for each prg, we add a class

.github/workflows/ci-cd.yml

@@ -0,0 +1,285 @@
+name: ATHENA CI/CD Pipeline
+
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main ]
+  release:
+    types: [ published ]
+
+env:
+  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
+  BUILD_TYPE: Release
+
+jobs:
+  # Build and test on multiple platforms
+  build-and-test:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-22.04, ubuntu-20.04]
+        compiler: [gcc, clang]
+        include:
+          - os: ubuntu-22.04
+            compiler: gcc
+            cc: gcc-11
+            cxx: g++-11
+          - os: ubuntu-22.04
+            compiler: clang
+            cc: clang-14
+            cxx: clang++-14
+          - os: ubuntu-20.04
+            compiler: gcc
+            cc: gcc-9
+            cxx: g++-9
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Cache dependencies
+      uses: actions/cache@v3
+      with:
+        path: |
+          ~/.cache/pip
+          ~/.apt-cache
+        key: ${{ runner.os }}-deps-${{ hashFiles('**/requirements.txt', '**/CMakeLists.txt') }}
+        restore-keys: |
+          ${{ runner.os }}-deps-
+
+    - name: Install system dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y \
+          build-essential \
+          cmake \
+          python3 \
+          python3-pip \
+          default-jre \
+          default-jdk \
+          fastqc \
+          trimmomatic \
+          velvet \
+          spades \
+          quast \
+          ncbi-blast+ \
+          samtools \
+          bcftools \
+          valgrind \
+          cppcheck
+
+    - name: Install compiler
+      if: matrix.compiler == 'clang'
+      run: |
+        sudo apt-get install -y ${{ matrix.cc }} ${{ matrix.cxx }}
+
+    - name: Setup Python dependencies
+      run: |
+        python3 -m pip install --upgrade pip
+        pip3 install pytest pytest-cov
+
+    - name: Configure CMake
+      env:
+        CC: ${{ matrix.cc }}
+        CXX: ${{ matrix.cxx }}
+      run: |
+        cmake -B ${{github.workspace}}/build \
+          -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} \
+          -DCMAKE_C_COMPILER=${{ matrix.cc }} \
+          -DCMAKE_CXX_COMPILER=${{ matrix.cxx }}
+
+    - name: Build ATHENA
+      run: |
+        cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}} -j$(nproc)
+
+    - name: Run basic tests
+      working-directory: ${{github.workspace}}
+      run: |
+        # Run original test suite
+        python3 test_cmd.py
+
+        # Run comprehensive test suite
+        python3 test_comprehensive.py --athena-path ./build/athena
+
+    - name: Run static analysis
+      run: |
+        # Run cppcheck
+        cppcheck --enable=all --std=c++17 --suppressions-list=.cppcheck-suppressions \
+          src/ include/ --error-exitcode=1 || true
+
+        # Run clang-tidy if clang compiler
+        if [[ "${{ matrix.compiler }}" == "clang" ]]; then
+          find src include -name "*.cpp" -o -name "*.hpp" | \
+            xargs clang-tidy -p build/ || true
+        fi
+
+    - name: Memory leak check
+      if: matrix.os == 'ubuntu-22.04' && matrix.compiler == 'gcc'
+      run: |
+        # Run valgrind on help command
+        valgrind --leak-check=full --error-exitcode=1 \
+          ./build/athena --help || true
+
+    - name: Upload test results
+      uses: actions/upload-artifact@v3
+      if: always()
+      with:
+        name: test-results-${{ matrix.os }}-${{ matrix.compiler }}
+        path: |
+          test_report.json
+          build/
+
+  # Docker build and test
+  docker-build:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+
+    - name: Build Docker image
+      uses: docker/build-push-action@v5
+      with:
+        context: .
+        push: false
+        tags: athena:test
+        cache-from: type=gha
+        cache-to: type=gha,mode=max
+
+    - name: Test Docker image
+      run: |
