python-package-conda.yml

name: Python Package using Conda

on:
  pull_request:
  workflow_dispatch:

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

    defaults:
      run:
        # Enable bash login shell to activate conda environment
        shell: bash -l {0}

    strategy:
      max-parallel: 5
      matrix:
        python-version: ["3.10", "3.11", "3.12"]

    steps:
    - name: Checkout 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 }}-${{ hashFiles('environment.yml') }}
    - name: Install prerequisite packages
      run: |
        sudo apt-get install -y gfortran libbz2-dev libblas-dev liblapack-dev libfftw3-dev clang cmake-data cmake
    - name: Get latest cpptraj commit hash
      id: get-hash
      run: |
        latest_hash=$(git ls-remote https://github.com/Amber-MD/cpptraj.git refs/heads/master | awk '{print $1}')
        echo "::set-output name=hash::$latest_hash"
    - name: Cache cpptraj
      uses: actions/cache@v4
      with:
        path: ~/cpptraj
        key: ${{ runner.os }}-cpptraj-${{ steps.get-hash.outputs.hash }}
        restore-keys: |
          ${{ runner.os }}-cpptraj-
    - name: Install CPPTRAJ dependencies
      run: |
        curl -OL https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.2.tar.gz
        tar -zxf v4.9.2.tar.gz
        cd netcdf-c-4.9.2
        ./configure --disable-byterange --disable-libxml2 --disable-netcdf-4 --disable-dap --disable-doxygen --prefix=$HOME
        make -j2
        make install
        cd ..
        export PATH=$HOME/bin:$PATH
    - name: Install cpptraj
      run: |
        if [ ! -d "$HOME/cpptraj" ]; then
          git clone https://github.com/Amber-MD/cpptraj
          cd cpptraj
          export CPPTRAJHOME=`pwd`
          yes | ./configure -shared -openmp gnu
          make libcpptraj
          cd ../
        fi
    - name: Set up Miniconda # Do this after installing cpptraj to avoid "yes: standard output: Broken pipe" error
      uses: conda-incubator/setup-miniconda@v3
      with:
        auto-update-conda: true
        auto-activate-base: false
        activate-environment: pytraj-gha
        environment-file: environment.yml
        mamba-version: "*"
        channels: conda-forge
        channel-priority: true
        python-version: ${{ matrix.python-version }}
    - name: Check conda environment
      run: |
        conda --version
        which conda
        which python
        which python3
    - 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