Add support for csi index #120
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| name: main | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| types: | |
| - opened | |
| - reopened | |
| - synchronize | |
| jobs: | |
| build-and-test: | |
| strategy: | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: git setup | |
| # Set up git and export env vars to be used in later steps. | |
| # Note the unconventional mechanism for exporting envs by appending to | |
| # $GITHUB_ENV. | |
| id: git-setup | |
| run: | | |
| git config --global user.email "action@github.com" | |
| git config --global user.name "GitHub Action" | |
| echo "BRANCH=${GITHUB_REF##*/}" >> $GITHUB_ENV | |
| echo "WORKDIR=$(pwd)" >> $GITHUB_ENV | |
| - name: cythonize and pip | |
| # Convert .pyx files to .cpp and package into sdist tarball. | |
| # | |
| # This only requires Cython, no other dependencies. | |
| run: | | |
| eval "$(conda shell.bash hook)" | |
| conda create -p ./cython-env -y cython python=${{ matrix.python-version }} numpy | |
| conda activate ./cython-env | |
| python setup.py clean cythonize sdist | |
| (cd dist && pip install pybedtools-*.tar.gz && cd $TMPDIR && python -c 'import pybedtools; print(pybedtools.__file__)') | |
| conda deactivate | |
| - name: conda env and install locally | |
| # Set up conda and install pybedtools into that env | |
| # | |
| # NOTE: Tests require *.so files that are created by installing the | |
| # package, otherwise we get: | |
| # | |
| # ModuleNotFoundError: No module named 'pybedtools.cbedtools' | |
| # | |
| # We could install from the source repo dir. However this may inadvertently | |
| # rely on files that are in the source repo but not in the actual sdist | |
| # package. So we extract the sdist tarball to another location and install | |
| # from there. | |
| # | |
| # Tests below will operate in this newly-installed directory. | |
| run: | | |
| eval "$(conda shell.bash hook)" | |
| conda install mamba python=${{ matrix.python-version }} -y --channel conda-forge | |
| # Only install non-python dependencies (like bedtools & ucsc tools); | |
| # let pip take care of the rest. | |
| grep -Ev "genomepy|matplotlib" optional-requirements.txt > optional-requirements-conda.txt | |
| grep -E "genomepy|matplotlib" optional-requirements.txt > optional-requirements-python.txt | |
| mamba create -y -p ./test-env \ | |
| --channel conda-forge \ | |
| --channel bioconda \ | |
| bedtools \ | |
| python=${{ matrix.python-version }} \ | |
| --file optional-requirements-conda.txt | |
| conda activate ./test-env | |
| pip install -r test-requirements.txt -r optional-requirements-python.txt | |
| mkdir -p /tmp/pybedtools-uncompressed | |
| cd /tmp/pybedtools-uncompressed | |
| tar -xf $WORKDIR/dist/pybedtools-*.tar.gz | |
| pip install -e /tmp/pybedtools-uncompressed/pybedtools-* | |
| # Trying import in the same directory will complain that cbedtools | |
| # can't be imported | |
| (cd / && python -c 'import pybedtools; print(pybedtools.__file__)') | |
| - name: tests | |
| # Run pytest and sphinx doctests | |
| run: | | |
| cd $WORKDIR | |
| eval "$(conda shell.bash hook)" | |
| conda activate ./test-env | |
| # Extract the package tarball built above, and use that for running the tests. | |
| cd /tmp/pybedtools-uncompressed/pybedtools-* | |
| pytest -v --doctest-modules | |
| pytest -v pybedtools/test/genomepy_integration.py | |
| cp -r $WORKDIR/docs . | |
| (cd docs && make clean doctest) | |
| - name: build-docs | |
| if: ${{ (matrix.python-version == 3.10) }} | |
| # Build docs and commit to gh-pages branch. Note that no push happens | |
| # unless we're on the master branch | |
| run: | | |
| eval "$(conda shell.bash hook)" | |
| conda activate ./test-env | |
| # Move to extracted tarball dir, see above notes | |
| cd /tmp/pybedtools-uncompressed/pybedtools-* | |
| (cd docs && make html) | |
| git clone \ | |
| --single-branch \ | |
| --branch gh-pages "https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY" \ | |
| /tmp/docs | |
| rm -rf /tmp/docs/* | |
| cp -r docs/build/html/* /tmp/docs | |
| touch /tmp/docs/.nojekyll | |
| cd /tmp/docs | |
| git add . | |
| if git diff --cached --quiet; then | |
| echo "no changes, nothing to commit" | |
| else | |
| git commit -m 'update docs' | |
| fi | |
| cd $WORKDIR | |
| - name: docs artifact | |
| # Upload built docs as an artifact for inspection, even on PRs | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: docs | |
| path: /tmp/docs | |
| - name: push docs to gh-pages branch | |
| # Push docs to gh-pages if this test is running on master branch | |
| if: ${{ (github.ref == 'refs/heads/master') && (matrix.python-version == 3.10) }} | |
| run: | | |
| cd /tmp/docs | |
| git push "https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY" gh-pages | |
| cd $WORKDIR |