+        # Test basic functionality in Docker
+        docker run --rm athena:test athena --help
+        docker run --rm athena:test athena --version
+
+    - name: Run Docker Compose tests
+      run: |
+        # Test with docker-compose
+        docker-compose -f docker-compose.yml up --build athena-test
+
+  # Security scanning
+  security-scan:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Run Trivy vulnerability scanner
+      uses: aquasecurity/trivy-action@master
+      with:
+        scan-type: 'fs'
+        format: 'sarif'
+        output: 'trivy-results.sarif'
+
+    - name: Upload Trivy scan results to GitHub Security tab
+      uses: github/codeql-action/upload-sarif@v2
+      if: always()
+      with:
+        sarif_file: 'trivy-results.sarif'
+
+  # Performance benchmarking
+  performance-test:
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y build-essential cmake fastqc trimmomatic
+
+    - name: Build ATHENA
+      run: |
+        cmake -B build -DCMAKE_BUILD_TYPE=Release
+        cmake --build build -j$(nproc)
+
+    - name: Generate test data
+      run: |
+        # Create larger test datasets for performance testing
+        mkdir -p perf_data
+        # This would generate larger synthetic datasets
+        python3 -c "
+import random
+bases = 'ACGT'
+with open('perf_data/large_input1.fastq', 'w') as f:
+    for i in range(10000):
+        seq = ''.join(random.choice(bases) for _ in range(100))
+        f.write(f'@read{i}\n{seq}\n+\n' + 'I'*100 + '\n')
+        "
+        cp perf_data/large_input1.fastq perf_data/large_input2.fastq
+
+    - name: Run performance tests
+      run: |
+        # Run performance benchmarks
+        python3 test_comprehensive.py --category performance --athena-path ./build/athena
+
+    - name: Store performance results
+      uses: actions/upload-artifact@v3
+      with:
+        name: performance-results
+        path: test_report.json
+
+  # Release builds
+  release:
+    if: github.event_name == 'release'
+    runs-on: ubuntu-latest
+    needs: [build-and-test, docker-build]
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y build-essential cmake
+
+    - name: Build release
+      run: |
+        cmake -B build -DCMAKE_BUILD_TYPE=Release
+        cmake --build build -j$(nproc)
+
+    - name: Package release
+      run: |
+        # Create release package
+        mkdir -p athena-release
+        cp build/athena athena-release/
+        cp README.md athena-release/
+        cp -r docs athena-release/ || true
+        tar -czf athena-${{ github.event.release.tag_name }}-linux-x64.tar.gz athena-release/
+
+    - name: Upload release assets
+      uses: actions/upload-release-asset@v1
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      with:
+        upload_url: ${{ github.event.release.upload_url }}
+        asset_path: ./athena-${{ github.event.release.tag_name }}-linux-x64.tar.gz
+        asset_name: athena-${{ github.event.release.tag_name }}-linux-x64.tar.gz
+        asset_content_type: application/gzip
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+
+    - name: Login to Docker Hub
+      uses: docker/login-action@v3
+      with:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+    - name: Build and push Docker image
+      uses: docker/build-push-action@v5
+      with:
+        context: .
+        push: true
+        tags: |
+          athena/athena:latest
+          athena/athena:${{ github.event.release.tag_name }}
+        cache-from: type=gha
+        cache-to: type=gha,mode=max

.gitignore

@@ -35,7 +35,7 @@ temp/
 # Development logs and TODO lists
 DEVELOPMENT_LOG.md
 PROJECT_TODO.md
-
+FASTQC_REFACTORING_REPORT.md
 # IDE files
 .vscode/
 .idea/

.vscode/settings.json

@@ -70,6 +70,7 @@
         "cinttypes": "cpp",
         "typeindex": "cpp",
         "typeinfo": "cpp",
-        "variant": "cpp"
+        "variant": "cpp",
+        "filesystem": "cpp"
     }
 }