Added workflow for vectra slides #16
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| name: Tests linux | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| branches: | |
| - dev | |
| - master | |
| push: | |
| branches: | |
| - dev | |
| - master | |
| jobs: | |
| build-linux: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 5 | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10"] | |
| timeout-minutes: 60 # add a timeout | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Display Python version | |
| run: python -c "import sys; print(sys.version)" | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install openslide-tools | |
| sudo apt-get install pandoc | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-activate-base: false | |
| activate-environment: pathml | |
| environment-file: requirements/environment_test.yml | |
| # mamba-version: "*" | |
| miniforge-version: latest | |
| use-mamba: true | |
| channels: conda-forge | |
| python-version: ${{ matrix.python-version }} | |
| - name: Debugging | |
| run: | | |
| echo "Printing the environment.yml file..." | |
| cat requirements/environment_test.yml | |
| echo "Checking the status of mamba..." | |
| mamba --version | |
| echo "Checking the available disk space..." | |
| df -h | |
| - name: Install dependencies with mamba | |
| shell: bash -l {0} | |
| run: mamba env update --file requirements/environment_test.yml --name pathml | |
| - name: Conda info | |
| shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda list | |
| - name: Set default Temurin JDK 17 | |
| run: | | |
| sudo update-java-alternatives --set temurin-17-jdk-amd64 || true | |
| java -version | |
| - name: Install PathML | |
| shell: bash -l {0} | |
| run: pip install -e . | |
| - name: Install torchvision | |
| shell: bash -l {0} | |
| run: pip install torchvision==0.14.1 | |
| - name: disk usage | |
| shell: bash -l {0} | |
| run: | | |
| sudo df -h | |
| sudo du -h | |
| - name: free disk space | |
| run: | | |
| sudo swapoff -a | |
| sudo rm -f /swapfile | |
| sudo apt clean | |
| docker rmi $(docker image ls -aq) | |
| sudo df -h | |
| sudo du -h | |
| # - name: Check Coverage Command | |
| # run: | | |
| # which coverage | |
| # coverage --version | |
| # - name: Test with pytest for tile_stitcher | |
| # run: | | |
| # java -version | |
| # python -m pytest tests/preprocessing_tests/test_tilestitcher.py | |
| # - name: Test with pytest and generate coverage report | |
| # shell: bash -l {0} | |
| # run: | | |
| # coverage run -m pytest -m "not slow and not exclude" | |
| # coverage xml | |
| # - name: Upload coverage to Codecov | |
| # uses: codecov/codecov-action@v2 | |
| # with: | |
| # token: ${{ secrets.CODECOV_TOKEN }} | |
| # env_vars: OS,PYTHON | |
| # fail_ci_if_error: true | |
| # files: ./coverage.xml | |
| # name: codecov-umbrella | |
| # verbose: true | |
| - name: Test other modules with pytest and generate coverage | |
| shell: bash -l {0} | |
| run: | | |
| COVERAGE_FILE=.coverage_others coverage run -m pytest -m "not slow and not exclude" | |
| - name: Test tile_stitcher with pytest and generate coverage | |
| shell: bash -l {0} | |
| run: | | |
| COVERAGE_FILE=.coverage_tilestitcher coverage run -m pytest tests/preprocessing_tests/test_tilestitcher.py | |
| - name: List Files in Directory | |
| shell: bash -l {0} | |
| run: | | |
| ls -la | |
| - name: Combine Coverage Data | |
| shell: bash -l {0} | |
| run: | | |
| coverage combine .coverage_tilestitcher .coverage_others | |
| - name: Generate Combined Coverage Report | |
| shell: bash -l {0} | |
| run: | | |
| coverage xml -o combined_coverage.xml | |
| # - name: Combine coverage data | |
| # shell: bash -l {0} | |
| # run: | | |
| # coverage combine coverage_tilestitcher.xml coverage_others.xml | |
| # coverage xml -o coverage_combined.xml | |
| - name: Upload combined coverage to Codecov | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| env_vars: OS,PYTHON | |
| fail_ci_if_error: true | |
| files: ./combined_coverage.xml | |
| name: codecov-umbrella | |
| verbose: true | |
| - name: Compile docs | |
| shell: bash -l {0} | |
| run: | | |
| cd docs | |
| pip install -r readthedocs-requirements.txt | |
| make html |