CI #37
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| name: CI | |
| on: | |
| # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming | |
| # Existing codes likely still have "master" as the primary branch | |
| # Both are tracked here to keep legacy and new codes working | |
| push: | |
| branches: | |
| - "main" | |
| paths-ignore: | |
| - '**/*.md' | |
| - '**/*.rst' | |
| - '**/*.ipynb' | |
| - '**/*.yml' | |
| - '**/*.yaml' | |
| - 'docs/**' | |
| - 'paper/**' | |
| - 'examples/**' | |
| - 'logos/**' | |
| pull_request: | |
| branches: | |
| - "main" | |
| paths-ignore: | |
| - '**/*.md' | |
| - '**/*.rst' | |
| - '**/*.ipynb' | |
| - '**/*.yml' | |
| - '**/*.yaml' | |
| - 'docs/**' | |
| - 'paper/**' | |
| - 'examples/**' | |
| - 'logos/**' | |
| schedule: | |
| # Nightly tests run on master 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 9 * * MON" | |
| workflow_dispatch: | |
| jobs: | |
| test: | |
| name: Test on ${{ matrix.cfg.os }}, Python ${{ matrix.cfg.python-version }} | |
| if: > | |
| !( | |
| (github.event_name == 'push' && contains(github.event.head_commit.message, '[skip ci]')) | |
| || | |
| (github.event_name == 'pull_request' && contains(github.event.pull_request.title, '[skip ci]')) | |
| || | |
| (github.event_name == 'pull_request' && contains(github.event.pull_request.head.ref, 'skip-ci')) | |
| ) | |
| runs-on: ${{ matrix.cfg.os }} | |
| strategy: | |
| fail-fast: false # do not cancel all in-progress jobs if any job variation fails | |
| matrix: | |
| cfg: | |
| - { os: ubuntu-latest, python-version: "3.10"} | |
| - { os: ubuntu-latest, python-version: "3.11"} | |
| - { os: ubuntu-latest, python-version: "3.12"} | |
| - { os: macos-latest, python-version: "3.10"} | |
| - { os: macos-latest, python-version: "3.11"} | |
| - { os: macos-latest, python-version: "3.12"} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Additional info about the build | |
| shell: bash | |
| run: | | |
| uname -a | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.cfg.python-version }} | |
| - name: Setup conda env | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: devtools/conda-envs/test_env.yaml | |
| environment-name: test | |
| condarc: | | |
| channels: | |
| - uibcdf | |
| - conda-forge | |
| - ambermd | |
| channel_priority: strict | |
| create-args: >- | |
| python=${{ matrix.cfg.python-version }} | |
| - name: Info conda | |
| shell: bash -l {0} | |
| run: | | |
| micromamba activate test | |
| micromamba info | |
| micromamba list | |
| - name: Install package | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install . --no-deps | |
| - name: Test import module | |
| shell: bash -l {0} | |
| run: | | |
| echo "::group::Importing module from home directory" | |
| cd | |
| pwd | |
| echo 'import molsysviewer; print("Version of the package: {}".format(molsysviewer.__version__))' | python | |
| echo "::endgroup::" | |
| - name: Run tests | |
| shell: bash -l {0} | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH:$(pwd) | |
| # pytest -n logical -v --cov-config=.coveragerc --cov=molsysviewer --cov-report=xml --junitxml=junit.xml --color=yes | |
| pytest -v --cov-config=.coveragerc --cov=molsysviewer --cov-report=xml --junitxml=junit.xml --color=yes | |
| - name: JS unit tests (Node) | |
| if: matrix.cfg.os == 'ubuntu-latest' && matrix.cfg.python-version == '3.12' | |
| shell: bash -l {0} | |
| run: | | |
| cd molsysviewer/js | |
| npm ci | |
| npm run build | |
| npm run test:js | |
| npm run coverage:js | |
| - name: Check coverage | |
| shell: bash -l {0} | |
| run: | | |
| cat ./coverage.xml | |
| if [ -f molsysviewer/js/coverage-js/lcov.info ]; then | |
| echo "JS coverage generated" | |
| fi | |
| - name: Upload coverage reports to Codecov | |
| if: matrix.cfg.os == 'ubuntu-latest' && matrix.cfg.python-version == '3.12' | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| verbose: true | |
| file: | | |
| ./coverage.xml | |
| ./molsysviewer/js/coverage-js/lcov.info | |
| flags: unittests | |
| name: codecov-${{ matrix.cfg.os }}-py${{ matrix.cfg.python-version }} | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - name: Upload test results to Codecov | |
| if: matrix.cfg.os == 'ubuntu-latest' && matrix.cfg.python-version == '3.12' && ${{ !cancelled() }} | |
| uses: codecov/test-results-action@v1 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} |