MinGW version of pysam

.github/workflows/ci.yaml

@@ -1,156 +1,152 @@
-name: CI
-
-on: [push, pull_request]
-
-jobs:
-  direct:
-    runs-on: ${{ matrix.os }}-latest
-    strategy:
-      matrix:
-        os: [ubuntu, macos]
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
-        exclude:
-          # Run only the latest few 3.x versions on macOS
-          - os: macos
-            python-version: 3.7
-          - os: macos
-            python-version: 3.8
-          - os: macos
-            python-version: 3.9
-
-    steps:
-      - name: Checkout pysam
-        uses: actions/checkout@v4
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install prerequisite Python libraries
-        run:  pip install cython pytest pytest-pep8 setuptools
-
-      - name: Install Linux build prerequisites
-        if:   runner.os == 'Linux'
-        run: |
-          sudo apt-get update
-          sudo apt-get install -q --no-install-recommends --no-install-suggests libcurl4-openssl-dev
-
-      - name: Update macOS build prerequisites
-        if:   runner.os == 'macOS'
-        run: |
-          brew unlink xz || true  # Remove brewed liblzma as it is not multiarch
-
-      - name: Build (directly from checkout)
-        run:  python setup.py build
-
-      - name: Install test prerequisites
-        run: |
-          case $RUNNER_OS in
-          Linux)
-              sudo apt-get install -q --no-install-recommends --no-install-suggests samtools bcftools tabix
-              ;;
-          macOS)
-              brew install -q samtools bcftools
-              ;;
-          esac
-
-      - name: Run tests
-        run: |
-          export PYTHONPATH=$(echo $GITHUB_WORKSPACE/build/lib.*)
-          export REF_PATH=':'
-          pytest
-
-
-  sdist:
-    runs-on: ${{ matrix.os }}-latest
-    strategy:
-      matrix:
-        os: [ubuntu, macos]
-        python-version: ['3.10']
-
-    steps:
-      - name: Checkout pysam
-        uses: actions/checkout@v4
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install prerequisite Python libraries
-        run:  pip install cython pytest pytest-pep8
-
-      - name: Install build prerequisites
-        if:   runner.os == 'Linux'
-        run: |
-          sudo apt-get update
-          sudo apt-get install -q --no-install-recommends --no-install-suggests libcurl4-openssl-dev
-
-      - name: Create source distribution
-        run:  python setup.py sdist --owner=root --group=root
-
-      - name: Build (via sdist tarball)
-        run:  pip install --verbose --no-deps --no-binary=':all:' pysam-*.tar.gz
-        working-directory: dist
-
-      - name: Install test prerequisites
-        run: |
-          case $RUNNER_OS in
-          Linux)
-              sudo apt-get install -q --no-install-recommends --no-install-suggests samtools bcftools tabix
-              ;;
-          macOS)
-              brew install -q samtools bcftools
-              ;;
-          esac
-
-      - name: Run tests
-        run:  REF_PATH=':' pytest
-
-      - name: Upload sdist tarball
-        if:   runner.os == 'Linux'
-        uses: actions/upload-artifact@v3
-        with:
-          name: sdist
-          path: dist/pysam-*.tar.gz
-          retention-days: 14
-
-
-  conda:
-    timeout-minutes: 20
-    runs-on: ${{ matrix.os }}-latest
-    strategy:
-      matrix:
-        os: [ubuntu]
-        python-version: ['3.7']
-    defaults:
-      run:
-        shell: bash -l {0}  # needed for conda activation
-    env:
-      HTSLIB_CONFIGURE_OPTIONS: "--disable-libcurl"
-
-    steps:
-      - name: Checkout pysam
-        uses: actions/checkout@v4
-
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          channel-priority: strict
-          activate-environment: testenv
-          auto-activate-base: false
-          use-only-tar-bz2: true
-
-      - name: Set up Conda and Python ${{ matrix.python-version }}
-        run: |
-          conda config --add channels bioconda --add channels conda-forge
-          conda install python=${{ matrix.python-version }} cython
-
-      - name: Build (directly from checkout)
-        run:  python setup.py install
-
-      - name: Install test prerequisites via Conda
-        run:  conda install "samtools>=1.11" "bcftools>=1.11" "htslib>=1.11" pytest
-
-      - name: Run tests
-        run:  REF_PATH=':' pytest
+name: CI
