Adding model to segment bones #155
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| jobs: | |
| Linting: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.7", "3.8", "3.9", "3.10"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: actions/cache@v2 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip | |
| - name: Install Dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| make dev | |
| pip install --upgrade click==8.0.2 | |
| - name: Lint with isort, black, docformatter, flake8 | |
| run: | | |
| make lint | |
| Documentation: | |
| needs: Linting | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.7", "3.8", "3.9", "3.10"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: actions/cache@v2 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip | |
| - name: Install Dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| make dev | |
| pip install -e '.[dev]' | |
| - name: Generate Docs | |
| run: | | |
| make build-docs | |
| Build: | |
| needs: Documentation | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ["3.7", "3.8", "3.9", "3.10"] # there are some issues with numpy multiarray in 3.7 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Dependencies | |
| # there are some issues with numpy multiarray in 3.7, affecting numba 0.54 installation | |
| # SimpleITK 2.1.0 does not support non-orthonormal directions | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install numba==0.53.1 | |
| pip install tensorflow>=2.0.0 | |
| pip install torch | |
| pip install sigpy | |
| pip install --upgrade simpleitk==2.0.2 | |
| make dev | |
| pip install -e '.[dev]' | |
| - name: Install Elastix | |
| run: | | |
| wget https://github.com/SuperElastix/elastix/releases/download/4.9.0/elastix-4.9.0-linux.tar.bz2 | |
| ELASTIX_FOLDER="elastix" | |
| mkdir -p $ELASTIX_FOLDER | |
| tar -xvf elastix-4.9.0-linux.tar.bz2 -C $ELASTIX_FOLDER | |
| ELASTIX_DIR="$(realpath $ELASTIX_FOLDER)" | |
| echo "PATH=${ELASTIX_DIR}/bin:${PATH}" >> $GITHUB_ENV | |
| echo "LD_LIBRARY_PATH=${ELASTIX_DIR}/lib:${LD_LIBRARY_PATH}" >> $GITHUB_ENV | |
| - name: Test with pytest | |
| run: | | |
| pip install pytest | |
| pip install pytest-cov | |
| make test-cov | |
| - name: Upload to codecov.io | |
| uses: codecov/codecov-action@v1 | |
| with: | |
| file: ./coverage.xml | |
| flags: unittests | |
| name: codecov-umbrella | |
| fail_ci_if_error: true |