WIP: Implement Pydra code-generators #57
Workflow file for this run
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| #This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| # For deployment, it will be necessary to create a PyPI API token and store it as a secret | |
| # https://docs.github.com/en/actions/reference/encrypted-secrets | |
| name: Pydra | |
| on: | |
| push: | |
| branches: [ master ] | |
| tags: [ '*' ] | |
| pull_request: | |
| branches: | |
| - master | |
| - dev | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| env: | |
| CFLAGS: -Werror | |
| QT_SELECT: qt6 | |
| SCCACHE_GHA_ENABLED: "true" | |
| SCCACHE_CACHE_SIZE: "2G" | |
| steps: | |
| - uses: actions/checkout@v1 | |
| with: | |
| submodules: true | |
| - name: Determine MRtrix3 version | |
| run: echo "MRTRIX3_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV | |
| - name: install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install clang qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build | |
| - name: Run sccache-cache | |
| uses: mozilla-actions/sccache-action@v0.0.3 | |
| - name: Get CMake | |
| uses: lukka/get-cmake@latest | |
| with: | |
| cmakeVersion: '3.16.3' | |
| - name: Print CMake version | |
| run: cmake --version | |
| - name: configure | |
| run: > | |
| cmake | |
| -B build | |
| -G Ninja | |
| -D CMAKE_BUILD_TYPE=Release | |
| -D MRTRIX_BUILD_TESTS=ON | |
| -D MRTRIX_STL_DEBUGGING=ON | |
| -D MRTRIX_WARNINGS_AS_ERRORS=ON | |
| -D CMAKE_C_COMPILER=clang | |
| -D CMAKE_CXX_COMPILER=clang++ | |
| -D CMAKE_INSTALL_PREFIX=$(pwd)/install | |
| - name: Build Mrtrix | |
| run: cmake --build build | |
| - name: Install Mrtrix | |
| run: cmake --install build | |
| - name: Set PATH Variable | |
| run: echo "PATH=$PATH:$(pwd)/install/bin" >> $GITHUB_ENV | |
| - name: Set LD_LIBRARY_PATH Variable | |
| run: echo "LD_LIBRARY_PATH=$(pwd)/install/lib" >> $GITHUB_ENV | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| - name: Install Python build dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| - name: Clone Pydra-MRtrix3 package | |
| run: git clone https://github.com/nipype/pydra-mrtrix3.git pydra | |
| - name: Install pydra-auto-gen requirements | |
| run: | | |
| pip install -e ./pydra/fileformats-medimage-mrtrix3 | |
| pip install -e ./pydra/fileformats-medimage-mrtrix3-extras | |
| pip install -e ./pydra[dev] | |
| - name: Generate task specifications | |
| run: > | |
| ./pydra/generate.py | |
| $(pwd)/install/bin | |
| $(pwd)/pydra/src | |
| $MRTRIX3_VERSION | |
| --log-errors | |
| --latest | |
| - name: Upload MRtrix3 install | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: MRtrix3 | |
| path: mrtrix3/install | |
| - name: Upload auto-gen pydra | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: AutoGen | |
| path: pydra/tasks/mrtrix3/$MRTRIX3_VERSION | |
| - name: Write version file | |
| run: echo $MRTRIX3_VERSION > mrtrix3_version.txt | |
| - name: Upload version file | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: VersionFile | |
| path: pydra/tasks/mrtrix3/$MRTRIX3_VERSION | |
| test: | |
| needs: [build] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.8, 3.11] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Download version file | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: VersionFile | |
| path: mrtrix3_version.txt | |
| - name: Extract Mrtrix version | |
| run: echo "MRTRIX3_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV | |
| - uses: actions/checkout@v2 | |
| - name: Install Minconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-activate-base: true | |
| activate-environment: "" | |
| - name: Install MRtrix via Conda | |
| run: | | |
| conda install -c mrtrix3 mrtrix3 | |
| mrconvert --version | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install build dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| - name: Install task package | |
| run: | | |
| pip install pydra/fileformats-medimage-mrtrix pydra/fileformats-medimage-mrtrix-extras '.[test]' | |
| python -c "import pydra.tasks.mrtrix3 as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| - name: Test with pytest | |
| run: | | |
| pytest -sv --doctest-modules pydra/tasks/mrtrix3 \ | |
| --cov pydra.tasks.mrtrix3 --cov-report xml | |
| - uses: codecov/codecov-action@v1 | |
| if: ${{ always() }} | |