check_stella.yml

# Run these tests automatically on Github on every push and pull request.
# Use the macOS operating system, which has 4 cores.
name: Check stella
on: [push, pull_request]

# We always run in a bash shell
defaults:
  run:
    shell: bash

# First build stella, and then perform python tests
jobs:

#-----------------------------------------------------------------------
#              Build stella on different operating systems              
#-----------------------------------------------------------------------
  build-stella:
  
    # Set environment variables
    env:
      OMPI_MCA_rmaps_base_oversubscribe: yes
      MPIRUN: mpiexec -np
    
    # Run the same set-up multiple times
    strategy:
      fail-fast: false
      matrix:
        os: [macos-12, macos-13, macos-14, ubuntu-20.04, ubuntu-22.04, ubuntu-24.04]
        compiler: [Make, CMake]
    
    # Operating system
    runs-on: ${{ matrix.os }}
      
    # Steps
    steps:
    
      # Set environment variables as echo "{name}={value}" >> $GITHUB_ENV
      - name: Set environment variables
        run: |
          # Set environment variables
          if [ ${{ matrix.os }} == 'macos-12' ] || [ ${{ matrix.os }} == 'macos-13' ]; then
            echo "Set STELLA_SYSTEM = macos"
            echo "STELLA_SYSTEM=macos" >> $GITHUB_ENV 
            echo "Set FFTW_LIB_DIR = /usr/local/Cellar/fftw/3.3.10_1/lib/"
            echo "FFTW_LIB_DIR=/usr/local/Cellar/fftw/3.3.10_1/lib/" >> $GITHUB_ENV
            echo "Set FFTW_INC_DIR = /usr/local/include/" 
            echo "FFTW_INC_DIR=/usr/local/include/" >> $GITHUB_ENV
            echo "Set NETCDF_LIB_DIR = /usr/local/lib -L/usr/local/Cellar/netcdf-fortran/4.6.1/lib/"
            echo "NETCDF_LIB_DIR=/usr/local/lib -L/usr/local/Cellar/netcdf-fortran/4.6.1/lib/" >> $GITHUB_ENV
            echo "Set NETCDF_INC_DIR = /usr/local/Cellar/netcdf-fortran/4.6.1/include/"
            echo "NETCDF_INC_DIR=/usr/local/Cellar/netcdf-fortran/4.6.1/include/" >> $GITHUB_ENV 
          elif [ ${{ matrix.os }} == 'macos-14' ]; then 
            echo "Set STELLA_SYSTEM = macos"
            echo "STELLA_SYSTEM=macos" >> $GITHUB_ENV 
            echo "Set FFTW_LIB_DIR = /opt/homebrew/Cellar/fftw/3.3.10_1/lib/"
            echo "FFTW_LIB_DIR=/opt/homebrew/Cellar/fftw/3.3.10_1/lib/" >> $GITHUB_ENV
            echo "Set FFTW_INC_DIR = /opt/homebrew/include/" 
            echo "FFTW_INC_DIR=/opt/homebrew/include/" >> $GITHUB_ENV
            echo "Set NETCDF_LIB_DIR = /opt/homebrew/lib -L/opt/homebrew/Cellar/netcdf-fortran/4.6.1/lib/"
            echo "NETCDF_LIB_DIR=/opt/homebrew/lib -L/opt/homebrew/Cellar/netcdf-fortran/4.6.1/lib/" >> $GITHUB_ENV
            echo "Set NETCDF_INC_DIR = /opt/homebrew/Cellar/netcdf-fortran/4.6.1/include/"
            echo "NETCDF_INC_DIR=/opt/homebrew/Cellar/netcdf-fortran/4.6.1/include/" >> $GITHUB_ENV 
          elif ${{ contains(matrix.os, 'ubuntu') }}; then  
            echo "Set STELLA_SYSTEM = gnu_ubuntu"
            echo "STELLA_SYSTEM=gnu_ubuntu" >> $GITHUB_ENV
          fi

