ci.yml

name: PeleLMeX-CI

on:
  workflow_dispatch:
  push:
    branches: [development]
  pull_request:
    branches: [development]

concurrency:
  group: ${{github.ref}}-${{github.head_ref}}-ci
  cancel-in-progress: true

jobs:
  Formatting:
    runs-on: ubuntu-24.04
    steps:
    - name: Clone
      uses: actions/checkout@v4
    - name: Check formatting
      uses: DoozyX/clang-format-lint-action@v0.18.2
      with:
        source: './Source ./Exec'
        exclude: '.'
        extensions: 'H,h,cpp'
        clangFormatVersion: 18
  CPU-GNUmake:
    needs: Formatting
    runs-on: ubuntu-24.04
    steps:
      - name: Clone
        uses: actions/checkout@v4
        with:
          submodules: recursive
      - name: Setup
        working-directory: ./Exec/RegTests/FlameSheet
        run: |
          echo "NPROCS=$(nproc)" >> $GITHUB_ENV
          echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
          echo "CCACHE_COMPRESSLEVEL=1" >> $GITHUB_ENV
          echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
          echo "CCACHE_MAXSIZE=200M" >> $GITHUB_ENV
          make COMP=gnu USE_MPI=FALSE DEBUG=TRUE TPL
          make COMP=llvm USE_MPI=FALSE DEBUG=TRUE PRECISION=FLOAT TPL
      - name: Install Ccache
        run: |
          wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
          tar xvf ccache-4.8-linux-x86_64.tar.xz
          sudo cp -f ccache-4.8-linux-x86_64/ccache /usr/local/bin/
      - name: Set Up Ccache
        uses: actions/cache@v4
        with:
          path: ~/.cache/ccache
          key: ccache-${{github.workflow}}-${{github.job}}-git-${{github.sha}}
          restore-keys: |
               ccache-${{github.workflow}}-${{github.job}}-git-
      - name: FlameSheet debug make
        working-directory: ./Exec/RegTests/FlameSheet
        run: |
          echo "::add-matcher::.github/problem-matchers/gcc.json"
          set -eu -o pipefail
          ccache -z
          make -j ${{env.NPROCS}} DIM=2 KEEP_BUILDINFO_CPP=TRUE USE_CCACHE=TRUE COMP=gnu USE_MPI=FALSE DEBUG=TRUE 2>&1 | tee -a build-output.txt
      - name: FlameSheet ccache report
        working-directory: ./Exec/RegTests/FlameSheet
        run: |
          ccache -s
          du -hs ~/.cache/ccache
      - name: FlameSheet debug test
        working-directory: ./Exec/RegTests/FlameSheet
        run: ./PeleLMeX2d.gnu.DEBUG.ex flamesheet-drm19-2d.inp amr.max_step=1 amr.plot_int=-1 amr.check_int=-1
      - name: FlameSheet debug report
        working-directory: ./Exec/RegTests/FlameSheet
        run: |
          egrep "Warning:|Error:|warning:|error:" build-output.txt \
            | egrep -v "Submodules/amrex|Submodules/sundials|Submodules/AMReX-Hydro|GNUmakefile|ThirdParty" \
            | egrep -v "ld: warning:" | sort | uniq \
            | awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > warnings.txt
          cat warnings.txt
          export return=$(tail -n 1 warnings.txt | awk '{print $2}')
          exit ${return}
  CPU-CMake:
    needs: Formatting
    runs-on: ${{matrix.os}}
    strategy:
      matrix:
        os: [ubuntu-22.04, macos-latest]
        build_type: [Release, Debug]
        enable_eb: [EB-OFF, EB-ON]
        include:
          - os: macos-latest
            install_deps: brew install mpich automake ccache
            comp: llvm
            procs: $(sysctl -n hw.ncpu)
            ccache_cache: /Users/runner/Library/Caches/ccache
          - os: ubuntu-22.04
            install_deps: sudo apt-get update && sudo apt-get install mpich libmpich-dev
            comp: gnu
            procs: $(nproc)
            ccache_cache: ~/.cache/ccache
          - build_type: Release
            ctest_args: -LE no-ci
            ccache_size: 100M
          - build_type: Debug
