ENH: Autoupdate hooks [pre-commit.ci] #1965
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| name: Pathology PR | |
| on: | |
| push: | |
| branches: [ main ] | |
| tags: | |
| - '*' | |
| pull_request: | |
| branches: [ main ] | |
| paths: | |
| - "hi-ml-cpath/**" | |
| - ".github/workflows/cpath-pr.yml" | |
| # When the core hi-ml libraries change, test the histo test too, to find problems with backwards compatibility | |
| - "hi-ml-azure/**" | |
| - "hi-ml/**" | |
| # Cancel previous runs of this workflow that are still in progress. | |
| concurrency: | |
| group: ${{ github.ref }}/cpath-pr | |
| cancel-in-progress: ${{ github.ref != 'refs/heads/master' }} | |
| permissions: | |
| # This is required for requesting the Azure login token | |
| id-token: write | |
| # This is required for actions/checkout | |
| contents: read | |
| env: | |
| pythonVersion: 3.9 | |
| folder: hi-ml-cpath | |
| HIML_TENANT_ID: ${{ secrets.HIML_TENANT_ID }} | |
| HIML_RESOURCE_GROUP: ${{ secrets.HIML_RESOURCE_GROUP }} | |
| HIML_SUBSCRIPTION_ID: ${{ secrets.HIML_SUBSCRIPTION_ID }} | |
| HIML_WORKSPACE_NAME: ${{ secrets.HIML_WORKSPACE_NAME }} | |
| HIML_SERVICE_PRINCIPAL_ID: ${{ secrets.HIML_SERVICE_PRINCIPAL_ID }} | |
| # Set the AML experiment name for all AML jobs submitted during tests. Github.ref looks like | |
| # "refs/pull/123/merge" for PR builds. | |
| HIML_EXPERIMENT_NAME: ${{ github.ref }} | |
| jobs: | |
| cancel-azureml: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Azure login using OpenID Connect | |
| uses: ./.github/actions/azure-login | |
| - name: Cancel previous AzureML runs | |
| uses: ./.github/actions/cancel_azureml_jobs | |
| cpath-flake8: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Set up Python ${{ env.pythonVersion }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.pythonVersion }} | |
| - name: flake8 | |
| run: | | |
| cd ${{ env.folder }} | |
| make pip_test | |
| make flake8 | |
| cpath-mypy: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Set up Python ${{ env.pythonVersion }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.pythonVersion }} | |
| - name: mypy | |
| run: | | |
| cd ${{ env.folder }} | |
| make pip_test | |
| make mypy | |
| cpath-pytest: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Prepare Conda environment | |
| uses: ./.github/actions/prepare_cpath_environment | |
| - name: Azure login using OpenID Connect | |
| uses: ./.github/actions/azure-login | |
| - name: Test with pytest | |
| run: | | |
| cd ${{ env.folder }} | |
| # Run tests | |
| make pip_test | |
| make pytest_coverage | |
| - name: Upload coverage reports to Codecov | |
| # Coverage should also be uploaded if tests still fail. | |
| # This will pick up the file coverage.xml from the test run | |
| if: always() | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| flags: ${{ env.folder }} | |
| cpath-pytest-gpu: | |
| runs-on: ubuntu-20.04 | |
| needs: [ cancel-azureml ] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Prepare Conda environment | |
| uses: ./.github/actions/prepare_cpath_environment | |
| - name: Azure login using OpenID Connect | |
| uses: ./.github/actions/azure-login | |
| - name: Run GPU tests | |
| run: | | |
| cd ${{ env.folder }} | |
| make pytest_gpu | |
| - name: Upload coverage reports to Codecov | |
| # Coverage should also be uploaded if tests still fail. | |
| # This will pick up the file pytest_gpu_coverage.xml from the GPU tests. | |
| if: always() | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| flags: ${{ env.folder }} | |
