cont_int.yml

name: CI

on:
  push:
    branches:
      - '*'
  pull_request:
    branches:
      - main
    types: [opened, synchronize, reopened, ready_for_review, review_requested]
  schedule:
    - cron: '0 0 * * *'


jobs:
  build:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -el {0}

    steps:
    - name: Checkout ARC
      uses: actions/checkout@v3

    - name: Clean Ubuntu Image
      uses: kfir4444/free-disk-space@main
      with:
        # This may remove tools actually needed - currently does not
        tool-cache: true
        android: true
        dotnet: true
        haskell: true
        large-packages: true
        swap-storage: true

    - name: Cache RMG-Py
      id: cache-rmg-py
      uses: actions/cache@v2
      with:
        path: RMG-Py
        key: ${{ runner.os }}-rmg-main
        restore-keys: |
          ${{ runner.os }}-rmg-

    - name: Checkout RMG-py
      if: steps.cache-rmg-py.outputs.cache-hit != 'true'
      uses: actions/checkout@v3
      with:
        repository: ReactionMechanismGenerator/RMG-Py
        path: RMG-Py
        ref: main
        fetch-depth: 1

    - name: Cache RMG-database
      id: cache-rmg-db
      uses: actions/cache@v2
      with:
          path: RMG-database
          key: ${{ runner.os }}-rmgdb-main
          restore-keys: |
            ${{ runner.os }}-rmgdb-
    - name: Checkout RMG-database
      if: steps.cache-rmg-db.outputs.cache-hit != 'true'
      uses: actions/checkout@v3
      with:
        repository: ReactionMechanismGenerator/RMG-database
        path: RMG-database
        ref: main
        fetch-depth: 1

    - name: Cache AutoTST
      id: cache-autotst
      uses: actions/cache@v2
      with:
          path: AutoTST
          key: ${{ runner.os }}-autotst-main
          restore-keys: |
            ${{ runner.os }}-autotst-
    - name: Checkout AutoTST
      if: steps.cache-autotst.outputs.cache-hit != 'true'
      uses: actions/checkout@v3
      with:
        repository: ReactionMechanismGenerator/AutoTST
        path: AutoTST
        ref: main
        fetch-depth: 1

    - name: Cache TS-GCN
      id: cache-tsgcn
      uses: actions/cache@v2
      with:
          path: TS-GCN
          key: ${{ runner.os }}-tsgcn-main
          restore-keys: |
            ${{ runner.os }}-tsgcn-
    - name: Checkout TS-GCN
      if: steps.cache-tsgcn.outputs.cache-hit != 'true'
      uses: actions/checkout@v3
      with:
        repository: ReactionMechanismGenerator/TS-GCN
        path: TS-GCN
        ref: main
        fetch-depth: 1
    
    - name: Cache KinBot
      id: cache-kinbot
      uses: actions/cache@v2
      with:
          path: KinBot
          key: ${{ runner.os }}-kinbot-2.0.6
          restore-keys: |
            ${{ runner.os }}-kinbot-

    - name: Checkout Kinbot 2.0.6
      if: steps.cache-kinbot.outputs.cache-hit != 'true'
      uses: actions/checkout@v3
      with:
        repository: zadorlab/KinBot
        path: KinBot
        ref: v2.0.6
        fetch-depth: 1

    - name: Cache Packages
      uses: actions/cache@v2
      env:
        CACHE_NUMBER: 0
      with:
        path: ~/conda_pkgs_dir
        key:
          ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
    
    - name: Set up miniconda
      uses: conda-incubator/setup-miniconda@v3
      with:
          auto-update-conda: true
          environment-file: environment.yml
          activate-environment: arc_env
          miniconda-version: latest
          conda-solver: libmamba

    - name: Cache ARC env
      uses: actions/cache@v2
      with:
        path: ${{ env.CONDA }}/envs/arc_env
        key: conda-${{ runner.os }}--${{ runner.arch }}-arcenv-${{ env.CACHE_NUMBER}}
      env:
        # Increase this value to reset cache if etc/example-environment.yml has not changed
        CACHE_NUMBER: 0
      id: cache-arc-env
    - name: Update environment
      run: conda env update -n arc_env -f environment.yml
      if: steps.cache-arc-env.outputs.cache-hit != 'true'

    - name: Install codecov
      run: conda install --force-reinstall ld_impl_linux-64 -y && conda install -y -c conda-forge codecov

    - name: Cythonize RMG-Py
      run: |
        cd RMG-Py
        echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> $GITHUB_ENV
        echo 'export PATH=$PATH:'"$(pwd)" >> $GITHUB_ENV
        echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> ~/.bashrc
        echo 'export PATH=$PATH:'"$(pwd)" >> ~/.bashrc
        make
        cd ..
  
    - name: Set ARC Path
      run: |
        echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> $GITHUB_ENV
        echo 'export PATH=$PATH:'"$(pwd)" >> $GITHUB_ENV
        echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> ~/.bashrc
        echo 'export PATH=$PATH:'"$(pwd)" >> ~/.bashrc
        
    - name: Install AutoTST
      run: |
        cd AutoTST
        echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> $GITHUB_ENV
        echo 'export PATH=$PATH:'"$(pwd)" >> $GITHUB_ENV
        echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> ~/.bashrc
        echo 'export PATH=$PATH:'"$(pwd)" >> ~/.bashrc
        conda env create -f environment.yml
        # install pyaml
        conda install -n tst_env -c conda-forge -y pyyaml
        cd ..
    
    - name: Install TS-GCN
      run: |
        cd TS-GCN
        echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> $GITHUB_ENV
        echo 'export PATH=$PATH:'"$(pwd)" >> $GITHUB_ENV
        echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> ~/.bashrc
        echo 'export PATH=$PATH:'"$(pwd)" >> ~/.bashrc
        bash devtools/create_env_cpu.sh
        conda env update -n ts_gcn -f environment.yml
        cd ..
    
    - name: Install KinBot
      run: |
        cd KinBot
        conda activate arc_env
        echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> $GITHUB_ENV
        echo 'export PATH=$PATH:'"$(pwd)" >> $GITHUB_ENV
        echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> ~/.bashrc
        echo 'export PATH=$PATH:'"$(pwd)" >> ~/.bashrc
        python setup.py build
        python setup.py install
        cd ..

    - name: Install OpenBabel
      run: |
        conda env create -f devtools/ob_environment.yml

    - name: Install Sella
      run: |
        conda env create -f devtools/sella_environment.yml

    - name: Install Torch Ani
      run: |
        conda env create -f devtools/tani_environment.yml
  
    - name: Install XTB
      run: |
        conda env create -f devtools/xtb_environment.yml
    
    - name: Test with pytest
      shell: bash -el {0} 
      run: |
        source ~/.bashrc
        conda activate arc_env
        make test
        codecov --token=f259713a-7f1d-4e9c-b140-bb3bb371d3ef

    - name: Functional Test
      run: |
        source ~/.bashrc
        conda activate arc_env
        make test-functional
    # Wait ten seconds before running the next step
    - name: Wait
      run: sleep 10

    - name: Code Coverage
      uses: codecov/codecov-action@v3
      with:
        token: f259713a-7f1d-4e9c-b140-bb3bb371d3ef
        file: ./coverage.xml
        flags: unittests
        name: codecov-umbrella
        verbose: true
        fail_ci_if_error: false