python-package-conda.yml

name: Testing pytraj

on: [push, pull_request, workflow_dispatch]

jobs:
  build-linux:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 5
      matrix:
        python-version: ['3.9', '3.10', '3.11', '3.12']

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

      - uses: actions/checkout@v3

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install mamba
        run: |
          conda install mamba -n base -c conda-forge

      - name: Add conda to system path
        run: echo $CONDA/bin >> $GITHUB_PATH

      - name: Install dependencies
        run: |
          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

      - name: Install cpptraj
        run: |
          git clone https://github.com/Amber-MD/cpptraj
          cd cpptraj
          export CPPTRAJHOME=`pwd`
          yes | ./configure -shared -openmp gnu
          make libcpptraj
          cd ../

      - name: Install conda packages with mamba
        run: |
          mamba create -n env python=${{ matrix.python-version }} -c conda-forge
          source activate env
          mamba update --file environment.yml

      - name: Install pytraj
        run: python setup.py install

      - name: Test with pytest
        run: |
          export CPPTRAJHOME=`pwd`/cpptraj
          cd tests
          pytest -vs --ignore=test_parallel_pmap --ignore=test