys: |
pre-commit | "$(Agent.OS)"
- script: python -m pip install --upgrade pip pre-commit
displayName: 'Install pre-commit'
- script: PRE_COMMIT_HOME=$(PRE_COMMIT_HOME) pre-commit run --all-files
displayName: 'Run pre-commit hooks'

- 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'

Comment on lines +41 to +55
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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.

Suggested change
- 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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- job: Smoke_Tests
displayName: 'Smoke tests'
pool:
vmImage: 'ubuntu-latest'
steps:
- task: UsePythonVersion@0
inputs:
versionSpec: '3.11'
addToPath: true
architecture: 'x64'
- script: python -m pip install --upgrade pip setuptools wheel
displayName: 'Install tools'
- script: >-
python -m pip install --only-binary=scipy,h5py
cython
h5py>=2.10
matplotlib
numpy
packaging
pytest
tqdm
threadpoolctl
filelock
Comment on lines +70 to +78
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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.

Suggested change
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

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displayName: 'Install smoke dependencies'
- script: >-
python -m pip install
./package
./testsuite
displayName: 'Install package and testsuite'
- script: >-
pytest testsuite/MDAnalysisTests/test_api.py
--disable-pytest-warnings
-q
displayName: 'Run smoke tests'

- job: Azure_Tests
dependsOn:
- Precommit_Lint
- Ruff_Lint
- Smoke_Tests
condition: and(succeeded(), ne(variables['Build.SourceBranch'], 'refs/heads/develop')) # skip for PR merges
variables:
MPLBACKEND: agg
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