Globally set RDKit to include all properties when pickling an RDKit Mol #2153
Workflow file for this run
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| name: "CI" | |
| on: | |
| # Allow for workflows to be manuallly triggered | |
| workflow_dispatch: | |
| pull_request: | |
| branches: | |
| - main | |
| push: | |
| branches: | |
| - main | |
| schedule: | |
| # At 07:00 UTC on Monday and Thursday. | |
| - cron: "0 7 * * *" | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.ref }}" | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| tests: | |
| runs-on: ${{ matrix.OS }} | |
| name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }} 🗃️${{ matrix.pydantic-version }}" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ['ubuntu-latest', macos-latest] | |
| pydantic-version: [">1"] | |
| python-version: | |
| - "3.10" | |
| - "3.11" | |
| - "3.12" | |
| include: | |
| # Note: we still need to add support for macos-13 | |
| # see https://github.com/OpenFreeEnergy/openfe/issues/842 | |
| - os: "ubuntu-latest" | |
| python-version: "3.11" | |
| pydantic-version: "<2" | |
| env: | |
| OE_LICENSE: ${{ github.workspace }}/oe_license.txt | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: "Setup Micromamba" | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| micromamba-binary-path: ~/.local/bin/micromamba | |
| environment-file: environment.yml | |
| environment-name: gufe | |
| cache-environment: true | |
| cache-downloads: true | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| init-shell: bash | |
| - name: "Install" | |
| run: python -m pip install --no-deps -e . | |
| - name: "Test imports" | |
| run: | | |
| # if we add more to this, consider changing to for + env vars | |
| python -Ic "import gufe; print(gufe.__version__)" | |
| - name: "Environment Information" | |
| run: | | |
| micromamba info | |
| micromamba list | |
| - name: "Run tests" | |
| run: | | |
| pytest -n 2 -v --cov=gufe --cov-report=xml | |
| - name: codecov | |
| if: ${{ github.repository == 'OpenFreeEnergy/gufe' | |
| && github.event != 'schedule' }} | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: coverage.xml | |
| fail_ci_if_error: False | |
| verbose: True | |
| package_build_and_test: | |
| runs-on: ubuntu-latest | |
| name: "package build and install test" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: "Setup Micromamba" | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yml | |
| environment-name: gufe | |
| cache-environment: true | |
| cache-downloads: true | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| init-shell: bash | |
| - name: "install extra deps" | |
| run: pip install pipx wheel twine readme-renderer | |
| - name: "build sdist" | |
| run: pipx run build --sdist --outdir dist | |
| - name: "check package build" | |
| run: | | |
| dist=$(ls -t1 dist/gufe-*tar.gz | head -n1) | |
| test -n "${dist}" || { echo "no distribution found"; exit 1; } | |
| twine check $dist | |
| - name: "install from source dist" | |
| working-directory: ./dist | |
| run: python -m pip install gufe-*tar.gz | |
| - name: "install checks" | |
| working-directory: ./dist | |
| run: | | |
| pip check | |
| python -Ic "import gufe; print(gufe.__version__)" | |
| - name: "run tests" | |
| working-directory: ./dist | |
| run: pytest -n auto --pyargs gufe |