python-test.yml

name: Python application test

on: [push, pull_request]

jobs:
  build:

    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v2
    - name: Set up Python
      uses: actions/setup-python@v2
      with:
        python-version: '3.9'  # Specify the Python version

    - name: Install dependencies
      run: |
        if [ -f pytest_requirements.txt ]; then 
          pip install -r pytest_requirements.txt; 
        fi
        export CONDA_ALWAYS_YES="true"
        pip install 'rdkit==2024.3.5'
        pip install 'scipy==1.11.1'
        pip install xtb
        pip install 'joblib==1.3.1'
        pip install 'PyYAML==6.0.1'
        pip install openbabel-wheel
        pip install 'pandas==2.0.3'
        pip install 'ase==3.22.1'
        conda install -y conda-forge::xtb
        pip install 'xgboost==1.7.6'
        pip install 'h5py==3.9.0'
        pip install pysisyphus
        conda install -y conda-forge::crest
        unset CONDA_ALWAYS_YES
        pip install --force-reinstall 'scikit-learn==1.3.0'
        pip install --force-reinstall 'numpy==1.24.4'
        pip install .

        # CHECK
        pip freeze

        # Prepare pysis env
        cp .pysisyphusrc /home/runner/.pysisyphusrc
        cond=asd
        sed -i "s|CONDA_ENV|${CONDA}|g" /home/runner/.pysisyphusrc

    - name: Run pytest
      run: |
               home=$(pwd)
               cd /opt/hostedtoolcache/Python/3.9.20/x64/bin/
               ls
               echo $CONDA
               cd $CONDA/bin
               
               #ls
               #echo $(pwd)
               #$CONDA/bin/xtb --version
               #$CONDA/bin/crest --version
               #pysis --version
               # test Organometallics
               #obabel --version
               #
               # run Organometallic YARP Example #
               cd $home/examples/
               pytest -s
               cd $home/pyTEST_Example/
               # xtb and crest are in conda bin, others in pip bin
               sed -i "s|CONDA_PATH|${CONDA}|g" test_rxn.py
               pytest -s
      shell: bash