add testing for HedwigZarrImage::rechunk method #223
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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}} |