CI #253
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: "CI" | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| branches: | |
| - main | |
| push: | |
| branches: | |
| - main | |
| schedule: | |
| # At 07:00 UTC | |
| - cron: "0 7 * * *" | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.ref }}" | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -leo pipefail {0} | |
| jobs: | |
| tests: | |
| runs-on: ${{ matrix.OS }}-latest | |
| name: "tests" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ['ubuntu',] | |
| python-version: | |
| - "3.9" | |
| - "3.10" | |
| - "3.11" | |
| include: | |
| - os: 'macos' | |
| python-version: "3.11" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Get current date | |
| id: date | |
| run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}" | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yml | |
| environment-name: kartograf | |
| cache-environment: true | |
| cache-downloads: true | |
| cache-environment-key: environment-${{ steps.date.outputs.date }} | |
| cache-downloads-key: downloads-${{ steps.date.outputs.date }} | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| lomap2 | |
| openfe | |
| - name: "Install" | |
| run: pip install --no-deps -e . | |
| - name: "Test imports" | |
| run: | | |
| # if we add more to this, consider changing to for + env vars | |
| python -Ic "import kartograf" | |
| - name: "Environment Information" | |
| run: | | |
| micromamba info | |
| micromamba list | |
| - name: "Run tests" | |
| run: | | |
| # add openfe-benchmarks | |
| pip install --no-deps git+https://github.com/OpenFreeEnergy/openfe-benchmarks.git | |
| # run tests | |
| pytest -n auto -v --cov=kartograf --cov-report=xml | |
| - name: "Test Notebooks" | |
| if: ${{ matrix.os != 'macos' }} | |
| run: | | |
| # Only need to test the notebook(s) in examples/ | |
| pytest -v --nbval-lax examples/ | |
| - name: codecov | |
| if: ${{ github.repository == 'OpenFreeEnergy/kartograf' && github.event != 'schedule'}} | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| env_vars: OS,PYTHON | |
| fail_ci_if_error: True | |
| verbose: True |