hi-ml/.github/workflows/cpath-pr.yml

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' }}

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 }}
  HIML_SERVICE_PRINCIPAL_PASSWORD: ${{ secrets.HIML_SERVICE_PRINCIPAL_PASSWORD }}
  # 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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@v1.8.5
        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@v1.8.5
        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."