      # Install dependencies
      - name: Install dependencies
        run: |
          # Install dependencies
          if ${{ contains(matrix.os, 'macos') }}; then  
            brew install gcc@11 make openmpi fftw netcdf-fortran gnu-sed
            if [ ${{ matrix.os }} == 'macos-12' ] || [ ${{ matrix.os }} == 'macos-13' ]; then
              sudo ln -s /usr/local/bin/gfortran-11 /usr/local/bin/gfortran
              sudo mkdir /usr/local/gfortran; sudo ln -s /usr/local/Cellar/gcc@11/*/lib/gcc/11 /usr/local/gfortran/lib 
            elif [ ${{ matrix.os }} == 'macos-14' ]; then 
              sudo ln -s /opt/homebrew/bin/gfortran-11 /opt/homebrew/bin/gfortran
            fi
          elif ${{ contains(matrix.os, 'ubuntu') }}; then  
            sudo apt update
            sudo apt install -y gfortran make libfftw3-dev libnetcdf-dev libnetcdff-dev 
            sudo apt install -y netcdf-bin python3 python3-pip openmpi-bin libopenmpi-dev 
            if [ ${{ matrix.os }} == 'ubuntu-24.04' ]; then sudo apt install -y libblas-dev liblapack-dev; fi
          fi

      # Check-out repository under $GITHUB_WORKSPACE
      - name: Check-out repository
        uses: actions/checkout@v4 
          
      # Build stella executable
      - name: Build stella
        run: |
          
          # Check system variables needed for Make
          if ${{ contains(matrix.os, 'macos') }}; then  
            echo " "; echo "System variables:" 
            echo "   FFTW_LIB_DIR = $FFTW_LIB_DIR"
            echo "   FFTW_INC_DIR = $FFTW_INC_DIR"
            echo "   NETCDF_LIB_DIR = $NETCDF_LIB_DIR"
            echo "   NETCDF_INC_DIR = $NETCDF_INC_DIR"
          fi
          
          # Download the submodules
          echo " "; echo "Download submodules:" 
          git submodule update --init --recursive
          
          # Build stella with Make or CMake
          echo " "; echo "Build stella with ${{ matrix.compiler }}:" 
          if [ ${{ matrix.compiler }} == 'Make' ]; then 
             make -j 4
          fi
          if [ ${{ matrix.compiler }} == 'CMake' ]; then 
             cmake . -B COMPILATION/build_cmake
             cmake --build COMPILATION/build_cmake -j 4
          fi

      # Print system information
      - name: System information
        run: |
          if ${{ contains(matrix.os, 'macos') }}; then  
            echo " "; echo "System information:"; echo "$(system_profiler SPHardwareDataType | sed 's/^/  /')"
            echo " "; echo "Gfortran version:"; echo "$(gfortran --version | sed 's/^/  /')"
            echo " "; echo "Clang version:"; echo "$(clang --version | sed 's/^/  /')"
            make numerical-tests-system
          elif ${{ contains(matrix.os, 'ubuntu') }}; then  
            echo " "; echo "System information:"; echo "$(cat /etc/*release | sed 's/^/  /')"
            echo " "; echo "Number of cores:"; echo "$(lscpu | egrep 'Model name|Socket|Thread|NUMA|CPU\(s\)' | sed 's/^/  /')"
            echo " "; echo "Gfortran version:"; echo "$(gfortran --version | sed 's/^/  /')"
            echo " "; echo "Netcdf version:"; echo "$(nf-config --all | sed 's/^/  /')"
            make numerical-tests-system
          fi
          
      # Check $GITHUB_WORKSPACE
      - name: Check Github Workspace
        run: | 
          echo " "; echo "Running directory:"; echo "  $(pwd)"
          echo " "; echo "Files in directory:"; echo "$(ls -la | sed 's/^/  /')"
          
