Pathlib object handling for Universe, SingleFrameReaderBase and Toplogy parsers (Issue #3937) #1911
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: "linters" | |
| on: | |
| pull_request: | |
| branches: | |
| - develop | |
| concurrency: | |
| # Probably overly cautious group naming. | |
| # Commits to develop will cancel each other, but PRs will only cancel | |
| # commits within the same PR | |
| group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}" | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| darker_lint: | |
| if: "github.repository == 'MDAnalysis/mdanalysis'" | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 10 | |
| permissions: | |
| pull-requests: write | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: darker-main-code | |
| id: darker-main-code | |
| uses: akaihola/[email protected] | |
| continue-on-error: true | |
| with: | |
| version: "~=1.6.1" | |
| options: "--check --diff --color" | |
| src: "./package/MDAnalysis" | |
| revision: "HEAD^" | |
| lint: "flake8" | |
| - name: darker-test-code | |
| id: darker-test-code | |
| uses: akaihola/[email protected] | |
| continue-on-error: true | |
| with: | |
| version: "~=1.6.1" | |
| options: "--check --diff --color" | |
| src: "./testsuite/MDAnalysisTests" | |
| revision: "HEAD^" | |
| lint: "flake8" | |
| - name: get-pr-info | |
| uses: actions/github-script@v7 | |
| with: | |
| script: | |
| const prNumber = context.payload.number; | |
| core.exportVariable('PULL_NUMBER', prNumber); | |
| - name: save-status | |
| env: | |
| MAIN: ${{ steps.darker-main-code.outcome }} | |
| TEST: ${{ steps.darker-test-code.outcome }} | |
| shell: python | |
| run: | | |
| import os | |
| import json | |
| from pathlib import Path | |
| Path('./darker_results/').mkdir(exist_ok=True) | |
| d = { | |
| 'main_stat': os.environ['MAIN'], | |
| 'test_stat': os.environ['TEST'], | |
| 'PR_NUM': os.environ['PULL_NUMBER'], | |
| 'RUN_ID': os.environ['GITHUB_RUN_ID'], | |
| } | |
| with open('darker_results/status.json', 'w') as f: | |
| json.dump(d, f) | |
| - name: check-json | |
| run: cat darker_results/status.json | |
| - name: upload-status | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: darkerlint | |
| path: darker_results/ | |
| retention-days: 1 | |
| pylint_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: "3.10" | |
| - name: install | |
| run: | | |
| python -m pip install pylint | |
| - name: pylint | |
| env: | |
| PYLINTRC: package/.pylintrc | |
| run: | | |
| pylint package/MDAnalysis && pylint testsuite/MDAnalysisTests | |
| mypy : | |
| if: "github.repository == 'MDAnalysis/mdanalysis'" | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 10 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: setup_micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-name: mda | |
| create-args: >- | |
| python=3.10 | |
| pip | |
| # using jaime's shim to avoid pulling down the cudatoolkit | |
| condarc: | | |
| channels: | |
| - jaimergp/label/unsupported-cudatoolkit-shim | |
| - conda-forge | |
| - bioconda | |
| - name: install_deps | |
| uses: ./.github/actions/setup-deps | |
| with: | |
| micromamba: true | |
| full-deps: true | |
| numpy: numpy=1.23.2 | |
| rdkit: rdkit=2023.09.3 | |
| - name: install | |
| run: | | |
| python -m pip install mypy | |
| - name: "Run mypy" | |
| run: | | |
| mypy package/MDAnalysis/ |