Update compile-and-publish.yml #4
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| name: Compile MSYS2 Dependencies | |
| on: | |
| push: | |
| branches: [ "main" ] | |
| pull_request: | |
| branches: [ "main" ] | |
| permissions: | |
| contents: read | |
| jobs: | |
| build: | |
| runs-on: windows-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set up MSYS2 | |
| uses: msys2/setup-msys2@v2 | |
| with: | |
| msystem: UCRT64 | |
| update: false | |
| install: >- | |
| git | |
| autotools | |
| gcc | |
| zlib-devel | |
| libbz2-devel | |
| liblzma-devel | |
| mingw-w64-x86_64-tools-git | |
| ncurses-devel | |
| - name: Clone repositories | |
| shell: msys2 {0} | |
| run: | | |
| git clone --depth 1 --recurse-submodules --branch 1.20 https://github.com/samtools/htslib | |
| git clone --depth 1 --recurse-submodules --branch 1.20 https://github.com/samtools/samtools | |
| git clone --depth 1 --recurse-submodules --branch 1.20 https://github.com/samtools/bcftools | |
| git clone --depth 1 --recurse-submodules --branch v0.7.18 https://github.com/lh3/bwa | |
| git clone --depth 1 --recurse-submodules --branch v2.28 https://github.com/lh3/minimap2 | |
| - name: Compile htslib | |
| shell: msys2 {0} | |
| run: | | |
| export PATH=$PATH:/mingw64/bin | |
| pushd . | |
| cd htslib | |
| autoreconf -i | |
| ./configure | |
| make -j32 | |
| popd | |
| - name: Compile samtools | |
| shell: msys2 {0} | |
| run: | | |
| export PATH=$PATH:/mingw64/bin | |
| pushd . | |
| cd samtools | |
| autoheader | |
| autoconf -Wno-syntax | |
| ./configure | |
| make -j32 | |
| popd | |
| - name: Compile bcftools | |
| shell: msys2 {0} | |
| run: | | |
| export PATH=$PATH:/mingw64/bin | |
| pushd . | |
| cd bcftools | |
| autoheader | |
| autoconf -Wno-syntax | |
| ./configure | |
| make -j32 | |
| popd | |
| - name: Compile bwa | |
| shell: msys2 {0} | |
| run: | | |
| export PATH=$PATH:/mingw64/bin | |
| pushd . | |
| cd bwa | |
| make -j32 | |
| popd | |
| - name: Compile minimap2 | |
| shell: msys2 {0} | |
| run: | | |
| export PATH=$PATH:/mingw64/bin | |
| pushd . | |
| cd minimap2 | |
| make -j32 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.x' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pefile | |
| pip install build | |
| - name: Scan imports | |
| run: | | |
| python -m pip install pefile | |
| python import_scanner.py | |
| - name: Build package | |
| run: python -m build | |
| - name: Publish package | |
| uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: third_party | |
| path: wgse/third_party/ | |
| retention-days: 1 |