update GHA to use main #128
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| name: Python Test and Package | |
| on: | |
| push: | |
| branches: | |
| - main | |
| tags: | |
| - 'v*' | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: 3.8 | |
| - name: Install tools | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install black flake8 | |
| - name: Lint with black | |
| run: | | |
| python -m black --check --diff . | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build for flake8 issues | |
| python -m flake8 . --show-source --statistics | |
| test: | |
| needs: linting | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.8, 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: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e .[dev] | |
| env: | |
| PIP_EXTRA_INDEX_URL: https://${{secrets.ARTIFACTORY_RO_USER}}:${{secrets.ARTIFACTORY_RO_TOKEN}}@artifactory.niaid.nih.gov/artifactory/api/pypi/bcbb-pypi/simple | |
| - name: Test with pytest | |
| run: | | |
| python -m pytest | |
| package_docs: | |
| needs: test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Create LFS file list | |
| run: | | |
| git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id | |
| - name: Restore LFS cache | |
| uses: actions/cache@v3 | |
| id: lfs-cache | |
| with: | |
| path: .git/lfs | |
| key: lfs-v1-${{ hashFiles('.lfs-assets-id') }} | |
| restore-keys: | | |
| lfs-v1- | |
| - name: Git LFS Pull | |
| run: | | |
| git lfs pull | |
| - name: Set up Python 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 build | |
| - name: Build package | |
| run: | | |
| python -m build | |
| ls -la dist | |
| - name: Upload package | |
| if: github.event_name == 'push' | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: python-packages | |
| path: dist | |
| - name: Build Sphinx Documentation | |
| run: | | |
| # install so that setuptools_scm generate version for package | |
| pip install -r docs/requirements.txt -e . | |
| make -C docs html | |
| env: | |
| PIP_EXTRA_INDEX_URL: https://${{secrets.ARTIFACTORY_RO_USER}}:${{secrets.ARTIFACTORY_RO_TOKEN}}@artifactory.niaid.nih.gov/artifactory/api/pypi/bcbb-pypi/simple | |
| - 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' | |
| publish_release: | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| needs: package_docs | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/download-artifact@v3 | |
| id: download | |
| with: | |
| name: python-packages | |
| - name: Extract Python Packages | |
| id: files | |
| run: | | |
| cd ${{steps.download.outputs.download-path}} | |
| echo ::set-output name=file1::$(ls tbpcxr*any.whl) | |
| echo ::set-output name=file2::$(ls tbpcxr*.tar.gz) | |
| - name: Create Release | |
| id: create_release | |
| uses: actions/create-release@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| tag_name: ${{ github.ref }} | |
| release_name: Release ${{ github.ref }} | |
| draft: false | |
| prerelease: false | |
| - name: Upload Release Asset Wheel | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| uses: actions/upload-release-asset@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include | |
| # a `upload_url`. See this blog post for more info: | |
| # https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps | |
| upload_url: ${{ steps.create_release.outputs.upload_url }} | |
| asset_path: ${{steps.download.outputs.download-path}}/${{steps.files.outputs.file1}} | |
| asset_name: ${{steps.files.outputs.file1}} | |
| asset_content_type: application/octet-stream | |
| - name: Upload Release Asset Source | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| uses: actions/upload-release-asset@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| upload_url: ${{ steps.create_release.outputs.upload_url }} | |
| asset_path: ${{steps.download.outputs.download-path}}/${{steps.files.outputs.file2}} | |
| asset_name: ${{steps.files.outputs.file2}} | |
| asset_content_type: application/octet-stream | |
| - name: bcbb-pypi upload | |
| run: | | |
| python -m pip install twine | |
| python -m twine check ${{steps.download.outputs.download-path}}/* | |
| python -m twine upload ${{steps.download.outputs.download-path}}/* | |
| 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}} |