      # Install python environment
      - name: Install python virtual environment
        run: |
          if [ ${{ matrix.os }} == 'ubuntu-24.04' ] || [ ${{ matrix.os }} == 'macos-14' ]; then 
            python3 -m venv AUTOMATIC_TESTS/venv
            source AUTOMATIC_TESTS/venv/bin/activate
            pip3 install -r AUTOMATIC_TESTS/requirements.txt
          else
            pip3 install --user -r AUTOMATIC_TESTS/requirements.txt
          fi
          if ${{ contains(matrix.os, 'macos') }}; then  
            gsed -i 's/nproc = 16/nproc = 4/g' AUTOMATIC_TESTS/config.ini 
          fi
        
      # Perform python tests  
      - name: Python tests 1 - Does stella run
        run: |
          if [ ${{ matrix.os }} == 'ubuntu-24.04' ] || [ ${{ matrix.os }} == 'macos-14' ]; then source AUTOMATIC_TESTS/venv/bin/activate; fi
          make numerical-tests-1
          
      - name: Python tests 2 - Geometry
        if: success() || failure() 
        run: |
          if [ ${{ matrix.os }} == 'ubuntu-24.04' ] || [ ${{ matrix.os }} == 'macos-14' ]; then source AUTOMATIC_TESTS/venv/bin/activate; fi
          make numerical-tests-2
          
      - name: Python tests 3 - Gyrokinetic equation
        if: success() || failure() 
        run: |
          if [ ${{ matrix.os }} == 'ubuntu-24.04' ] || [ ${{ matrix.os }} == 'macos-14' ]; then source AUTOMATIC_TESTS/venv/bin/activate; fi
          make numerical-tests-3
          
      - name: Python tests 4 - Flux tube
        if: success() || failure() 
        run: |
          if [ ${{ matrix.os }} == 'ubuntu-24.04' ] || [ ${{ matrix.os }} == 'macos-14' ]; then source AUTOMATIC_TESTS/venv/bin/activate; fi
          make numerical-tests-4
          
      - name: Python tests 5 - Diagnostics
        if: success() || failure() 
        run: |
          if [ ${{ matrix.os }} == 'ubuntu-24.04' ] || [ ${{ matrix.os }} == 'macos-14' ]; then source AUTOMATIC_TESTS/venv/bin/activate; fi
          make numerical-tests-5
          
      - name: Python tests 6 - Full Flux Surface
        if: success() || failure() 
        run: |
          if [ ${{ matrix.os }} == 'ubuntu-24.04' ] || [ ${{ matrix.os }} == 'macos-14' ]; then source AUTOMATIC_TESTS/venv/bin/activate; fi
          make numerical-tests-6
          
      - name: Python tests 7 - Electromagnetic effects"
        if: success() || failure() 
        run: |
          if [ ${{ matrix.os }} == 'ubuntu-24.04' ] || [ ${{ matrix.os }} == 'macos-14' ]; then source AUTOMATIC_TESTS/venv/bin/activate; fi
          make numerical-tests-7

#-----------------------------------------------------------------------
#                              Quick build                              
#-----------------------------------------------------------------------

  # Build stella to perform python and fortran tests
  build-stella-quick: 
    name: Build stella quickly
    runs-on: ubuntu-22.04
    env:
      OMPI_MCA_rmaps_base_oversubscribe: yes
      MPIRUN: mpiexec -np
      STELLA_SYSTEM: gnu_ubuntu

    steps:

      # Check-out repository under $GITHUB_WORKSPACE
      - name: Check out repository
        uses: actions/checkout@v4

      # Install dependencies
      - name: Install dependencies
        run: |
          sudo apt update
          sudo apt install -y gfortran make libfftw3-dev libnetcdf-dev libnetcdff-dev 
          sudo apt install -y netcdf-bin python3 python3-pip openmpi-bin libopenmpi-dev

      # Build stella executable
      - name: Build stella
        run: |
          git submodule update --init --recursive
          make -j 12
          
          # Stella is bugged when compiling without the falg debug = on
          # So the python tests will break when compiling with CMake
          #cmake . -B COMPILATION/build_cmake
          #cmake --build COMPILATION/build_cmake -j 4

      # Upload stella
      - name: Upload stella  
        uses: actions/upload-artifact@v4
        with:
          name: stella-executable
          path: stella
          retention-days: 1

