Use tiered testing for the Build and ctest action

.github/actions/build-test/action.yml

@@ -0,0 +1,39 @@
+name: 'Build and Test LevioSAM2'
+description: 'Build and test LevioSAM2 with CMake'
+inputs:
+  build-type:
+    description: 'CMake build type'
+    required: false
+    default: 'Release'
+  cache-enabled:
+    description: 'Enable caching for CMake builds'
+    required: false
+    default: 'true'
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Cache CMake build
+      if: inputs.cache-enabled == 'true'
+      uses: actions/cache@v3
+      with:
+        path: ${{github.workspace}}/build
+        key: cmake-build-${{ runner.os }}-${{ inputs.build-type }}-${{ hashFiles('**/CMakeLists.txt', '**/src/**') }}
+        restore-keys: |
+          cmake-build-${{ runner.os }}-${{ inputs.build-type }}-
+          cmake-build-${{ runner.os }}-
+
+    - name: Configure CMake
+      shell: bash
+      run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{ inputs.build-type }}
+
+    - name: Build
+      shell: bash
+      run: |
+        gcc -v &&
+        cmake --build ${{github.workspace}}/build --config ${{ inputs.build-type }}
+
+    - name: Test
+      shell: bash
+      working-directory: ${{github.workspace}}/build
+      run: ./leviosam2 -h && ctest -C ${{ inputs.build-type }}

.github/actions/setup-htslib/action.yml

@@ -0,0 +1,43 @@
+name: 'Setup htslib'
+description: 'Install and configure htslib with caching'
+inputs:
+  version:
+    description: 'htslib version to install'
+    required: true
+  cache-enabled:
+    description: 'Enable caching for htslib builds'
+    required: false
+    default: 'true'
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Cache htslib
+      if: inputs.cache-enabled == 'true'
+      uses: actions/cache@v3
+      with:
+        path: /tmp/htslib-${{ inputs.version }}
+        key: htslib-${{ inputs.version }}-${{ runner.os }}-${{ hashFiles('**/CMakeLists.txt') }}
+        restore-keys: |
+          htslib-${{ inputs.version }}-${{ runner.os }}-
+          htslib-${{ inputs.version }}-
+
+    - name: Set up SDSL
+      shell: bash
+      run: sudo apt-get -y install libsdsl-dev
+
+    - name: Set up htslib
+      shell: bash
+      run: |
+        if [ ! -d "/tmp/htslib-${{ inputs.version }}" ]; then
+          sudo apt-get -y install libbz2-dev liblzma-dev &&
+          wget https://github.com/samtools/htslib/releases/download/${{ inputs.version }}/htslib-${{ inputs.version }}.tar.bz2 &&
+          tar -vxjf htslib-${{ inputs.version }}.tar.bz2 &&
+          cd htslib-${{ inputs.version }} &&
+          ./configure --prefix=/tmp/htslib-${{ inputs.version }} &&
+          make &&
+          make install &&
+          cd ../ &&
+          rm htslib-${{ inputs.version }}.tar.bz2
+        fi
+        sudo cp -r /tmp/htslib-${{ inputs.version }}/* /usr/local/

.github/workflows/cmake_htslib.yml

@@ -1,4 +1,4 @@
-name: Build and ctest
+name: Build and ctest (with cache)
 
 on:
   push:
@@ -11,63 +11,107 @@ on:
       - 'CMakeLists.txt.in'
       - 'testdata/**'
   pull_request:
-    branches:
-      - 'main'
+    branches: [ main ]
     paths:
       - '.github/**'
       - 'src/**'
       - 'leviosam-test.py'
       - 'CMakeLists.txt'
       - 'CMakeLists.txt.in'
       - 'testdata/**'
+  workflow_dispatch:
+    inputs:
+      test_level:
+        description: 'Test level to run'
+        required: true
+        default: 'smart'
+        type: choice
+        options:
+        - smart
+        - extended
+        - full
 
 env:
-  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
   BUILD_TYPE: Release
 
