bump version v4.6.3 -> v4.6.4 #311
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| name: ci | |
| on: [push, pull_request, workflow_dispatch] | |
| jobs: | |
| examples: | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| fail-fast: False | |
| matrix: | |
| python-version: | |
| - "3.6" | |
| - "3.7" | |
| - "3.8" | |
| - "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: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get install libpython2.7 # required by paup | |
| python -m pip install --upgrade pip | |
| - name: Install paup | |
| run: | | |
| temp_dir=$(mktemp -d) | |
| wget -P ${temp_dir} http://phylosolutions.com/paup-test/paup4a168_ubuntu64.gz | |
| gunzip ${temp_dir}/paup4a168_ubuntu64.gz | |
| chmod +x ${temp_dir}/paup4a168_ubuntu64 | |
| sudo mv ${temp_dir}/paup4a168_ubuntu64 /usr/local/bin/paup | |
| echo "export DENDROPY_PAUP_EXECUTABLE_PATH=/usr/local/bin/paup" >> "${GITHUB_ENV}" | |
| - name: Install dendropy | |
| run: | | |
| python -m pip install . | |
| - name: Run examples | |
| run: | | |
| cd docs/source/examples | |
| # only allow known failures | |
| # and enforce removal of working examples from known failures | |
| for f in *.py; do | |
| echo "${f}" | |
| if timeout 60 python "${f}" && ! grep -q "${f}" backlogged-fail-whitelist.txt; then | |
| : | |
| elif grep -q "${f}" backlogged-fail-whitelist.txt; then | |
| : | |
| else | |
| echo FAIL "${f}" | |
| exit 1 | |
| fi | |
| done | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install ruff==0.0.292 | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Lint with ruff | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| ./lint.sh | |
| tests: | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| fail-fast: False | |
| matrix: | |
| python-version: | |
| - "2.7" | |
| - "3.5" | |
| - "3.6" | |
| - "3.7" | |
| - "3.8" | |
| - "3.9" | |
| - "3.10" | |
| - "3.11" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| continue-on-error: true | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install python2 libpython2.7 # required by paup | |
| python -m pip install --upgrade pip | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Install paup | |
| run: | | |
| temp_dir=$(mktemp -d) | |
| wget -P ${temp_dir} http://phylosolutions.com/paup-test/paup4a168_ubuntu64.gz | |
| gunzip ${temp_dir}/paup4a168_ubuntu64.gz | |
| chmod +x ${temp_dir}/paup4a168_ubuntu64 | |
| sudo mv ${temp_dir}/paup4a168_ubuntu64 /usr/local/bin/paup | |
| echo "export DENDROPY_PAUP_EXECUTABLE_PATH=/usr/local/bin/paup" >> "${GITHUB_ENV}" | |
| - name: Python2 compatibility workaround # TODO remove when Python2 compatibility dropped | |
| if: matrix.python-version == '2.7' | |
| run: | | |
| rm tests/dendropy | |
| curl --silent --show-error --retry 5 https://bootstrap.pypa.io/pip/2.7/get-pip.py | sudo python2 | |
| python2 -m pip install setuptools --upgrade | |
| python2 setup.py test | |
| - name: Test with setup.py | |
| if: matrix.python-version != '2.7' | |
| run: | | |
| python setup.py test | |
| entrypoints: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: False | |
| matrix: | |
| python-version: | |
| - "2.7" | |
| - "3.5" | |
| - "3.6" | |
| - "3.7" | |
| - "3.8" | |
| - "3.9" | |
| - "3.10" | |
| - "3.11" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| continue-on-error: true | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install python2 libpython2.7 # required by paup | |
| python -m pip install --upgrade pip | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| python -m pip install . | |
| - name: Test sumtrees | |
| run: | | |
| which sumtrees | |
| sumtrees --help | |
| sumtrees 2>&1 | grep sumtrees || exit 1 | |
| - name: Test sumlabels | |
| run: | | |
| which sumlabels | |
| sumlabels --help | |
| sumlabels 2>&1 | grep sumlabels || exit 1 | |
| - name: Test dendropy-format | |
| run: | | |
| which dendropy-format | |
| dendropy-format --help | |
| dendropy-format 2>&1 | grep dendropy-format || exit 1 | |
| - name: Test deprecated entrypoints | |
| run: | | |
| which sumtrees.py | |
| sumtrees.py --help | |
| sumtrees.py 2>&1 | grep sumtrees.py || exit 1 | |
| which sumlabels.py | |
| sumlabels.py --help | |
| sumlabels.py 2>&1 | grep sumlabels.py || exit 1 | |
| coverage: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: Setup Python | |
| uses: actions/setup-python@master | |
| with: | |
| python-version: 3.8 | |
| - name: Install paup | |
| run: | | |
| sudo apt-get install libpython2.7 # required by paup | |
