FIX: Select function in segmentation resampling workflow #1541
Workflow file for this run
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| name: Stable tests | |
| on: | |
| push: | |
| branches: [ '*' ] | |
| tags: [ '*' ] | |
| pull_request: | |
| branches: [ master, 'maint/*', 'next' ] | |
| schedule: | |
| - cron: '0 0 * * *' | |
| defaults: | |
| run: | |
| shell: bash | |
| concurrency: | |
| group: python-${{ github.ref }} | |
| cancel-in-progress: true | |
| permissions: | |
| contents: read | |
| jobs: | |
| check_if_skip: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| commit_message: ${{ steps.get_commit_message.outputs.commit_message }} | |
| steps: | |
| - name: Get repo | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| - name: Print head git commit message | |
| id: get_commit_message | |
| run: | | |
| if [[ -z "$COMMIT_MSG" ]]; then | |
| COMMIT_MSG=$(git show -s --format=%s) | |
| else | |
| COMMIT_MSG=$(echo $COMMIT_MSG | head -n 1) | |
| fi | |
| echo $COMMIT_MSG | |
| echo "commit_message=$COMMIT_MSG" >> $GITHUB_OUTPUT | |
| env: | |
| COMMIT_MSG: ${{ github.event.head_commit.message }} | |
| build: | |
| needs: check_if_skip | |
| if: "!contains(needs.check_if_skip.outputs.commit_message, '[skip ci]')" | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Display Python version | |
| run: python -c "import sys; print(sys.version)" | |
| - name: Build smriprep | |
| run: pipx run build | |
| - name: Check distributions | |
| run: pipx run twine check dist/* | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: dist | |
| path: dist/ | |
| test: | |
| needs: [build] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.10", "3.11", "3.12"] | |
| install: [repo] | |
| include: | |
| - python-version: "3.11" | |
| install: sdist | |
| - python-version: "3.11" | |
| install: wheel | |
| - python-version: "3.11" | |
| install: editable | |
| env: | |
| INSTALL_TYPE: ${{ matrix.install }} | |
| FSLOUTPUTTYPE: NIFTI_GZ | |
| steps: | |
| - uses: actions/checkout@v4 | |
| if: matrix.install == 'repo' || matrix.install == 'editable' | |
| - name: Fetch packages | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: dist | |
| path: dist/ | |
| if: matrix.install == 'sdist' || matrix.install == 'wheel' | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Select archive | |
| run: | | |
| if [ "$INSTALL_TYPE" = "sdist" ]; then | |
| ARCHIVE=$( ls dist/*.tar.gz ) | |
| elif [ "$INSTALL_TYPE" = "wheel" ]; then | |
| ARCHIVE=$( ls dist/*.whl ) | |
| elif [ "$INSTALL_TYPE" = "repo" ]; then | |
| ARCHIVE="." | |
| elif [ "$INSTALL_TYPE" = "editable" ]; then | |
| ARCHIVE="-e ." | |
| fi | |
| echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV | |
| - name: Install package | |
| run: python -m pip install $ARCHIVE | |
| - name: Install test dependencies | |
| run: python -m pip install "smriprep[tests]" | |
| - name: Run tests | |
| run: pytest -sv --doctest-modules --cov smriprep --pyargs smriprep | |
| - uses: codecov/codecov-action@v4 | |
| name: Submit to CodeCov | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| style: | |
| if: "!contains(github.event.head_commit.message, '[skip ci]')" | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - run: pipx run ruff check smriprep | |
| - run: pipx run ruff format --diff smriprep |