WIP: Implement Pydra code-generators #37
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| #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: qt5 | |
| SCCACHE_GHA_ENABLED: "true" | |
| SCCACHE_CACHE_SIZE: "2G" | |
| CXX_COMPILER_LAUNCHER: sccache | |
| steps: | |
| - uses: actions/checkout@v1 | |
| - name: Install MRtrix dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install clang libqt5opengl5-dev libqt5svg5-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev | |
| - name: Run sccache-cache | |
| uses: mozilla-actions/sccache-action@v0.0.3 | |
| - name: Configure MRtrix | |
| run: ./configure -assert || { cat configure.log; false; } | |
| - name: Build MRtrix | |
| run: ./build -nowarnings -persistent -nopaginate || { cat build.log; false; } | |
| - name: Set PATH Variable | |
| run: echo "PATH=$PATH:$(pwd)/bin" >> $GITHUB_ENV | |
| - name: Set LD_LIBRARY_PATH Variable | |
| run: echo "LD_LIBRARY_PATH=$(pwd)/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 -r pydra/fileformats-mrtrix | |
| pip install -r pydra/fileformats-mrtrix-extras | |
| pip install -r pydra/requirements.txt | |
| - name: Generate task specifications | |
| run: | | |
| python pydra/pydra-auto-gen.py | |
| - name: Upload auto-gen pydra | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: AutoGen | |
| path: pydra/src/pydra/tasks/mrtrix3/latest | |
| 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: pydra/src/pydra/tasks/mrtrix3/latest | |
| - 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 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 ".[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() }} | |
| 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: pydra/src/pydra/tasks/mrtrix3/latest | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install build tools | |
| run: python -m pip install --upgrade pip twine build | |
| - name: Build source and wheel distributions | |
| working-directory: ./pydra/src | |
| run: python -m build | |
| - name: Check distributions | |
| run: twine check pydra/src/dist/* | |
| - name: Upload sdist | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: SDist | |
| path: pydra/src/dist/*.tar.gz | |
| # Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets. | |
| # Secrets are not accessible in the if: condition [0], so set an output variable [1] | |
| # [0] https://github.community/t/16928 | |
| # [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter | |
| - name: Check for PyPI token on tag | |
| id: deployable | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| env: | |
| PYPI_API_TOKEN: "${{ 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: pydra/src/dist/ |