| temp_dir=$(mktemp -d) | |
| wget -P ${temp_dir} http://phylosolutions.com/paup-test/paup4a168_ubuntu64.gz | |
| gunzip ${temp_dir}/paup4a168_ubuntu64.gz | |
| chmod +x ${temp_dir}/paup4a168_ubuntu64 | |
| sudo mv ${temp_dir}/paup4a168_ubuntu64 /usr/local/bin/paup | |
| echo "export DENDROPY_PAUP_EXECUTABLE_PATH=/usr/local/bin/paup" >> "${GITHUB_ENV}" | |
| - name: Install coverage dependencies | |
| run: | | |
| python3 -m pip install pytest | |
| python3 -m pip install pytest-cov | |
| - name: Generate coverage report | |
| run: | | |
| python3 -m pytest tests --cov=tests/dendropy --cov-report=xml | |
| - uses: codecov/codecov-action@v4 | |
| with: | |
| token: ae13d715-bae4-4e6d-9dce-f47e7d7c7c01 | |
| flags: unittests # optional | |
| fail_ci_if_error: true # optional (default = false) | |
| verbose: true # optional (default = false) | |
| packaging-bdist: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Install build tools | |
| run: python3 -m pip install pip setuptools wheel --upgrade | |
| - name: Build bdist | |
| run: | | |
| python3 setup.py bdist_wheel | |
| tree dist | |
| - name: Upgrade pip | |
| run: python3 -m pip install pip --upgrade | |
| - name: Install from bdist | |
| run: python3 -m pip install dist/*.whl | |
| - name: Test install | |
| run: | | |
| find . -type f -name '*.py' -exec rm {} \; | |
| python3 -c "import dendropy; print(dendropy.__version__)" | |
| packaging-sdist: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Install build tools | |
| run: python3 -m pip install pip setuptools wheel --upgrade | |
| - name: Build sdist | |
| run: | | |
| python3 setup.py sdist | |
| tree dist | |
| - name: Install from sdist | |
| run: python3 -m pip install dist/*.tar.gz | |
| - name: Test install | |
| run: | | |
| find . -type f -name '*.py' -exec rm {} \; | |
| python3 -c "import dendropy; print(dendropy.__version__)" | |
| packaging-source: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Upgrade pip | |
| run: python3 -m pip install pip --upgrade | |
| - name: Install from source | |
| run: python3 -m pip install . | |
| - name: Test install | |
| run: | | |
| find . -type f -name '*.py' -exec rm {} \; | |
| python3 -c "import dendropy; print(dendropy.__version__)" | |
| docs: | |
| permissions: | |
| contents: write | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v4 | |
| continue-on-error: true | |
| with: | |
| python-version: 3.9 | |
| - name: Upgrade pip | |
| run: python3 -m pip install pip --upgrade | |
| - name: Install from source | |
| run: python3 -m pip install . | |
| - name: Install documentation build dependencies | |
| run: python3 -m pip install -r docs/requirements.txt | |
| - name: Build documentation | |
| run: make -C docs html | |
| - name: Deploy docs | |
| if: github.ref == 'refs/heads/main' | |
| uses: actions/upload-pages-artifact@v3 | |
| with: | |
| path: docs/build/html # The folder the action should deploy. | |
| # uses: JamesIves/github-pages-deploy-action@v4 | |
| # with: | |
| # folder: docs/build/html # The folder the action should deploy. | |
| # uses: jsmrcaga/[email protected] | |
| # with: | |
| # NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }} | |
| # NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }} | |
| # NETLIFY_DEPLOY_MESSAGE: "Prod deploy v${{ github.ref }}" | |
| # NETLIFY_DEPLOY_TO_PROD: true | |
| # install_command: "echo Skipping installing the dependencies" | |
| # build_command: "echo Skipping building the web files" | |
| # build_directory: docs/build/html | |
| deploy-docs: | |
| if: github.ref == 'refs/heads/main' | |
| # Add a dependency to the build job | |
| needs: docs | |
| # Grant GITHUB_TOKEN the permissions required to make a Pages deployment | |
| permissions: | |
| pages: write # to deploy to Pages | |
| id-token: write # to verify the deployment originates from an appropriate source | |
| # Deploy to the github-pages environment | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| # Specify runner + deployment step | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@v4 # or specific "vX.X.X" version tag for this | |
| deploy: | |
| runs-on: ubuntu-latest | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| needs: | |
| - examples | |
| - lint | |
| - tests | |
| steps: | |
| - uses: actions/checkout@v1 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install setuptools wheel twine | |
| - run: python setup.py sdist bdist_wheel | |
| - name: Publish package | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} |