WIP: Implement Pydra code-generators #53
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: | |
| generate-pydra: | |
| 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: Install pydra-auto-gen requirements | |
| run: | | |
| pip install -e interfaces/pydra/fileformats-medimage-mrtrix3 | |
| pip install -e interfaces/pydra/fileformats-medimage-mrtrix3-extras | |
| pip install -e interfaces/pydra/src | |
| pip install -r interfaces/pydra/requirements.txt | |
| - name: Generate task specifications | |
| run: > | |
| ./interfaces/pydra/generate.py | |
| $(pwd)/install/bin | |
| $(pwd)/interfaces/pydra/src | |
| $MRTRIX3_VERSION | |
| --log-errors | |
| --latest | |
| - name: Upload auto-gen pydra | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: AutoGen | |
| path: interfaces/pydra/src/pydra/tasks/mrtrix3/v3_0 | |
| devcheck: | |
| needs: [generate-pydra] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.8, 3.11] # Check oldest and newest versions | |
| pip-flags: ['', '--editable'] | |
| pydra: | |
| - 'pydra' | |
| - '--editable git+https://github.com/nipype/pydra.git#egg=pydra' | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Download auto-gen pydra | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: AutoGen | |
| path: interfaces/pydra/src/pydra/tasks/mrtrix3/v3_0 | |
| - 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 Pydra | |
| run: | | |
| pip install ${{ matrix.pydra }} | |
| python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| - name: Install task package | |
| run: | | |
| pip install ${{ matrix.pip-flags }} "pydra/src[dev]" | |
| python -c "import pydra.tasks.mrtrix3 as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| python -c "import pydra.tasks.mrtrix3.v3_0" | |
| python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| # test: | |
| # needs: [generate] | |
| # runs-on: ubuntu-latest | |
| # strategy: | |
| # matrix: | |
| # python-version: [3.8, 3.11] | |
| # defaults: | |
| # run: | |
| # shell: bash -l {0} | |
| # steps: | |
| # - 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 interfaces/pydra/fileformats-medimage-mrtrix interfaces/pydra/fileformats-medimage-mrtrix-extras 'interfaces/pydra/src[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 interfaces/src/pydra/tasks/mrtrix3 \ | |
| # --cov pydra.tasks.mrtrix3 --cov-report xml | |
| # - uses: codecov/codecov-action@v1 | |
| # if: ${{ always() }} | |
| deploy: | |
| needs: [devcheck] # , test] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.11] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Download auto-gen pydra | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: AutoGen | |
| path: interfaces/pydra/src/pydra/tasks/mrtrix3/v3_0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install build tools | |
| run: python -m pip install --upgrade pip twine build | |
| - name: Build source and wheel distributions | |
| working-directory: ./interfaces/pydra/src | |
| run: python -m build | |
| - name: Check distributions | |
| run: twine check interfaces/pydra/src/dist/* | |
| - name: Upload sdist | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: SDist | |
| path: interfaces/pydra/src/dist/*.tar.gz | |
| # Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets. | |
| # Secrets are not accessible in the if: condition [0], so set an output variable [1] | |
| # [0] https://github.community/t/16928 | |
| # [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter | |
| - name: Check for PyPI token on tag | |
| id: deployable | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| env: | |
| PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}" | |
| run: if [ -n "$PYPI_API_TOKEN" ]; then echo ::set-output name=DEPLOY::true; fi | |
| - name: Upload to PyPI | |
| if: steps.deployable.outputs.DEPLOY | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| packages-dir: interfaces/pydra/src/dist/ |