            ctest_args: -R covo
            ccache_size: 500M
          - enable_eb: EB-OFF
            use_eb: "OFF"
          - enable_eb: EB-ON
            use_eb: "ON"
        exclude:
          - os: macos-latest
            build_type: Debug
    steps:
      - name: Clone
        uses: actions/checkout@v4
        with:
          submodules: recursive
      - name: Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.12'
      - name: Setup
        run: |
          echo "NPROCS=${{matrix.procs}}" >> $GITHUB_ENV
          echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
          echo "CCACHE_COMPRESSLEVEL=1" >> $GITHUB_ENV
          echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
          echo "CCACHE_MAXSIZE=${{matrix.ccache_size}}" >> $GITHUB_ENV
          cmake -E make_directory ${{runner.workspace}}/deps
          if [ "${RUNNER_OS}" != "macOS" ]; then
            ${{github.workspace}}/Submodules/PelePhysics/Submodules/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
          fi
      - name: Dependencies
        run: |
          # Install MPI
          ${{matrix.install_deps}}
          # Install Python packages
          python -m pip install --upgrade pip
          pip install pynose numpy pandas
      - name: Install Ccache
        run: |
          if [ "${RUNNER_OS}" != "macOS" ]; then
            wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
            tar xvf ccache-4.8-linux-x86_64.tar.xz
            sudo cp -f ccache-4.8-linux-x86_64/ccache /usr/local/bin/
          fi
      - name: Set Up Ccache
        uses: actions/cache@v4
        with:
          path: ${{matrix.ccache_cache}}
          key: ccache-${{github.workflow}}-${{github.job}}-${{matrix.os}}-${{matrix.build_type}}-${{matrix.enable_eb}}-git-${{github.sha}}
          restore-keys: |
               ccache-${{github.workflow}}-${{github.job}}-${{matrix.os}}-${{matrix.build_type}}-${{matrix.enable_eb}}-git-
      - name: Configure
        run: |
          (for DIM in 2 3; do \
            printf "\n-------- Configuring ${DIM}D --------\n"; \
            cmake -B${{runner.workspace}}/build-${DIM}d-${{matrix.os}}-${{matrix.build_type}}-${{matrix.enable_eb}} \
            -DCMAKE_INSTALL_PREFIX:PATH=${{runner.workspace}}/install-${DIM}d-${{matrix.os}}-${{matrix.build_type}}-${{matrix.enable_eb}} \
            -DCMAKE_BUILD_TYPE:STRING=${{matrix.build_type}} \
            -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
            -DPELE_DIM:STRING=${DIM} \
            -DPELE_ENABLE_MPI:BOOL=ON \
            -DPELE_ENABLE_EB:BOOL=${{matrix.use_eb}} \
            -DPELE_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
            -DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
            ${{github.workspace}}; \
            if [ $? -ne 0 ]; then exit 1; fi \
          done)
      - name: Build
        run: |
          ccache -z
          (for DIM in 2 3; do \
            printf "\n-------- Building ${DIM}D --------\n"; \
            cmake --build ${{runner.workspace}}/build-${DIM}d-${{matrix.os}}-${{matrix.build_type}}-${{matrix.enable_eb}} \
              --parallel ${{env.NPROCS}} 2>&1 | tee -a ${{runner.workspace}}/build-output.txt; \
            if [ ${PIPESTATUS[0]} -ne 0 ]; then exit 1; fi \
          done)
      - name: Ccache Report
        run: |
          ccache -s
          du -hs ${{matrix.ccache_cache}}
      - name: Report
        run: |
          echo "::add-matcher::.github/problem-matchers/gcc.json"
          egrep "Warning:|Error:|warning:|error:" ${{runner.workspace}}/build-output.txt \
            | egrep -v "Submodules/amrex|Submodules/sundials|Submodules/AMReX-Hydro" \
            | egrep -v "ld: warning:" | egrep -v "lto-wrapper: warning:" | sort | uniq \
            | awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > ${{runner.workspace}}/build-output-warnings.txt
          cat ${{runner.workspace}}/build-output-warnings.txt
          export return=$(tail -n 1 ${{runner.workspace}}/build-output-warnings.txt | awk '{print $2}')
          exit ${return}
      - name: Test
        run: |
          (for DIM in 2 3; do \
            printf "\n-------- Testing ${DIM}D --------\n"; \
            cd ${{runner.workspace}}/build-${DIM}d-${{matrix.os}}-${{matrix.build_type}}-${{matrix.enable_eb}}; \
            ctest ${{matrix.ctest_args}} --output-on-failure; \
            if [ $? -ne 0 ]; then exit 1; fi \
          done)
  GPU-Nvidia:
    name: GPU-CUDA
    needs: [Formatting, CPU-GNUmake]
    runs-on: ubuntu-24.04
    steps:
      - name: Clone
        uses: actions/checkout@v4
        with:
          submodules: recursive
      - name: Setup
        run: |
          echo "NPROCS=$(nproc)" >> $GITHUB_ENV
          echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
          echo "CCACHE_COMPRESSLEVEL=1" >> $GITHUB_ENV
          echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
          echo "CCACHE_MAXSIZE=300M" >> $GITHUB_ENV
      - name: Dependencies
        run: |
          ${{github.workspace}}/Submodules/PelePhysics/Submodules/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
          wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/cuda-keyring_1.1-1_all.deb
          sudo dpkg -i cuda-keyring_1.1-1_all.deb
          sudo apt-get update
          sudo apt-get install -y cuda-command-line-tools-12-6 \
              cuda-compiler-12-6 cuda-minimal-build-12-6 \
              cuda-nvml-dev-12-6 cuda-nvtx-12-6 \
              libcurand-dev-12-6 cuda-cupti-dev-12-6 \
              libcusolver-dev-12-6 libcusparse-dev-12-6 \
              libcublas-dev-12-6 libcurand-dev-12-6 libnvjitlink-12-6
      - name: Install Ccache
        run: |
          wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
          tar xvf ccache-4.8-linux-x86_64.tar.xz
          sudo cp -f ccache-4.8-linux-x86_64/ccache /usr/local/bin/
      - name: Set Up Ccache
        uses: actions/cache@v4
        with:
          path: ~/.cache/ccache
          key: ccache-${{github.workflow}}-${{github.job}}-git-${{github.sha}}
          restore-keys: |
               ccache-${{github.workflow}}-${{github.job}}-git-
      - name: Configure
        run: |
          export PATH=/usr/local/nvidia/bin:/usr/local/cuda-12.6/bin:${PATH}
          export LD_LIBRARY_PATH=/usr/local/nvidia/lib:/usr/local/nvidia/lib64:/usr/local/cuda-12.6/lib:${LD_LIBRARY_PATH}
          cmake -Bbuild-cuda \
            -DCMAKE_BUILD_TYPE:STRING=Release \
            -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
            -DPELE_ENABLE_MPI:BOOL=OFF \
            -DPELE_ENABLE_CUDA:BOOL=ON \
            -DAMReX_CUDA_ERROR_CAPTURE_THIS:BOOL=ON \
            -DCMAKE_CUDA_ARCHITECTURES:STRING=80 \
            -DCMAKE_CUDA_COMPILER_LAUNCHER:STRING=ccache \
            -DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
            ${{github.workspace}}
      - name: Build
        run: |
          ccache -z
          cmake --build build-cuda --parallel ${{env.NPROCS}}
      - name: Ccache Report
        run: |
          ccache -s
          du -hs ~/.cache/ccache
  GPU-AMD:
    name: GPU-HIP
    needs: [Formatting, CPU-GNUmake]
    runs-on: ubuntu-24.04
    steps:
      - name: Clone
        uses: actions/checkout@v4
        with:
          submodules: recursive
      - name: Setup
        run: |
          echo "NPROCS=$(nproc)" >> $GITHUB_ENV
          echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
          echo "CCACHE_COMPRESSLEVEL=1" >> $GITHUB_ENV
          echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
          echo "CCACHE_MAXSIZE=80M" >> $GITHUB_ENV
      - name: Dependencies
        run: |
          ${{github.workspace}}/Submodules/PelePhysics/Submodules/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
          sudo mkdir --parents --mode=0755 /etc/apt/keyrings
          wget https://repo.radeon.com/rocm/rocm.gpg.key -O - | gpg --dearmor | sudo tee /etc/apt/keyrings/rocm.gpg > /dev/null
          echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/rocm.gpg] https://repo.radeon.com/rocm/apt/6.2.1 noble main" | sudo tee --append /etc/apt/sources.list.d/rocm.list
          echo -e 'Package: *\nPin: release o=repo.radeon.com\nPin-Priority: 600' | sudo tee /etc/apt/preferences.d/rocm-pin-600
          echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' | sudo tee -a /etc/profile.d/rocm.sh
          sudo apt-get update
          sudo apt-get install -y rocm-dev rocrand-dev rocprim-dev hiprand-dev
      - name: Install Ccache
        run: |
          wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
          tar xvf ccache-4.8-linux-x86_64.tar.xz
          sudo cp -f ccache-4.8-linux-x86_64/ccache /usr/local/bin/
      - name: Set Up Ccache
        uses: actions/cache@v4
        with:
          path: ~/.cache/ccache
          key: ccache-${{github.workflow}}-${{github.job}}-git-${{github.sha}}
          restore-keys: |
               ccache-${{github.workflow}}-${{github.job}}-git-
      - name: Configure
        run: |
          source /etc/profile.d/rocm.sh
          which clang
          which clang++
          which hipcc
          hipcc --version
          hipconfig --full
          cmake -B${{runner.workspace}}/build-hip \
          -DCMAKE_BUILD_TYPE:STRING=Release \
          -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
          -DCMAKE_CXX_COMPILER:STRING=$(which clang++) \
          -DCMAKE_C_COMPILER:STRING=$(which clang) \
          -DPELE_ENABLE_MPI:BOOL=OFF \
          -DPELE_ENABLE_HIP:BOOL=ON \
          -DAMReX_AMD_ARCH:STRING=gfx90a \
          -DCMAKE_HIP_ARCHITECTURES:STRING=gfx90a \
          -DAMDGPU_TARGETS:STRING=gfx90a \
          -DGPU_TARGETS:STRING=gfx90a \
          -DAMReX_GPU_RDC:BOOL=OFF \
          -DPELE_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
          -DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
          ${{github.workspace}}
      - name: Build
        run: |
          echo "::add-matcher::.github/problem-matchers/gcc.json"
          source /etc/profile.d/rocm.sh
          ccache -z
          cmake --build ${{runner.workspace}}/build-hip --parallel ${{env.NPROCS}}
      - name: Ccache Report
        run: |
          ccache -s
          du -hs ~/.cache/ccache
  GPU-Intel:
    name: GPU-SYCL
    needs: [Formatting, CPU-GNUmake]
    runs-on: ubuntu-24.04
    steps:
      - name: Clone
        uses: actions/checkout@v4
        with:
          submodules: recursive
      - name: Setup
        run: |
          echo "NPROCS=$(nproc)" >> $GITHUB_ENV
          echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
          echo "CCACHE_COMPRESSLEVEL=1" >> $GITHUB_ENV
          echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
          echo "CCACHE_MAXSIZE=80M" >> $GITHUB_ENV
          echo "CCACHE_DEPEND=1" >> $GITHUB_ENV
      - name: Dependencies
        run: |
          ${{github.workspace}}/Submodules/PelePhysics/Submodules/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
          sudo wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
          sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
          echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
          sudo apt-get update
