[ENH] add methods section #149
Workflow file for this run
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| --- | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - maint/* | |
| tags: | |
| - '*' | |
| pull_request: | |
| branches: | |
| - main | |
| - maint/* | |
| defaults: | |
| run: | |
| shell: bash | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| permissions: | |
| contents: read | |
| jobs: | |
| check_skip_flags: | |
| name: Check skip flags | |
| runs-on: ubuntu-latest | |
| outputs: | |
| head-commit-message: ${{ steps.get_head_commit_message.outputs.headCommitMsg }} | |
| steps: | |
| - name: Get repo | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| - name: Print head git commit message | |
| id: get_head_commit_message | |
| run: echo "headCommitMsg=$(git show -s --format=%s)" >> $GITHUB_OUTPUT | |
| download-test-data: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/cache@v3 | |
| id: cache | |
| env: | |
| cache-name: ds000017 | |
| with: | |
| path: /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data | |
| key: ${{ env.cache-name }} | |
| - if: ${{ steps.cache.outputs.cache-hit != 'true' }} | |
| name: Download fmriprep derivative of ds000017 | |
| id: download | |
| run: | | |
| mkdir -p /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data | |
| cd /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data | |
| wget --retry-connrefused \ | |
| --waitretry=5 \ | |
| --read-timeout=20 \ | |
| --timeout=15 \ | |
| -t 0 \ | |
| -q \ | |
| -O ds000017.tar.gz \ | |
| "https://zenodo.org/record/8091903/files/ds000017-fmriprep22.0.1-downsampled-nosurface.tar.gz?download=1" | |
| tar -xzf ds000017.tar.gz | |
| rm ds000017.tar.gz | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3 | |
| - run: pip install --upgrade build twine | |
| - name: Build sdist and wheel | |
| run: python -m build | |
| - run: twine check dist/* | |
| - name: Upload sdist and wheel artifacts | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: dist | |
| path: dist/ | |
| - name: Build git archive | |
| run: mkdir archive && git archive -v -o archive/archive.tgz HEAD | |
| - name: Upload git archive artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: archive | |
| path: archive/ | |
| test-package: | |
| runs-on: ubuntu-latest | |
| needs: [build] | |
| strategy: | |
| matrix: | |
| package: [wheel, sdist, archive] | |
| steps: | |
| - name: Download sdist and wheel artifacts | |
| if: matrix.package != 'archive' | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: dist | |
| path: dist/ | |
| - name: Download git archive artifact | |
| if: matrix.package == 'archive' | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: archive | |
| path: archive/ | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3 | |
| - name: Display Python version | |
| run: python -c "import sys; print(sys.version)" | |
| - name: Update pip | |
| run: pip install --upgrade pip | |
| - name: Install wheel | |
| if: matrix.package == 'wheel' | |
| run: pip install dist/*.whl | |
| - name: Install sdist | |
| if: matrix.package == 'sdist' | |
| run: pip install dist/*.tar.gz | |
| - name: Install archive | |
| if: matrix.package == 'archive' | |
| run: pip install archive/archive.tgz | |
| test-coverage: | |
| runs-on: ubuntu-latest | |
| needs: [build, download-test-data, check_skip_flags] | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.9', '3.10', '3.11', '3.12'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| name: Set up Python ${{ matrix.python-version }} | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Restore cached data ds000017 | |
| id: cache | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data | |
| key: ds000017 | |
| - name: Install build dependencies | |
| run: python -m pip install --upgrade pip | |
| - name: Install task package | |
| run: pip install -e .[test] | |
| - name: Test with pytest - ignore smoke test. | |
| if: ${{ !contains(needs.check_skip_flags.outputs.head-commit-message, 'full_test') }} | |
| run: | | |
| pytest -m "not smoke" --cov=giga_connectome --cov-report=xml --doctest-modules -v --pyargs giga_connectome | |
| - name: Full test - run all the test to generate accurate coverage report. | |
| if: ${{ contains(needs.check_skip_flags.outputs.head-commit-message, 'full_test') }} || ${{ github.event.pull_request.merged }} | |
| run: pytest --cov=giga_connectome --cov-report=xml --doctest-modules -v --pyargs giga_connectome | |
| - uses: codecov/codecov-action@v3 | |
| if: ${{ always() }} | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| docker: | |
| # build and test docker image | |
| if: ${{ contains(needs.check_skip_flags.outputs.head-commit-message, 'full_test') }} | |
| runs-on: ubuntu-latest | |
| needs: [download-test-data, check_skip_flags] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Build the Docker image | |
| run: | | |
| user_name="bids" | |
| docker build . --file Dockerfile --tag ${user_name}/giga_connectome | |
| mkdir -p "${HOME}/docker" | |
| docker save "${user_name}/giga_connectome" > "${HOME}/docker/image.tar" | |
| - name: Restore cached data ds000017 | |
| id: cache | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data | |
| key: ds000017 | |
| - name: Test the Docker image | |
| run: | | |
| docker load -i ${HOME}/docker/image.tar | |
| docker run --rm --read-only \ | |
| -v /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data:/test_data \ | |
| -v ./outputs:/outputs \ | |
| -v ./outputs/working_dir:/work \ | |
| bids/giga_connectome \ | |
| /test_data/ds000017-fmriprep22.0.1-downsampled-nosurface \ | |
| /outputs \ | |
| participant \ | |
| -w /work \ | |
| --participant_label 1 \ | |
| --reindex-bids | |
| - name: Upload output artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: connectome | |
| path: ./outputs/ | |
| - name: Upload docker image artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: docker-image | |
| path: ${HOME}/docker/image.tar | |
| # publish: | |
| # runs-on: ubuntu-latest | |
| # needs: [test-package, test-coverage] | |
| # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/') | |
| # steps: | |
| # - uses: actions/download-artifact@v3 | |
| # with: | |
| # name: dist | |
| # path: dist/ | |
| # - uses: pypa/gh-action-pypi-publish@release/v1 | |
| # with: | |
| # user: __token__ | |
| # password: ${{ secrets.PYPI_API_TOKEN }} |