Add exception when duplicate series zarr paths are detected. #273
Workflow file for this run
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| name: Python Test and Package | |
| on: | |
| push: | |
| branches: | |
| - master | |
| tags: | |
| - 'v*' | |
| pull_request: | |
| branches: | |
| - master | |
| jobs: | |
| linting_test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| - name: set PY | |
| run: echo "PY=$(python -VV | sha256sum | cut -d' ' -f1)" >> $GITHUB_ENV | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pre-commit | |
| key: pre-commit|${{ env.PY }}|${{ hashFiles('.pre-commit-config.yaml') }} | |
| - name: Linting | |
| run: | | |
| pip install pre-commit "trufflehog3>=3.0" | |
| pre-commit run --all-files | |
| - name: Run trufflehog3 detector | |
| run: | | |
| trufflehog3 -v -c trufflehog3.yml . && echo "tufflehog3 OK" | |
| test_package: | |
| needs: linting_test | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.8, 3.9, '3.10', '3.11'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Create LFS file list | |
| run: | | |
| git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id | |
| - name: Restore LFS cache | |
| uses: actions/cache@v3 | |
| id: lfs-cache | |
| with: | |
| path: .git/lfs | |
| key: lfs-v1-${{ hashFiles('.lfs-assets-id') }} | |
| restore-keys: | |
| lfs-v1- | |
| - name: Git LFS Pull | |
| run: | | |
| git lfs pull | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements-dev.txt twine build | |
| pip install -e . | |
| - name: Test with pytest | |
| run: | | |
| python -m pytest --junitxml=junit/test-results-${{ matrix.python-version }}.xml | |
| - name: Upload pytest test results | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: pytest-results-${{ matrix.python-version }} | |
| path: junit/test-results-${{ matrix.python-version }}.xml | |
| # Use always() to always run this step to publish test results when there are test failures | |
| if: ${{ always() }} | |
| - name: Build package | |
| run: | | |
| python -m build --wheel --sdist | |
| python -m twine check dist/* | |
| ls -la dist | |
| - name: Upload package | |
| if: github.event_name == 'push' | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: python-packages | |
| path: dist | |
| docs: | |
| needs: linting_test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install -r requirements-dev.txt -r docs/requirements.txt | |
| # install so that setuptools_scm generate version for package | |
| pip install -e . | |
| - name: Build Sphinx Documentation | |
| run: | | |
| make -C docs html | |
| - name: Upload documentation | |
| if: github.event_name == 'push' | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: sphinx-docs | |
| path: docs/_build/html | |
| - name: Update gh-pages | |
| if: github.ref == 'refs/heads/master' | |
| run: | | |
| rm docs/_build/html/.buildinfo | |
| touch docs/_build/html/.nojekyll | |
| git update-ref refs/heads/${TARGET_BRANCH} origin/${TARGET_BRANCH} | |
| ./utils/update-gh-pages.sh docs/_build/html | |
| repo_uri="https://x-access-token:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git" | |
| git push $repo_uri ${TARGET_BRANCH} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.github_token }} | |
| TARGET_BRANCH: 'gh-pages' | |
| github_publish: | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| needs: test_package | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install twine | |
| - uses: actions/download-artifact@v3 | |
| id: download | |
| with: | |
| name: python-packages | |
| - name: Create Release and Upload | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| id: create_release | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| gh release create ${{ github.ref_name }} --repo ${{ github.repository }} --verify-tag --generate-notes --title "Release ${{ github.ref_name }}" | |
| gh release upload ${{ github.ref_name }} --repo ${{ github.repository }} ${{ steps.download.outputs.download-path }}/pytools* | |
| - name: bcbb-pypi upload | |
| run: | | |
| python -m twine check ${{steps.download.outputs.download-path}}/pytools* | |
| python -m twine upload ${{steps.download.outputs.download-path}}/pytools* | |
| env: | |
| TWINE_REPOSITORY_URL: https://artifactory.niaid.nih.gov/artifactory/api/pypi/bcbb-pypi | |
| TWINE_PASSWORD: ${{secrets.BCBB_PYPI_PASSWORD}} | |
| TWINE_USERNAME: ${{secrets.BCBB_PYPI_USERNAME}} |