When re-runing with the same atlases, load segmentations #378
Workflow file for this run
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| --- | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - maint/* | |
| tags: | |
| - '*' | |
| pull_request: | |
| branches: | |
| - main | |
| - maint/* | |
| paths: ['giga_connectome/*', 'pyproject.toml', 'requirements.txt', 'Dockerfile'] | |
| 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/setup-python@v5 | |
| - name: install tox | |
| run: pip install tox | |
| - uses: actions/cache@v4 | |
| 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: tox -e test_data | |
| 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@v4 | |
| 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@v4 | |
| 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@v4 | |
| with: | |
| name: dist | |
| path: dist/ | |
| - name: Download git archive artifact | |
| if: matrix.package == 'archive' | |
| uses: actions/download-artifact@v4 | |
| 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: | |
| fail-fast: false | |
| 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@v4 | |
| 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 --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 --pyargs giga_connectome | |
| - uses: codecov/codecov-action@v4 | |
| if: ${{ always() }} | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} |