#-----------------------------------------------------------------------
#                             Python tests                              
#-----------------------------------------------------------------------

  # Perform python tests one by one
  python-tests: 
    runs-on: ubuntu-22.04
    needs: build-stella-quick
    env:
      OMPI_MCA_rmaps_base_oversubscribe: yes
      MPIRUN: mpiexec -np
      STELLA_SYSTEM: gnu_ubuntu
    
    # Run the same set-up multiple times
    strategy:
      fail-fast: false
      matrix:
        config:
          - name: "1 - Does stella run "
          - name: "2 - Geometry"
          - name: "3 - Gyrokinetic equation"
          - name: "4 - Flux tube"
          - name: "5 - Diagnostics"
          - name: "6 - Full Flux Surface"
          - name: "7 - Electromagnetic effects"

    steps:

      # Check-out repository under $GITHUB_WORKSPACE
      - name: Check out repository
        uses: actions/checkout@v4

      # Install dependencies
      - name: Install dependencies and python virtual environment
        run: |
          sudo apt update
          sudo apt install -y gfortran make libfftw3-dev libnetcdf-dev libnetcdff-dev 
          sudo apt install -y netcdf-bin python3 python3-pip openmpi-bin libopenmpi-dev
          pip3 install --user -r AUTOMATIC_TESTS/requirements.txt
          sed -i 's/nproc = 16/nproc = 4/g' AUTOMATIC_TESTS/config.ini 

      # Download stella executable from previous job
      - name: Download stella 
        uses: actions/download-artifact@v4
        with:
           name: stella-executable
    
      # Perform python tests  
      - name: Numerical python tests
        run: |
          # Make stella executable
          chmod +x stella
          
          # Run one of the python tests
          if ${{ contains(matrix.config.name, '1 -') }}; then make numerical-tests-1; fi
          if ${{ contains(matrix.config.name, '2 -') }}; then make numerical-tests-2; fi
          if ${{ contains(matrix.config.name, '3 -') }}; then make numerical-tests-3; fi
          if ${{ contains(matrix.config.name, '4 -') }}; then make numerical-tests-4; fi
          if ${{ contains(matrix.config.name, '5 -') }}; then make numerical-tests-5; fi
          if ${{ contains(matrix.config.name, '6 -') }}; then make numerical-tests-6; fi
          if ${{ contains(matrix.config.name, '7 -') }}; then make numerical-tests-7; fi



  # Perform python on 1 processor.
  python-tests-nproc1: 
    name: Python tests on 1 processor
    runs-on: ubuntu-22.04
    needs: build-stella-quick
    env:
      OMPI_MCA_rmaps_base_oversubscribe: yes
      MPIRUN: mpiexec -np
      STELLA_SYSTEM: gnu_ubuntu

    steps:

      # Check-out repository under $GITHUB_WORKSPACE
      - name: Check out repository
        uses: actions/checkout@v4

      # Install dependencies
      - name: Install dependencies and python virtual environment
        run: |
          sudo apt update
          sudo apt install -y gfortran make libfftw3-dev libnetcdf-dev libnetcdff-dev 
          sudo apt install -y netcdf-bin python3 python3-pip openmpi-bin libopenmpi-dev
          pip3 install --user -r AUTOMATIC_TESTS/requirements.txt
          sed -i 's/nproc = 16/nproc = 1/g' AUTOMATIC_TESTS/config.ini 

      # Download stella executable from previous job
      - name: Download stella 
        uses: actions/download-artifact@v4
        with:
           name: stella-executable
    
      # Make stella executable  
      - name: Make stella executable
        run: chmod +x stella
        
      # Perform python tests  
      - name: Python tests 1 - Does stella run
        run: make numerical-tests-1
          
      - name: Python tests 2 - Geometry
        if: success() || failure() 
        run: make numerical-tests-2
          
      - name: Python tests 3 - Gyrokinetic equation
        if: success() || failure() 
        run: make numerical-tests-3
          
