debugging running tests #168
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| name: CI/CD | |
| on: | |
| push: | |
| branches: [ main, develop ] | |
| pull_request: | |
| branches: [ main, develop ] | |
| release: | |
| types: [published] | |
| defaults: | |
| run: | |
| shell: bash | |
| jobs: | |
| download-task-template: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Download task template | |
| run: | | |
| LATEST=$(curl -s https://api.github.com/repos/nipype/pydra-tasks-template/releases/latest | grep tag_name | awk -F\" '{print $4}') | |
| curl -Lo pydra-tasks-template.tar.gz https://github.com/nipype/pydra-tasks-template/archive/refs/tags/$LATEST.tar.gz | |
| tar xzf pydra-tasks-template.tar.gz | |
| rm pydra-tasks-template.tar.gz | |
| mv pydra-tasks-template-${LATEST#v} pydra-tasks-template | |
| tar czf pydra-tasks-template.tar.gz pydra-tasks-template | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: tasks-template | |
| path: pydra-tasks-template.tar.gz | |
| test: | |
| needs: [download-task-template] | |
| strategy: | |
| matrix: | |
| os: [macos-latest, ubuntu-latest] | |
| python-version: ["3.8", "3.11"] | |
| fail-fast: false | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Download the pydra-tasks-template artefact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: tasks-template | |
| path: . | |
| - name: Extract the pydra-tasks-template | |
| run: tar xzf pydra-tasks-template.tar.gz | |
| - name: Unset header | |
| # checkout@v2 adds a header that makes branch protection report errors | |
| # because the Github action bot is not a collaborator on the repo | |
| run: | | |
| git config --local --unset http.https://github.com/.extraheader | |
| git config --global init.defaultBranch main | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "Dummy User" | |
| - name: Fetch tags | |
| run: git fetch --prune --unshallow | |
| - name: Disable etelemetry | |
| run: echo "NO_ET=TRUE" >> $GITHUB_ENV | |
| - name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Update build tools | |
| run: python3 -m pip install --break-system-packages --upgrade pip setuptools wheel | |
| - name: Install required file-formats packages | |
| run: | | |
| pushd required-fileformats | |
| python3 -m pip install --break-system-packages -r requirements.txt | |
| popd | |
| - name: Install Dipy separately as it was causing trouble | |
| run: python3 -m pip install --break-system-packages dipy | |
| - name: Install Package | |
| run: python3 -m pip install --break-system-packages .[test] | |
| - name: Pytest | |
| run: >- | |
| NIPYPE2PYDRA_PYDRA_TASK_TEMPLATE=$PWD/pydra-tasks-template | |
| pytest -vvs --cov nipype2pydra --cov-config .coveragerc --cov-report xml | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| fail_ci_if_error: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| deploy: | |
| needs: [test] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Unset header | |
| # checkout@v2 adds a header that makes branch protection report errors | |
| # because the Github action bot is not a collaborator on the repo | |
| run: git config --local --unset http.https://github.com/.extraheader | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' | |
| - name: Install build tools | |
| run: python3 -m pip install --break-system-packages build twine | |
| - name: Build source and wheel distributions | |
| run: python3 -m build . | |
| - name: Check distributions | |
| run: twine check dist/* | |
| - name: Check for PyPI token on tag | |
| id: deployable | |
| if: github.event_name == 'release' | |
| env: | |
| PYPI_API_TOKEN: "${{ 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@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| trigger_post_release: | |
| needs: [deploy] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| repo: | |
| - afni | |
| - ants | |
| - fsl | |
| - freesurfer | |
| - mriqc | |
| - niworkflows | |
| - nireports | |
| steps: | |
| - name: Trigger post-release on downstream repos | |
| if: github.event_name == 'release' | |
| run: | | |
| curl -XPOST -u "${{ env.POST_RELEASE_PAT }}" -H "Accept: application/vnd.github.everest-preview+json" \ | |
| "https://api.github.com/repos/nipype/pydra-${{ matrix.repo }}/dispatches" \ | |
| -d '{"event_type": "create-post-release"}' | |
| env: | |
| PAT: ${{ env.POST_RELEASE_PAT }} |