+
+on: [push, pull_request]
+
+jobs:
+  direct:
+    runs-on: ${{ matrix.os }}-latest
+    strategy:
+      matrix:
+        os: [ubuntu, macos, windows]
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
+        include:
+          # Add specific configuration for Windows
+          - os: windows
+            msystem: ucrt64
+        exclude:
+          - os: ubuntu
+            python-version: '3.7'
+          - os: ubuntu
+            python-version: '3.8'
+          - os: ubuntu
+            python-version: '3.9'
+          - os: ubuntu
+            python-version: '3.10'
+          - os: ubuntu
+            python-version: '3.11'
+          - os: ubuntu
+            python-version: '3.12'
+          # Run only the latest few 3.x versions on macOS
+          - os: macos
+            python-version: '3.7'
+          - os: macos
+            python-version: '3.8'
+          - os: macos
+            python-version: '3.9'
+          - os: macos
+            python-version: '3.10'
+          - os: macos
+            python-version: '3.11'
+          - os: macos
+            python-version: '3.12'
+          # Exclude all Windows Python versions except 3.11
+          - os: windows
+            python-version: '3.7'
+          - os: windows
+            python-version: '3.8'
+          - os: windows
+            python-version: '3.9'
+          - os: windows
+            python-version: '3.10'
+          - os: windows
+            python-version: '3.12'
+
+    steps:
+      - name: Checkout pysam
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        if: runner.os != 'Windows'
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install prerequisite Python libraries
+        if: runner.os != 'Windows'
+        run: pip install cython pytest pytest-pep8 setuptools
+
+      - name: Install Linux build prerequisites
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -q --no-install-recommends --no-install-suggests libcurl4-openssl-dev
+
+      - name: Update macOS build prerequisites
+        if: runner.os == 'macOS'
+        run: |
+          brew unlink xz || true
+
+      - name: Install MSYS2 build prerequisites
+        if: runner.os == 'Windows'
+        uses: msys2/setup-msys2@v2
+        with:
+          msystem: ucrt64
+          update: true
+          install: >-
+            base-devel
+            mingw-w64-ucrt-x86_64-toolchain
+            mingw-w64-ucrt-x86_64-cython
+            mingw-w64-ucrt-x86_64-python
+            mingw-w64-ucrt-x86_64-python-pip
+            mingw-w64-ucrt-x86_64-python-setuptools
+            mingw-w64-ucrt-x86_64-curl
+            mingw-w64-ucrt-x86_64-libdeflate
+            mingw-w64-ucrt-x86_64-bzip2
+            mingw-w64-ucrt-x86_64-zlib
+            mingw-w64-ucrt-x86_64-python-pytest
+            mingw-w64-ucrt-x86_64-xz
+            mingw-w64-ucrt-x86_64-openssl
+            mingw-w64-ucrt-x86_64-libtre
+            mingw-w64-ucrt-x86_64-libiconv
+
+      - name: Build (Windows)
+        if: runner.os == 'Windows'
+        shell: msys2 {0}
+        run: |
+          python setup.py build
+
+      - name: Build (Unix)
+        if: runner.os != 'Windows'
+        run: |
+          python setup.py build
+
+      - name: Install test prerequisites (Windows)
+        if: runner.os == 'Windows'
+        shell: msys2 {0}
+        run: |
+          pacman -S --noconfirm mingw-w64-ucrt-x86_64-samtools mingw-w64-ucrt-x86_64-bcftools
+
+      - name: Install test prerequisites (Unix)
+        if: runner.os != 'Windows'
+        shell: bash
+        run: |
+          if [ "$RUNNER_OS" == "Linux" ]; then
+            sudo apt-get install -q --no-install-recommends --no-install-suggests samtools bcftools tabix
+          elif [ "$RUNNER_OS" == "macOS" ]; then
+            brew install -q samtools bcftools
+          fi
+
+      - name: Run tests (Windows)
+        if: runner.os == 'Windows'
+        shell: msys2 {0}
+        run: |
+          export PYTHONPATH=$(echo $GITHUB_WORKSPACE/build/lib.*)
+          export REF_PATH=':'
+          pytest
+
+      - name: Run tests (Unix)
+        if: runner.os != 'Windows'
+        shell: bash
+        run: |
+          export PYTHONPATH=$(echo $GITHUB_WORKSPACE/build/lib.*)
+          export REF_PATH=':'
+          pytest
+
+
+
+
+
+
+
+      - name: Run tests
+        run:  REF_PATH=':' pytest