      - name: Python tests 4 - Flux tube
        if: success() || failure() 
        run: make numerical-tests-4
          
      - name: Python tests 5 - Diagnostics
        if: success() || failure() 
        run: make numerical-tests-5
          
      - name: Python tests 6 - Full Flux Surface
        if: success() || failure() 
        run: make numerical-tests-6
          
      - name: Python tests 7 - Electromagnetic effects"
        if: success() || failure() 
        run: make numerical-tests-7

#-----------------------------------------------------------------------
#                             Fortran tests                              
#-----------------------------------------------------------------------

  fortran-tests:
    runs-on: ubuntu-22.04
    name: "Automated Fortran tests"  
    env:
      OMPI_MCA_rmaps_base_oversubscribe: yes
      MPIRUN: mpiexec -np 
      STELLA_SYSTEM: gnu_ubuntu

    steps:

      # Check-out repository under $GITHUB_WORKSPACE
      - name: Check out repository
        uses: actions/checkout@v4

      # Install dependencies
      - name: Install dependencies
        run: |
          sudo apt update
          sudo apt install -y gfortran make libfftw3-dev libnetcdf-dev libnetcdff-dev netcdf-bin 
          sudo apt install -y python3 python3-pip openmpi-bin libopenmpi-dev libblas-dev liblapack-dev
          pip3 install --user -r AUTOMATIC_TESTS/requirements.txt
      
      # Build stella executable and pFUnit library
      - name: Build stella and perform automated Fortran tests
        run: |
          git submodule update --init --recursive
          cmake . -B build -DSTELLA_ENABLE_TESTS=on
          cmake --build build -j1 --target check

#-----------------------------------------------------------------------
#                          Build in debug mode                          
#-----------------------------------------------------------------------

  # Build stella with Make in debug mode, here the python tests do not work!
  # Specifically, the flush statement in mini_libstell's 
  # read_wout_mod.F module in the readw_and_open() routine breaks 
  # when reading a VMEC equilibirium during the python tests.
  debug-build:
    runs-on: ubuntu-22.04
    name: "Build stella in debug mode"  
    env:
      OMPI_MCA_rmaps_base_oversubscribe: yes
      MPIRUN: mpiexec -np 
      STELLA_SYSTEM: gnu_ubuntu_debug

    steps:

      # Check-out repository under $GITHUB_WORKSPACE
      - name: Check out repository
        uses: actions/checkout@v4

      # Install dependencies
      - name: Install dependencies
        run: |
          sudo apt update
          sudo apt install -y gfortran make libfftw3-dev libnetcdf-dev libnetcdff-dev netcdf-bin 
          sudo apt install -y python3 python3-pip openmpi-bin libopenmpi-dev libblas-dev liblapack-dev 
           
      # Build stella executable
      - name: Build stella in debug mode
        run: make -j 4


# If the operating system is changed, we can check where modules are installed
# by reading the CMake cache file:
#    echo " "; echo "--------- DIRECTORIES ----------"
#    cat COMPILATION/build_cmake/CMakeCache.txt

# We can also install Homebrew and use the following lines of code
#    echo "Install Homebrew:"
#    /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"; brew update
#    echo "FFTW_LIB_DIR=/opt/homebrew/lib/" >> $GITHUB_ENV; echo "Set FFTW_LIB_DIR"
#    echo "FFTW_INC_DIR=/opt/homebrew/include/" >> $GITHUB_ENV; echo "Set FFTW_INC_DIR"
#    echo "NETCDF_LIB_DIR=/opt/homebrew/lib/" >> $GITHUB_ENV; echo "Set NETCDF_LIB_DIR"
#    echo "NETCDF_INC_DIR=/opt/homebrew/include/" >> $GITHUB_ENV; echo "Set NETCDF_INC_DIR"
#    brew install gcc fftw netcdf netcdf-fortran open-mpi python
#    ln -sn /opt/homebrew/bin/gfortran-12 /opt/homebrew/bin/gfortran

# if:  github.event_name == 'push'

    # Turn this job off for now !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    #if: false