Updating documentation #11
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: 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: | |
| main-tests: | |
| if: "github.repository == 'MDAnalysis/helanal'" | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macOS-latest, windows-latest] | |
| mdanalysis-version: ["latest", "develop"] | |
| python-version: ["3.10", "3.11", "3.12"] | |
| exclude: | |
| # Entries here exclude particular combinations of the matrix | |
| # Edit or remove as particular combinations come into or out of date | |
| # Below we exclude runs with the latest release and Python 3.12 | |
| - mdanalysis-version: "latest" | |
| python-version: "3.12" | |
| 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 | |
| miniforge-variant: Mambaforge | |
| use-mamba: true | |
| channels: conda-forge, defaults | |
| activate-environment: helanal-test | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| show-channel-urls: true | |
| - name: Install MDAnalysis version | |
| uses: MDAnalysis/install-mdanalysis@main | |
| with: | |
| version: ${{ matrix.mdanalysis-version }} | |
| install-tests: true | |
| installer: mamba | |
| shell: bash -l {0} | |
| - name: Install package | |
| run: | | |
| python --version | |
| python -m pip install . --no-deps | |
| - name: Python information | |
| run: | | |
| which python | |
| which pip | |
| pip list | |
| conda info | |
| conda list | |
| - name: Run tests | |
| run: | | |
| pytest -n 2 -v --cov=helanal --cov-report=xml --color=yes helanal/tests/ | |
| - name: codecov | |
| if: github.repository == 'MDAnalysis/helanal' && github.event_name != 'schedule' | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| file: coverage.xml | |
| name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} | |
| verbose: True | |
| # to upload coverage reports, set a secret called CODECOV_TOKEN | |
| # in the repository settings | |
| # (Obtain this from the Codecov website after setting up the repository there) | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| # To fail the CI if there's an error, keep this set to true | |
| # If repository forks need to run CI, you may need to set this to false | |
| # Forks can't access the CODECOV_TOKEN secret, | |
| # and a failed upload registers as an error | |
| fail_ci_if_error: true | |
| pylint_check: | |
| if: "github.repository == 'MDAnalysis/helanal'" | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| - name: Install Pylint | |
| run: | | |
| which pip | |
| which python | |
| pip install pylint mdanalysis | |
| - name: Run Pylint | |
| env: | |
| PYLINTRC: .pylintrc | |
| run: | | |
| pylint helanal | |
| pypi_check: | |
| if: "github.repository == 'MDAnalysis/helanal'" | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| - name: Install dependencies | |
| run: | | |
| pip install pipx twine | |
| - name: Build package | |
| run: | | |
| python -m pipx run build --sdist | |
| - name: Check package build | |
| run: | | |
| DISTRIBUTION=$(ls -t1 dist/helanal-*.tar.gz | head -n 1) | |
| test -n "${DISTRIBUTION}" || { echo "no distribution dist/helanal-*.tar.gz found"; exit 1; } | |
| echo "twine check $DISTRIBUTION" | |
| twine check $DISTRIBUTION |