python-package-conda.yml

name: Python Package using Conda

on:
  push:
  pull_request:
  workflow_dispatch:

jobs:
  build-linux:
    runs-on: ubuntu-latest

    strategy:
      max-parallel: 5
      matrix:
        python-version: ["3.8", "3.9", "3.10", "3.11"]

    steps:
    - name: Checkout nglview repository
      uses: actions/checkout@v4
    - name: Cache conda
      uses: actions/cache@v4
      env:
        CACHE_NUMBER: 1  # Increase this value to reset cache if environment.yml has changed
      with:
        path: ~/conda_pkgs_dir
        key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('.github/workflows/environment.yml') }}
    - name: Set up Miniconda
      uses: conda-incubator/setup-miniconda@v3
      with:
        auto-update-conda: true
        auto-activate-base: false
        activate-environment: pytraj-gha
        environment-file: .github/workflows/environment.yml
        mamba-version: "*"
        channels: conda-forge
        channel-priority: true
        python-version: ${{ matrix.python-version }}
    - name: Install prerequisite packages
      run: |
        sudo apt-get install gfortran
        sudo apt-get install libbz2-dev
        sudo apt-get install libblas-dev liblapack-dev
        sudo apt-get install libfftw3-dev
        sudo apt-get install clang
        sudo apt-get install cmake-data cmake
    - name: Install cpptraj dependencies
      run: |
        curl -OL https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.2.tar.gz
        tar -zxf v4.9.2.tar.gz
        cd netcdf-c-4.9.2
        ./configure --disable-byterange --disable-libxml2 --disable-netcdf-4 --disable-dap --disable-doxygen --prefix=$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 pytraj
      run: |
        which python3
        python3 setup.py install
    - name: Test with pytest
      run: |
        export CPPTRAJHOME=`pwd`/cpptraj && cd tests && pytest -vs --ignore=test_parallel_pmap --ignore=test_run_mpi.py --ignore=test_energy/test_pmap_sander.py --ignore=test_parallel_mpi --ignore=test_actionlist.py