merge-gate.yml

name: Cpptraj Tests
on:
  push:
    branches: [master]
  pull_request:
    branches: [master]

jobs:
  linux_build:
    runs-on: ubuntu-latest
    name: Build ${{ matrix.compiler }} with CMake ${{ matrix.use_cmake }}
    strategy:
      fail-fast: false
      matrix:
        compiler: ["gnu", "clang"]
        use_cmake: ["0", "1"]
        use_openmp: ["no"]
        use_mpi: ["no"]
        include:
          - use_openmp: "yes"
            compiler: "gnu"
            use_mpi: "no"
            use_cmake: "0"
          - use_openmp: "no"
            compiler: "gnu"
            use_mpi: "yes"
            use_cmake: "0"
          - use_openmp: "yes"
            compiler: "gnu"
            use_mpi: "yes"
            use_cmake: "0"
          - use_openmp: "no"
            compiler: "gnu"
            use_mpi: "yes"
            use_cmake: "1"

    env:
      COMPILER: ${{ matrix.compiler }}
      USE_CMAKE: ${{ matrix.use_cmake }}
      BUILD_TYPE: "install"
      TEST_TYPE: "test.showerrors"
      USE_MPI: ${{ matrix.use_mpi }}
      USE_OPENMP: ${{ matrix.use_openmp }}

    steps:
      - name: Install prerequisite packages
        run: |
          sudo apt-get install gfortran
          sudo apt-get install libbz2-dev
          sudo apt-get install libblas-dev liblapack-dev
          sudo apt-get install libfftw3-dev
          sudo apt-get install clang
          sudo apt-get install cmake-data cmake

      - name: Checkout source code
        uses: actions/checkout@v4

      - name: Compile and test cpptraj
        shell: bash -lex {0}
        run: |
          curl -OL https://anaconda.org/AmberMD/amber_phenix/0.9.6/download/linux-64/amber_phenix-0.9.6-0.tar.bz2
          tar jxf amber_phenix-0.9.6-0.tar.bz2 lib/libsander.so AmberTools/src/sander/sander.h
          mkdir -p include && mv AmberTools/src/sander/sander.h include
          mv lib include $HOME

          if [ $USE_OPENMP = "yes" ]; then
            export OPT="openmp"
            export OMP_NUM_THREADS=4
            if [ "$USE_CMAKE" = "1" ]; then
              export BUILD_FLAGS="-DOPENMP=TRUE"
            else
              export BUILD_FLAGS="-openmp"
            fi
          fi

          if [ $USE_MPI = "yes" ]; then
            curl -OL http://www.mpich.org/static/downloads/3.4.2/mpich-3.4.2.tar.gz
            tar -zxf mpich-3.4.2.tar.gz
            cd mpich-3.4.2
            export FFLAGS=-fallow-argument-mismatch
            ./configure --with-device=ch3 --prefix=$HOME
            make -j2
            make install
            cd ..
            export PATH=$HOME/bin:$PATH
            export LD_LIBRARY_PATH=$HOME/lib:$LD_LIBRARY_PATH
            export DO_PARALLEL="mpirun -n 2"
            if [ $USE_OPENMP = "yes" ]; then
              export OMP_NUM_THREADS=1
            fi
            if [ "$USE_CMAKE" = "1" ]; then
              export BUILD_FLAGS="-DMPI=TRUE ${BUILD_FLAGS}"
            else
              export BUILD_FLAGS="-mpi ${BUILD_FLAGS}"
            fi
          fi

          if [ "$USE_CMAKE" = "1" ]; then
            curl -OL https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.2.tar.gz
            tar -zxf v4.9.2.tar.gz
            cd netcdf-c-4.9.2
            ./configure --disable-byterange --disable-libxml2 --disable-netcdf-4 --disable-dap --disable-doxygen --prefix=$HOME
            make -j2
            make install
            cd ..
            export PATH=$HOME/bin:$PATH
            export LD_LIBRARY_PATH=$HOME/lib:${LD_LIBRARY_PATH}

            mkdir build install
            installdir=$(pwd)
            cd build
            cmake .. $BUILD_FLAGS -DCOMPILER=${COMPILER^^} -DINSTALL_HEADERS=FALSE \
                     -DCMAKE_INSTALL_PREFIX=$installdir -DCMAKE_LIBRARY_PATH=$HOME/lib \
                     -DPRINT_PACKAGING_REPORT=TRUE -DNetCDF_LIBRARIES_C=$HOME/lib/libnetcdf.so \
                     -DNetCDF_INCLUDES=$HOME/include
            make -j2 install
            cd ..
            export PATH=$installdir/bin:$PATH
          else
            export LD_LIBRARY_PATH=$HOME/lib:${LD_LIBRARY_PATH}
            ./configure --buildlibs ${BUILD_FLAGS} ${COMPILER}
            source cpptraj.sh
            make -j2 install
          fi
          cd test && make $TEST_TYPE

  build-pytraj:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 5
    steps:
    - name: Install prerequisite packages
      run: |
        sudo apt-get install clang
        sudo apt-get install cmake-data cmake    
    - uses: actions/checkout@v4
    - name: Set up Python 3.12
      uses: actions/setup-python@v5
      with:
        python-version: '3.12'
    - name: Add conda to system path
      run: |
        # $CONDA is an environment variable pointing to the root of the miniconda directory
        echo $CONDA/bin >> $GITHUB_PATH
    - name: Install conda packages
      run: |
        which conda
        conda install conda python=3.12
        conda --version
        conda env update --file devtools/ci/environment.yml --name base
    - name: Install cpptraj
      run: |
        export PATH=$HOME/bin:${PATH}
        export LD_LIBRARY_PATH=$HOME/lib:${LD_LIBRARY_PATH}
        export PATH=$CONDA/bin:${PATH}
        export LD_LIBRARY_PATH=$CONDA/lib:${LD_LIBRARY_PATH}
        echo $PATH
        echo $LD_LIBRARY_PATH
        ls $CONDA/lib
        export MAKE_COMMAND="make -j2"
        ./configure --buildlibs -openmp -shared --with-zlib=$CONDA --with-bzlib=$CONDA --with-hdf5=$CONDA --with-netcdf=$CONDA --with-fftw3=$CONDA gnu
        source cpptraj.sh
        make -j2 libcpptraj
    - name: Install pytraj
      run: |        
        git clone https://github.com/Amber-MD/pytraj.git
        export PATH=$CONDA/bin:${PATH}
        export LD_LIBRARY_PATH=$CONDA/lib:${LD_LIBRARY_PATH}
        source cpptraj.sh
        cd pytraj
        python setup.py install
        cd ..
    - name: Test with pytest
      run: |
        export PATH=$CONDA/bin:${PATH}
        export LD_LIBRARY_PATH=$CONDA/lib:${LD_LIBRARY_PATH}
        source cpptraj.sh && cd pytraj/tests && pytest -vs --ignore=test_parallel_pmap