 jobs:
-  htslib_matrix:
+  # Setup job to define version lists
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      all_versions: ${{ steps.versions.outputs.all }}
+      critical_versions: ${{ steps.versions.outputs.critical }}
+      extended_versions: ${{ steps.versions.outputs.extended }}
+    steps:
+      - name: Define version lists
+        id: versions
+        run: |
+          ALL_VERSIONS='["1.12", "1.19.1", "1.20", "1.21", "1.22.1"]'
+          CRITICAL_VERSIONS='["1.12", "1.22.1"]'
+          EXTENDED_VERSIONS='["1.19.1", "1.20", "1.21"]'
+
+          echo "all=$ALL_VERSIONS" >> $GITHUB_OUTPUT
+          echo "critical=$CRITICAL_VERSIONS" >> $GITHUB_OUTPUT
+          echo "extended=$EXTENDED_VERSIONS" >> $GITHUB_OUTPUT
+
+  # Critical matrix testing - tests edge cases and representative versions
+  critical_tests:
+    needs: setup
+    if: github.event_name == 'workflow_dispatch' && github.event.inputs.test_level == 'smart' || github.event_name != 'workflow_dispatch'
     strategy:
       matrix:
-        version: [1.12, 1.13, 1.14, 1.15, 1.16, 1.17, 1.18]
-        os: [ubuntu-22.04, ubuntu-latest]
-
-    # The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
-    # You can convert this to a matrix build if you need cross-platform coverage.
-    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
+        version: ${{ fromJSON(needs.setup.outputs.critical_versions) }}  # Oldest and newest supported versions
+        os: ['ubuntu-latest']
     runs-on: ${{ matrix.os }}
-
     steps:
       - uses: actions/checkout@v3
-
-      - name: Set up SDSL
-        run: sudo apt-get -y install libsdsl-dev
-
-      - name: Set up htslib
-        run:
-          sudo apt-get -y install libbz2-dev liblzma-dev &&
-          wget https://github.com/samtools/htslib/releases/download/${{ matrix.version }}/htslib-${{ matrix.version }}.tar.bz2 &&
-          tar -vxjf htslib-${{ matrix.version }}.tar.bz2 &&
-          cd htslib-${{ matrix.version }} &&
-          ./configure &&
-          make &&
-          sudo make install &&
-          cd ../ &&
-          rm htslib-${{ matrix.version }}.tar.bz2
-
-      - name: Configure CMake
-        # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
-        # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
-        run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}
+      - uses: ./.github/actions/setup-htslib
+        with:
+          version: ${{ matrix.version }}
+          cache-enabled: 'true'
+      - uses: ./.github/actions/build-test
+        with:
+          build-type: ${{ env.BUILD_TYPE }}
+          cache-enabled: 'true'
 
-      - name: Build
-        # Build your program with the given configuration
-        run: 
-          gcc -v &&
-          cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
+  # Extended testing for PRs
+  extended_tests:
+    needs: setup
+    if: github.event_name == 'pull_request' || (github.event_name == 'workflow_dispatch' && github.event.inputs.test_level == 'extended')
+    strategy:
+      matrix:
+        # Representative middle versions
+        version: ${{ fromJSON(needs.setup.outputs.extended_versions) }}
+        os: ['ubuntu-22.04']
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: ./.github/actions/setup-htslib
+        with:
+          version: ${{ matrix.version }}
+          cache-enabled: 'true'
+      - uses: ./.github/actions/build-test
+        with:
+          build-type: ${{ env.BUILD_TYPE }}
+          cache-enabled: 'true'
 
-      - name: Test
-        working-directory: ${{github.workspace}}/build
-        # Execute tests defined by the CMake configuration.  
-        # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
-        run: ./leviosam2 -h && ctest -C ${{env.BUILD_TYPE}}
+  # Full compatibility matrix - only for releases or manual trigger
+  full_tests:
+    needs: setup
+    if: github.ref == 'refs/heads/main' || (github.event_name == 'workflow_dispatch' && github.event.inputs.test_level == 'full')
+    strategy:
+      matrix:
+        # Test all supported versions
+        version: ${{ fromJSON(needs.setup.outputs.all_versions) }}
+        os: ['ubuntu-22.04', 'ubuntu-latest']
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: ./.github/actions/setup-htslib
+        with:
+          version: ${{ matrix.version }}
+          cache-enabled: 'true'
+      - uses: ./.github/actions/build-test
+        with:
+          build-type: ${{ env.BUILD_TYPE }}
+          cache-enabled: 'true'