doc changes and adding test_ files #4
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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: | |
| main-tests: | |
| if: "github.repository == 'BecksteinLab/mdaadb-kit'" | |
| 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| # Edit or remove as particular combinations come into or out of date | |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@v3 | |
| 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: mdaadb-kit-test | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| show-channel-urls: true | |
| - name: Install MDAnalysis version | |
| uses: MDAnalysis/install-mdanalysis@main | |
| with: | |
| version: ${{ matrix.mdanalysis-version }} | |
| install-tests: false | |
| installer: mamba | |
| shell: bash -l {0} | |
| - name: Install package | |
| run: | | |
| python --version | |
| python -m pip install . --no-deps | |
| - name: Python information | |
| run: | | |
| which python | |
| which pip | |
| pip list | |
| conda info | |
| conda list | |
| - name: Run tests | |
| run: | | |
| pytest -n 2 -v --cov=mdaadb --cov-report=xml --color=yes mdaadb/tests/ | |
| - name: codecov | |
| if: github.repository == 'BecksteinLab/mdaadb-kit' && github.event_name != 'schedule' | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| file: coverage.xml | |
| name: codecov-${{ 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: ${{ secrets.CODECOV_TOKEN }} | |
| # To fail the CI if there's an error, keep this set to true | |
| # If repository forks need to run CI, you may need to set this to false | |
| # Forks can't access the CODECOV_TOKEN secret, | |
| # and a failed upload registers as an error | |
| fail_ci_if_error: true | |
| pylint_check: | |
| if: "github.repository == 'BecksteinLab/mdaadb-kit'" | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install Pylint | |
| run: | | |
| which pip | |
| which python | |
| pip install pylint mdanalysis | |
| - name: Run Pylint | |
| env: | |
| PYLINTRC: .pylintrc | |
| run: | | |
| pylint mdaadb-kit | |
| pypi_check: | |
| if: "github.repository == 'BecksteinLab/mdaadb-kit'" | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install dependencies | |
| run: | | |
| pip install pipx twine | |
| - name: Build package | |
| run: | | |
| python -m pipx run build --sdist | |
| - name: Check package build | |
| run: | | |
| DISTRIBUTION=$(ls -t1 dist/mdaadb_kit-*.tar.gz | head -n 1) | |
| test -n "${DISTRIBUTION}" || { echo "no distribution dist/mdaadb-kit-*.tar.gz found"; exit 1; } | |
| echo "twine check $DISTRIBUTION" | |
| twine check $DISTRIBUTION |