name: "CodeQL"

on:
  push:
    branches: [ "develop" ]
  pull_request:
    branches: [ "develop" ]
  schedule:
    - cron: "16 7 * * 0"
  workflow_dispatch:  # Allow manual triggering

jobs:
  analyze:
    name: Analyze
    runs-on: ubuntu-latest
    permissions:
      actions: read
      contents: read
      security-events: write

    strategy:
      fail-fast: false

    steps:
      - name: Install Dependencies (Linux)
        run: |
          sudo apt-get update
          sudo apt-get install -y \
            openmpi-bin openmpi-common mpi-default-dev \
            zlib1g-dev libaec-dev

          # Set env vars
          echo "CC=mpicc" >> $GITHUB_ENV
          echo "FC=mpif90" >> $GITHUB_ENV
          echo "F77=mpif90" >> $GITHUB_ENV

      - name: Checkout
        uses: actions/checkout@v6

      - name: Configure HDF5
        run: |
          mkdir build; cd build
          cmake -G "Unix Makefiles" \
            -DCMAKE_INSTALL_PREFIX=$PWD/hdf5 \
            -DCMAKE_BUILD_TYPE=Debug \
            -DHDF5_ENABLE_PARALLEL:BOOL=ON \
            -DHDF5_ENABLE_SUBFILING_VFD:BOOL=ON \
            -DHDF5_BUILD_TOOLS:BOOL=ON \
            -DBUILD_SHARED_LIBS:BOOL=ON \
            -DBUILD_STATIC_LIBS:BOOL=OFF \
            -DHDF5_BUILD_FORTRAN:BOOL=OFF \
            -DHDF5_BUILD_JAVA:BOOL=OFF \
            -DBUILD_TESTING:BOOL=OFF \
            -DHDF5_BUILD_EXAMPLES:BOOL=OFF \
            -DHDF5_ENABLE_ZLIB_SUPPORT:BOOL=ON \
            -DZLIB_INCLUDE_DIR=/usr/include \
            -DZLIB_LIBRARY=/usr/lib/x86_64-linux-gnu/libz.so \
            ..

      - name: Initialize CodeQL
        uses: github/codeql-action/init@v4.32.2
        with:
          languages: c-cpp
          build-mode: manual
          queries: +security-and-quality
          
          config: |
             query-filters:
               - exclude:
                   id: cpp/toctou-race-condition
               - exclude:
                   id: cpp/short-global-name

      - name: Build
        run: |
          cd build
          cmake --build . --config Debug
        shell: bash

      - name: Perform CodeQL Analysis
        uses: github/codeql-action/analyze@v4.32.2
        with:
          category: "/language:c-cpp"
          output: sarif-results
          upload: failure-only

      - name: filter-sarif
        uses: advanced-security/filter-sarif@v1
        with:
          patterns: |
            -**/test/**
            -**/testpar/**
            -**/tools/test/**
          input: sarif-results/cpp.sarif
          output: sarif-results/cpp.sarif

      - name: Upload SARIF
        uses: github/codeql-action/upload-sarif@v4.32.2
        with:
          sarif_file: sarif-results/cpp.sarif