finish addressing #228 #119
Workflow file for this run
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| name: main | |
| on: [push] | |
| jobs: | |
| build-and-test: | |
| strategy: | |
| matrix: | |
| python-version: ["3.7", "3.8", "3.9", "3.10"] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: git setup | |
| id: git-setup | |
| run: | | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "GitHub Action" | |
| echo "BRANCH=${GITHUB_REF##*/}" >> $GITHUB_ENV | |
| echo "WORKDIR=$(pwd)" >> $GITHUB_ENV | |
| - name: conda env | |
| run: | | |
| wget -O Mambaforge.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh" | |
| curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh" | |
| bash Mambaforge.sh -b -p "${HOME}/conda" | |
| source "${HOME}/conda/etc/profile.d/conda.sh" | |
| source "${HOME}/conda/etc/profile.d/mamba.sh" | |
| which conda | |
| conda config --system --add channels defaults | |
| conda config --system --add channels bioconda | |
| conda config --system --add channels conda-forge | |
| conda config --system --set channel_priority strict | |
| mamba create -y -n gffutils-env \ | |
| python=${{ matrix.python-version }} \ | |
| --file requirements.txt | |
| conda activate gffutils-env | |
| python setup.py clean sdist | |
| (cd dist && pip install gffutils-*.tar.gz) | |
| cd $TMPDIR | |
| python -c "import gffutils; print(gffutils.__file__)" | |
| conda deactivate | |
| - name: run unit tests | |
| run: | | |
| source "${HOME}/conda/etc/profile.d/conda.sh" | |
| source "${HOME}/conda/etc/profile.d/mamba.sh" | |
| mamba install -y -n gffutils-env --file optional-requirements.txt pytest hypothesis | |
| conda activate gffutils-env | |
| pytest -v --doctest-modules gffutils | |
| conda deactivate | |
| - name: doctests | |
| # Specifically in 3.8 (but not 3.6, 3.7, 3.9) we get: | |
| # | |
| # Handler <function process_generate_options at 0x7f6eb70ba790> | |
| # for event 'builder-inited' threw an exception (exception: no | |
| # module named gffutils.pybedtools_integration) | |
| # | |
| # ...and this is difficult or impossible to replicate locally. | |
| # The workaround is to just not build the html docs on 3.8. | |
| if: ${{ (matrix.python-version != 3.8) }} | |
| run: | | |
| source "${HOME}/conda/etc/profile.d/conda.sh" | |
| source "${HOME}/conda/etc/profile.d/mamba.sh" | |
| mamba install -y -n gffutils-env --file docs-requirements.txt | |
| conda activate gffutils-env | |
| (cd doc && make clean doctest) | |
| conda deactivate | |
| - name: build docs | |
| # See above for note about 3.8 | |
| if: ${{ (matrix.python-version != 3.8) }} | |
| run: | | |
| source "${HOME}/conda/etc/profile.d/conda.sh" | |
| source "${HOME}/conda/etc/profile.d/mamba.sh" | |
| conda activate gffutils-env | |
| (cd doc && make html) | |
| conda deactivate | |
| # Clone the gh-pages branch to a temporary location | |
| git clone \ | |
| --single-branch \ | |
| --branch gh-pages "https://x-acess-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY" \ | |
| /tmp/docs | |
| # clean it out and add newly-built docs | |
| rm -rf /tmp/docs/* | |
| cp -r doc/build/html/* /tmp/docs | |
| # so that sphinx-built docs show up correctly on github.io | |
| touch /tmp/docs/.nojekyll | |
| cd /tmp/docs | |
| git add . | |
| if git diff --cached --quiet; then | |
| echo "no changes to docs, nothing to commit" | |
| else | |
| git commit -m "update docs" | |
| fi | |
| cd $WORKDIR | |
| - name: push artifact | |
| if: ${{ (matrix.python-version == 3.9) }} | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: doc | |
| path: /tmp/docs | |
| - name: push docs to gh-pages branch | |
| # Push docs to gh-pages if this test is running on master branch, and | |
| # restrict to a single Python version. | |
| if: ${{ (github.ref == 'refs/heads/master') && (matrix.python-version == 3.9) }} | |
| run: | | |
| cd /tmp/docs | |
| git push "https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY" gh-pages | |
| cd $WORKDIR |