Clean examples -- CLI protein-ligand example for Tyk2 (#1223) #3262
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| name: CI | |
| on: | |
| merge_group: | |
| pull_request: | |
| branches: | |
| - "main" | |
| - "0.10.*" | |
| schedule: | |
| # nightly tests | |
| - cron: "0 0 * * *" | |
| push: | |
| branches: | |
| - main | |
| - "0.10.x" | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Test on ubuntu-latest, Python ${{ matrix.python-version }}, OpenMM ${{ matrix.openmm }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.9, "3.10"] | |
| openmm: ["8.0", "7.7"] | |
| include: | |
| - openmm: "dev" | |
| python-version: "3.10" | |
| env: | |
| OPENMM: ${{ matrix.openmm }} | |
| OE_LICENSE: ${{ github.workspace }}/oe_license.txt | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Additional info about the build | |
| shell: bash | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| - name: Setup micromamba dev | |
| if: ${{ matrix.openmm == 'dev' }} | |
| uses: mamba-org/provision-with-micromamba@main | |
| with: | |
| environment-file: devtools/conda-envs/test_env.yaml | |
| environment-name: test | |
| channels: jaimergp/label/unsupported-cudatoolkit-shim,conda-forge/label/openmm_dev,conda-forge,openeye | |
| channel-priority: flexible | |
| cache-env: true | |
| cache-downloads: true | |
| extra-specs: | | |
| python==${{ matrix.python-version }} | |
| openmmtools==0.23.0 | |
| openmm==8.0.0dev3 | |
| - name: Setup micromamba | |
| if: ${{ matrix.openmm != 'dev' }} | |
| uses: mamba-org/provision-with-micromamba@main | |
| with: | |
| environment-file: devtools/conda-envs/test_env.yaml | |
| environment-name: test | |
| cache-env: true | |
| cache-downloads: true | |
| extra-specs: | | |
| python==${{ matrix.python-version }} | |
| openmm==${{ matrix.openmm }} | |
| openmmtools==0.23.0 | |
| - name: Install package | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install --no-deps -v . | |
| - name: Environment Information | |
| shell: bash -l {0} | |
| run: | | |
| micromamba info | |
| micromamba list | |
| - name: Decrypt OpenEye license | |
| shell: bash -l {0} | |
| env: | |
| OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }} | |
| run: | | |
| echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE} | |
| python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'OpenEye license checks failed!'" | |
| - name: Test the package | |
| shell: bash -l {0} | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.S3_TEST_KEY }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.S3_TEST_SECRET }} | |
| run: | | |
| export TRAVIS=true | |
| pytest -v --cov-report xml --cov=perses --durations=0 -a "not advanced" -n auto -m "not gpu_needed" perses/tests | |
| - name: Codecov | |
| if: ${{ github.repository == 'choderalab/perses' | |
| && github.event != 'schedule' }} | |
| uses: codecov/codecov-action@v1 | |
| with: | |
| file: ./coverage.xml | |
| fail_ci_if_error: true |