relax mda requirements #189
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| name: GH Actions CI | |
| 'on': | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| schedule: | |
| # Weekly tests at midnight on Sundays run on main by default: | |
| # Scheduled workflows run on the latest commit on the default or base branch. | |
| # (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule) | |
| - cron: 0 0 * * 0 | |
| concurrency: | |
| # Specific group naming so CI is only cancelled | |
| # within same PR or on merge to main | |
| group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| environment-config: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| stable-python-version: ${{ steps.get-compatible-python.outputs.stable-python }} | |
| python-matrix: ${{ steps.get-compatible-python.outputs.python-versions }} | |
| steps: | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' | |
| - id: get-compatible-python | |
| uses: MDAnalysis/mdanalysis-compatible-python@main | |
| with: | |
| release: latest | |
| main-tests: | |
| if: github.repository == 'Becksteinlab/zarrtraj' | |
| needs: environment-config | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: | |
| - macOS-latest | |
| - ubuntu-latest | |
| - windows-latest | |
| python-version: ["3.10", "3.11", "3.12"] | |
| mdanalysis-version: | |
| - latest | |
| - develop | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Build information | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| # More info on options: https://github.com/conda-incubator/setup-miniconda | |
| - name: Install conda dependencies | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: devtools/conda-envs/test_env.yaml | |
| add-pip-as-python-dependency: true | |
| architecture: x64 | |
| channels: defaults | |
| activate-environment: zarrtraj-test | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| show-channel-urls: true | |
| # Need this to ensure miniconda installed | |
| # if not already on MacOS | |
| miniconda-version: latest | |
| - name: Install MDAnalysis version | |
| uses: MDAnalysis/install-mdanalysis@main | |
| with: | |
| version: ${{ matrix.mdanalysis-version }} | |
| install-tests: true | |
| installer: conda | |
| shell: bash -l {0} | |
| - name: Install package | |
| run: | | |
| python --version | |
| python -m pip install . --no-deps | |
| - name: Python information | |
| run: | | |
| which python | |
| which pip | |
| pip list | |
| conda info | |
| conda list | |
| - name: Run tests | |
| run: | | |
| pytest -v -x --cov=zarrtraj --cov-report=xml --color=yes zarrtraj/tests/ | |
| - name: codecov | |
| if: github.repository == 'Becksteinlab/zarrtraj' && github.event_name != | |
| 'schedule' | |
| uses: codecov/[email protected] | |
| with: | |
| file: coverage.xml | |
| name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} | |
| verbose: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| slug: Becksteinlab/zarrtraj | |
| pylint_check: | |
| if: github.repository == 'Becksteinlab/zarrtraj' | |
| needs: environment-config | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ needs.environment-config.outputs.stable-python-version }} | |
| - name: Install Pylint | |
| run: | | |
| which pip | |
| which python | |
| pip install pylint mdanalysis | |
| - name: Run Pylint | |
| env: | |
| PYLINTRC: .pylintrc | |
| run: | | |
| pylint zarrtraj | |
| pypi_check: | |
| if: github.repository == 'Becksteinlab/zarrtraj' | |
| needs: environment-config | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ needs.environment-config.outputs.stable-python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ needs.environment-config.outputs.stable-python-version }} | |
| - name: Install dependencies | |
| run: | | |
| pip install pipx twine | |
| - name: Build package | |
| run: | | |
| python -m pipx run build --sdist | |
| - name: Check package build | |
| run: | | |
| DISTRIBUTION=$(ls -t1 dist/zarrtraj-*.tar.gz | head -n 1) | |
| test -n "${DISTRIBUTION}" || { echo "no distribution dist/zarrtraj-*.tar.gz found"; exit 1; } | |
| echo "twine check $DISTRIBUTION" | |
| twine check $DISTRIBUTION |