Add an AnalysisCollection class
#1805
Workflow file for this run
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| 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@v4 | |
| 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@v6 | |
| 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@v3 | |
| 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@v4 | |
| 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/ |