Improve kraken list robustness
#780
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| name: Lint, test, build, and publish | |
| on: | |
| push: | |
| jobs: | |
| lint_and_test: | |
| name: Runs the linter and tests | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.9, '3.10', '3.11'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies and kraken | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install .[test] flake8 | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Run tests, except training tests | |
| run: | | |
| pytest -k 'not test_train and not test_pageseg' | |
| build-n-publish-pypi: | |
| name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI | |
| needs: lint_and_test | |
| runs-on: ubuntu-latest | |
| if: startsWith(github.ref, 'refs/tags/') | |
| 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: Build a binary wheel and a source tarball | |
| run: | | |
| python -m pip install build --user | |
| python -m build --sdist --wheel --outdir dist/ . | |
| - name: Publish a Python distribution to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| - name: Upload PyPI artifacts to GH storage | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: pypi_packages | |
| path: dist/* | |
| build-n-publish-anaconda: | |
| name: Build and publish anaconda packages | |
| needs: lint_and_test | |
| runs-on: ubuntu-latest | |
| if: startsWith(github.ref, 'refs/tags/') | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: 3.9 | |
| miniforge-variant: Mambaforge | |
| - name: install dependencies build | |
| shell: bash -l {0} | |
| run: mamba install "conda-build>=3.20" colorama pip ruamel ruamel.yaml rich jsonschema conda-verify anaconda-client mamba | |
| # Runs the action with the following inputs or defaults if not specified. | |
| - name: install boa | |
| shell: bash -l {0} | |
| run: pip install https://github.com/mamba-org/boa/archive/refs/tags/0.14.0.zip | |
| - name: validate recipe | |
| shell: bash -l {0} | |
| id: conda_validation | |
| run: | | |
| PACKAGE_PATHS=$(conda mambabuild . --output --check -c conda-forge | tail -n 1) | |
| echo "package_paths=$PACKAGE_PATHS" >> $GITHUB_OUTPUT | |
| - name: run build | |
| shell: bash -l {0} | |
| run: conda mambabuild . -c conda-forge | |
| - name: convert packages | |
| shell: bash -l {0} | |
| run: | | |
| conda convert -p osx-arm64 -p osx-64 -o conda_convert ${{ steps.conda_validation.outputs.package_paths }} | |
| mkdir conda_convert/linux-64 | |
| cp -f ${{ steps.conda_validation.outputs.package_paths }} conda_convert/linux-64 | |
| - name: upload to anaconda | |
| shell: bash -l {0} | |
| run: anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload --no-progress --force conda_convert/*/* | |
| - name: Upload conda artifacts to GH storage | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: conda_packages | |
| path: conda_convert/*/*.tar.bz2 | |
| autodraft-gh-release: | |
| name: Create github release | |
| needs: [build-n-publish-anaconda, build-n-publish-pypi] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| name: conda_packages | |
| path: conda | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| name: pypi_packages | |
| path: pypi | |
| - uses: "marvinpinto/action-automatic-releases@latest" | |
| with: | |
| repo_token: "${{ secrets.GITHUB_TOKEN }}" | |
| prerelease: false | |
| draft: true | |
| files: | | |
| conda/*/*.tar.bz2 | |
| pypi/* | |
| publish-gh-pages: | |
| name: Update kraken.re github pages | |
| needs: lint_and_test | |
| runs-on: ubuntu-latest | |
| if: | | |
| github.ref == 'refs/heads/main' || | |
| startsWith(github.ref, 'refs/tags/') | |
| 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 sphinx-multiversion | |
| run: python -m pip install sphinx-multiversion sphinx-autoapi | |
| - name: Create docs | |
| run: sphinx-multiversion docs build/html | |
| - name: Create redirect | |
| run: cp docs/redirect.html build/html/index.html | |
| - name: Push gh-pages | |
| uses: crazy-max/ghaction-github-pages@v3 | |
| with: | |
| target_branch: gh-pages | |
| build_dir: build/html | |
| fqdn: kraken.re | |
| jekyll: false | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} |