          sudo apt-get install -y intel-oneapi-compiler-dpcpp-cpp=2024.2.1-1079 intel-oneapi-mkl-devel=2024.2.2-15
      - name: Install Ccache
        run: |
          wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
          tar xvf ccache-4.8-linux-x86_64.tar.xz
          sudo cp -f ccache-4.8-linux-x86_64/ccache /usr/local/bin/
      - name: Set Up Ccache
        uses: actions/cache@v4
        with:
          path: ~/.cache/ccache
          key: ccache-${{github.workflow}}-${{github.job}}-git-${{github.sha}}
          restore-keys: |
               ccache-${{github.workflow}}-${{github.job}}-git-
      - name: Configure
        run: |
          set +e
          source /opt/intel/oneapi/setvars.sh
          set -e
          cmake -B${{runner.workspace}}/build-sycl \
            -DCMAKE_BUILD_TYPE:STRING=Release \
            -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
            -DCMAKE_CXX_COMPILER:STRING=$(which icpx) \
            -DCMAKE_C_COMPILER:STRING=$(which icx) \
            -DCMAKE_CXX_FLAGS:STRING=-fsycl \
            -DPELE_ENABLE_MPI:BOOL=OFF \
            -DPELE_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
            -DPELE_ENABLE_SYCL:BOOL=ON \
            -DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
            ${{github.workspace}}
      - name: Build
        run: |
          set +e
          source /opt/intel/oneapi/setvars.sh
          set -e
          ccache -z
          cmake --build ${{runner.workspace}}/build-sycl --parallel ${{env.NPROCS}}
      - name: Ccache Report
        run: |
          ccache -s
          du -hs ~/.cache/ccache
  Lint-clang-tidy:
    needs: Formatting
    runs-on: ubuntu-24.04
    strategy:
      matrix:
        enable_eb: [EB-OFF, EB-ON]
        include:
          - enable_eb: EB-OFF
            use_eb: "OFF"
          - enable_eb: EB-ON
            use_eb: "ON"
      fail-fast: false
    steps:
      - name: Setup
        run: |
          echo "NPROCS=$(nproc)" >> $GITHUB_ENV
          echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
          echo "CCACHE_COMPRESSLEVEL=1" >> $GITHUB_ENV
          echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
          echo "CCACHE_EXTRAFILES=${{github.workspace}}/.clang-tidy" >> $GITHUB_ENV
          echo "CCACHE_MAXSIZE=50M" >> $GITHUB_ENV
          echo "CTCACHE_DIR=~/.cache/ctcache" >> $GITHUB_ENV
      - name: Clone
        uses: actions/checkout@v4
        with:
          submodules: recursive
      - name: Install Ccache
        run: |
          wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
          sudo curl https://raw.githubusercontent.com/matus-chochlik/ctcache/7fd516e91c17779cbc6fc18bd119313d9532dd90/clang-tidy-cache -Lo /usr/bin/clang-tidy-cache
          tar xvf ccache-4.8-linux-x86_64.tar.xz
          sudo cp -f ccache-4.8-linux-x86_64/ccache /usr/local/bin/
          sudo chmod +x /usr/bin/clang-tidy-cache
          mkdir -p ~/.cache/ctcache
      - name: Set Up Ccache
        uses: actions/cache@v4
        with:
          path: ~/.cache
          key: ccache-${{github.workflow}}-${{github.job}}-${{matrix.enable_eb}}-git-${{github.sha}}
          restore-keys: |
               ccache-${{github.workflow}}-${{github.job}}-${{matrix.enable_eb}}-git-
      - name: Configure
        run: |
          cmake -B${{runner.workspace}}/build-clang-tidy \
          -DCMAKE_BUILD_TYPE:STRING=Release \
          -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
          -DCMAKE_CXX_COMPILER:STRING=clang++ \
          -DCMAKE_C_COMPILER:STRING=clang \
          -DPELE_ENABLE_EB:BOOL=${{matrix.use_eb}} \
          -DPELE_ENABLE_MPI:BOOL=OFF \
          -DPELE_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
          -DPELE_ENABLE_CLANG_TIDY:BOOL=ON \
