Add AtomMappingError
#2114
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: | |
| # 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 |