CMake rewrite

.github/workflows/cd.yml

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+name: CD
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  build-conda-package:
+    name: Conda package (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@v0.8.3
+
+      - name: Build conda package
+        run: |
+          mkdir -p dist
+          pixi build
+          # Copy built package to dist/ for upload
+          find .pixi/build -name '*.conda' -o -name '*.tar.bz2' | xargs -I{} cp {} dist/ 2>/dev/null || true
+
+      - name: Upload conda package artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: conda-package-${{ matrix.os }}
+          path: dist/
+          if-no-files-found: warn
+          retention-days: 30
+
+  build-release-binaries:
+    name: Release binaries (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            artifact: bgen-linux-x86_64
+          - os: macos-latest
+            artifact: bgen-macos-arm64
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install dependencies (Ubuntu)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            libboost-all-dev \
+            libsqlite3-dev \
+            zlib1g-dev \
+            libzstd-dev \
+            ninja-build
+
+      - name: Install dependencies (macOS)
+        if: runner.os == 'macOS'
+        run: brew install boost sqlite zstd ninja
+
+      - name: Configure
+        run: |
+          cmake -S . -B build -G Ninja \
+            -DCMAKE_BUILD_TYPE=Release \
+            -DBGEN_BUILD_TESTS=OFF
+
+      - name: Build
+        run: cmake --build build --parallel
+
+      - name: Package binaries
+        run: |
+          cmake --install build --prefix staging
+          tar -czf ${{ matrix.artifact }}.tar.gz -C staging .
+
+      - name: Upload release artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ matrix.artifact }}
+          path: ${{ matrix.artifact }}.tar.gz
+
+  create-release:
+    name: Create GitHub Release
+    needs: [build-conda-package, build-release-binaries]
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Download all artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: artifacts/
+
+      - name: Create release
+        uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true
+          files: |
+            artifacts/bgen-linux-x86_64/*.tar.gz
+            artifacts/bgen-macos-x86_64/*.tar.gz
+            artifacts/bgen-macos-arm64/*.tar.gz
+            artifacts/conda-package-*/*.conda
+            artifacts/conda-package-*/*.tar.bz2

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main, master, develop]
+  pull_request:
+    branches: [main, master, develop]
+
+jobs:
+  build-cmake:
+    name: CMake (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install dependencies (Ubuntu)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            libboost-all-dev \
+            libsqlite3-dev \
+            zlib1g-dev \
+            libzstd-dev \
+            ninja-build
+
+      - name: Install dependencies (macOS)
+        if: runner.os == 'macOS'
+        run: brew install boost sqlite zstd ninja
+
+      - name: Configure
+        run: |
+          cmake -S . -B build -G Ninja \
+            -DCMAKE_BUILD_TYPE=Release \
+            -DBGEN_BUILD_TESTS=ON
+
+      - name: Build
+        run: cmake --build build --parallel
+
+      - name: Test
+        run: ctest --test-dir build --output-on-failure
+
+      - name: Install
+        run: cmake --install build --prefix build/install
+
+      - name: Verify CMake package config files installed
+        run: |
+          test -f build/install/lib/cmake/bgen/bgenConfig.cmake
+          test -f build/install/lib/cmake/bgen/bgenConfigVersion.cmake
+          test -f build/install/lib/cmake/bgen/bgenTargets.cmake
+          echo "CMake package config files present"
+
+  build-pixi:
+    name: Pixi package (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@v0.8.3
+
+      - name: Run tests via pixi tasks
+        run: pixi run test
+
+      - name: Build conda package
+        run: pixi build
+
+      - name: Test R package
+        working-directory: R/package
+        run: pixi run test

.gitignore

@@ -0,0 +1,56 @@
+# Build directories
+build/
+dist/
+.waf-1.8.13*
+.waf-2.0.6*
+
+# CMake
+CMakeFiles/
+CMakeCache.txt
+cmake_install.cmake
+CTestTestfile.cmake
+build.ninja
+Testing/
+
+# Compiled binaries and libraries
+*.o
+*.a
+*.so
+*.so.*
+*.dylib
+*.dll
+*.exe
+*.out
+
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.egg-info/
+dist/
+build/
+.Python
+*.conda
+
+# IDE and editor files
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+.DS_Store
+.clang_complete
+
+# Pixi/Conda
+.pixi/
+pixi-lock.yaml
+
+# Local environment files
+.env
+.env.local
+*.lock
+
+# Temporary files
+*.tmp
+*.bak
+*.orig