          -DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
          ${{github.workspace}}
      - name: Check
        working-directory: ${{runner.workspace}}/build-clang-tidy
        run: |
          #set -eu -o pipefail
          cmake --build . --parallel ${{env.NPROCS}} 2>&1 | tee -a clang-tidy-full-report.txt
          egrep "Warning:|Error:|warning:|error:" clang-tidy-full-report.txt \
            | egrep -v "Submodules/amrex|Submodules/sundials|Submodules/AMReX-Hydro" \
            | egrep -v "ld: warning:" | sort | uniq \
            | awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > clang-tidy-warnings.txt
      - name: Ccache Report
        run: |
          ls ~/.cache
          ls ~/.cache/ccache
          du -hs ~/.cache/ccache
          ls ~/.cache/ctcache
          du -hs ~/.cache/ctcache
          ccache -s
      - name: Full report
        working-directory: ${{runner.workspace}}/build-clang-tidy
        run: cat clang-tidy-full-report.txt
      - name: Short report
        working-directory: ${{runner.workspace}}/build-clang-tidy
        run: |
          echo "::add-matcher::.github/problem-matchers/gcc.json"
          cat clang-tidy-warnings.txt
          export return=$(tail -n 1 clang-tidy-warnings.txt | awk '{print $2}')
          exit ${return}
  Lint-codeql:
    needs: Formatting
    runs-on: ubuntu-24.04
    steps:
      - name: Clone
        uses: actions/checkout@v4
        with:
          submodules: recursive
      - name: Initialize CodeQL
        uses: github/codeql-action/init@v3
        with:
          languages: cpp
          queries: +security-and-quality
          config-file: ./.github/codeql/codeql-config.yml
      - name: Configure
        run: |
          echo "NPROCS=$(nproc)" >> $GITHUB_ENV
          cmake -B${{runner.workspace}}/build-codeql \
          -DCMAKE_BUILD_TYPE:STRING=Debug \
          -DCMAKE_CXX_COMPILER:STRING=clang++ \
          -DCMAKE_C_COMPILER:STRING=clang \
          -DPELE_ENABLE_MPI:BOOL=OFF \
          -DPELE_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
          -DPELE_ENABLE_CLANG_TIDY:BOOL=OFF \
          ${{github.workspace}}
      - name: Build
        run: |
          cmake --build ${{runner.workspace}}/build-codeql --parallel ${{env.NPROCS}}
      - name: Perform CodeQL Analysis
        uses: github/codeql-action/analyze@v3
        with:
          category: "/language:cpp"
          upload: False
          output: sarif-results
      - name: Filter CodeQL sarif
        uses: advanced-security/filter-sarif@v1
        with:
          patterns: |
            -**/Submodules/sundials/**
            -**/Submodules/amrex/**
            -**/Submodules/AMReX-Hydro/**
          input: sarif-results/cpp.sarif
          output: sarif-results/cpp.sarif
      - name: Upload CodeQL sarif
        uses: github/codeql-action/upload-sarif@v3
        with:
          sarif_file: sarif-results/cpp.sarif
  Lint-codespell:
    needs: Formatting
    runs-on: ubuntu-24.04
    steps:
      - name: Clone
        uses: actions/checkout@v4
        with:
          submodules: false
      - name: Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.10'
      - name: Dependencies
        run: |
          # Install Python packages
          python -m pip install --upgrade pip
          pip install codespell
      - name: Run codespell
        run: codespell
  Save-PR-Number:
    if: github.event_name == 'pull_request'
    runs-on: ubuntu-24.04
    steps:
      - name: Save PR number
        env:
          PR_NUMBER: ${{ github.event.number }}
        run: |
          echo $PR_NUMBER > pr_number.txt
      - uses: actions/upload-artifact@v4
        with:
          name: pr_number
          path: pr_number.txt
          retention-days: 1