| smoke_test_cucim_slidespandaimagenetmil: | |
| runs-on: ubuntu-20.04 | |
| needs: [ cancel-azureml ] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Prepare Conda environment | |
| uses: ./.github/actions/prepare_cpath_environment | |
| - name: Azure login using OpenID Connect | |
| uses: ./.github/actions/azure-login | |
| - name: smoke test | |
| run: | | |
| cd ${{ env.folder }} | |
| make smoke_test_cucim_slidespandaimagenetmil_aml | |
| smoke_test_openslide_slidespandaimagenetmil: | |
| runs-on: ubuntu-20.04 | |
| needs: [ cancel-azureml ] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Prepare Conda environment | |
| uses: ./.github/actions/prepare_cpath_environment | |
| - name: Azure login using OpenID Connect | |
| uses: ./.github/actions/azure-login | |
| - name: smoke test | |
| run: | | |
| cd ${{ env.folder }} | |
| make smoke_test_openslide_slidespandaimagenetmil_aml | |
| smoke_test_tilespandaimagenetmil: | |
| runs-on: ubuntu-20.04 | |
| needs: [ cancel-azureml ] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Prepare Conda environment | |
| uses: ./.github/actions/prepare_cpath_environment | |
| - name: Azure login using OpenID Connect | |
| uses: ./.github/actions/azure-login | |
| - name: smoke test | |
| run: | | |
| cd ${{ env.folder }} | |
| make smoke_test_tilespandaimagenetmil_aml | |
| smoke_test_tcgacrckimagenetmil: | |
| runs-on: ubuntu-20.04 | |
| needs: [ cancel-azureml ] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Prepare Conda environment | |
| uses: ./.github/actions/prepare_cpath_environment | |
| - name: Azure login using OpenID Connect | |
| uses: ./.github/actions/azure-login | |
| - name: smoke test | |
| run: | | |
| cd ${{ env.folder }} | |
| make smoke_test_tcgacrckimagenetmil_aml | |
| smoke_test_tcgacrcksslmil: | |
| runs-on: ubuntu-20.04 | |
| needs: [ cancel-azureml ] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Prepare Conda environment | |
| uses: ./.github/actions/prepare_cpath_environment | |
| - name: Azure login using OpenID Connect | |
| uses: ./.github/actions/azure-login | |
| - name: smoke test | |
| run: | | |
| cd ${{ env.folder }} | |
| make smoke_test_tcgacrcksslmil_aml | |
| smoke_test_crck_simclr: | |
| runs-on: ubuntu-20.04 | |
| needs: [ cancel-azureml ] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Prepare Conda environment | |
| uses: ./.github/actions/prepare_cpath_environment | |
| - name: Azure login using OpenID Connect | |
| uses: ./.github/actions/azure-login | |
| - name: smoke test | |
| run: | | |
| cd ${{ env.folder }} | |
| make smoke_test_crck_simclr_aml | |
| smoke_test_crck_flexible_finetuning: | |
| runs-on: ubuntu-20.04 | |
| needs: [ cancel-azureml ] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Prepare Conda environment | |
| uses: ./.github/actions/prepare_cpath_environment | |
| - name: Azure login using OpenID Connect | |
| uses: ./.github/actions/azure-login | |
| - name: smoke test | |
| run: | | |
| cd ${{ env.folder }} | |
| make smoke_test_crck_flexible_finetuning_aml | |
| smoke_test_crck_loss_analysis: | |
| runs-on: ubuntu-20.04 | |
| needs: [ cancel-azureml ] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Prepare Conda environment | |
| uses: ./.github/actions/prepare_cpath_environment | |
| - name: Azure login using OpenID Connect | |
| uses: ./.github/actions/azure-login | |
| - name: smoke test | |
| run: | | |
| cd ${{ env.folder }} | |
| make smoke_test_crck_loss_analysis_aml | |
| smoke_test_slides_panda_loss_analysis: | |
| runs-on: ubuntu-20.04 | |
| needs: [ cancel-azureml ] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Prepare Conda environment | |
| uses: ./.github/actions/prepare_cpath_environment | |
| - name: Azure login using OpenID Connect | |
| uses: ./.github/actions/azure-login | |
| - name: smoke test | |
| run: | | |
| cd ${{ env.folder }} | |
| make smoke_test_slides_panda_loss_analysis_aml | |
| smoke_test_slides_panda_no_ddp_sampler: | |
| runs-on: ubuntu-20.04 | |
| needs: [ cancel-azureml ] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Prepare Conda environment | |
| uses: ./.github/actions/prepare_cpath_environment | |
| - name: Azure login using OpenID Connect | |
| uses: ./.github/actions/azure-login | |
| - name: smoke test | |
| run: | | |
| cd ${{ env.folder }} | |
| make smoke_test_slides_panda_no_ddp_sampler_aml | |
| smoke_test_tiles_panda_no_ddp_sampler: | |
| runs-on: ubuntu-20.04 | |
| needs: [ cancel-azureml ] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Prepare Conda environment | |
| uses: ./.github/actions/prepare_cpath_environment | |
| - name: Azure login using OpenID Connect | |
| uses: ./.github/actions/azure-login | |
| - name: smoke test | |
| run: | | |
| cd ${{ env.folder }} | |
| make smoke_test_tiles_panda_no_ddp_sampler_aml | |
| smoke_test_montage_creation: | |
| runs-on: ubuntu-20.04 | |
| needs: [ cancel-azureml ] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Prepare Conda environment | |
| uses: ./.github/actions/prepare_cpath_environment | |
| - name: Azure login using OpenID Connect | |
| uses: ./.github/actions/azure-login | |
| - name: smoke test | |
| run: | | |
| cd ${{ env.folder }} | |
| make smoke_test_montage_creation | |
| cpath-publish-pypi-package: | |
| runs-on: ubuntu-20.04 | |
| needs: [ | |
| cpath-flake8, | |
| cpath-mypy, | |
| cpath-pytest, | |
| cpath-pytest-gpu, | |
| smoke_test_cucim_slidespandaimagenetmil, | |
| smoke_test_openslide_slidespandaimagenetmil, | |
| smoke_test_tilespandaimagenetmil, | |
| smoke_test_tcgacrckimagenetmil, | |
| smoke_test_tcgacrcksslmil, | |
| smoke_test_crck_simclr, | |
| smoke_test_crck_flexible_finetuning, | |
| smoke_test_crck_loss_analysis, | |
| smoke_test_slides_panda_loss_analysis, | |
| smoke_test_slides_panda_no_ddp_sampler, | |
| smoke_test_tiles_panda_no_ddp_sampler, | |
| smoke_test_montage_creation, | |
| ] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Set up Python ${{ env.pythonVersion }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.pythonVersion }} | |
| - name: Install build tools | |
| run: make pip_build | |
| - name: Build a binary wheel and a source tarball | |
| run: | | |
| cd ${{ env.folder }} | |
| make build | |
| - name: Test the binary wheel | |
| run: | | |
| cd ${{ env.folder }} | |
| make test_wheel | |
| - name: Publish package to TestPyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_TEST_API_TOKEN }} | |
| packages_dir: ${{ env.folder }}/dist/ | |
| repository_url: https://test.pypi.org/legacy/ | |
| verbose: true | |
| skip_existing: true | |
| - name: Publish package to PyPI | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v') | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| packages_dir: ${{ env.folder }}/dist/ | |
| verbose: true | |
| cpath-pr-completed: | |
| runs-on: ubuntu-20.04 | |
| if: "!startsWith(github.ref, 'refs/tags/v')" | |
| needs: [ cpath-publish-pypi-package ] | |
| steps: | |
| - name: Final PR Job | |
| run: | | |
| echo "All cpath PR jobs have passed." |