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 T3
      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 ARC
      id: cache-arc
      uses: actions/cache@v2
      with:
          path: ARC
          key: ${{ runner.os }}-arc-main
          restore-keys: |
            ${{ runner.os }}-arc-

    - name: Checkout ARC
      if: steps.cache-arc.outputs.cache-hit != 'true'
      uses: actions/checkout@v3
      with:
        repository: ReactionMechanismGenerator/ARC
        path: ARC
        ref: no_ase
        fetch-depth: 1

    - name: Setup ARC paths
      run: |
        cd ARC
        echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> $GITHUB_ENV
        echo "PATH=$(pwd):$PATH" >> $GITHUB_ENV
        echo "export arc_path=$(pwd)" >> $GITHUB_ENV
        echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> ~/.bashrc
        echo "PATH=$(pwd):$PATH" >> ~/.bashrc
        echo "export arc_path=$(pwd)" >> ~/.bashrc

    - 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: Setup ARC Env
      uses: conda-incubator/setup-miniconda@v2
      with:
          miniforge-variant: Mambaforge
          miniforge-version: latest
          activate-environment: arc_env
          use-mamba: true

    - name: Cache RMG-Py env
      uses: actions/cache@v2
      with:
        path: ${{ env.CONDA }}/envs/rmg_env
        key:
          conda-${{ runner.os }}--${{ runner.arch }}-rmgpyenv-${{ env.CACHE_NUMBER}}
      env:
        # Increase this value to reset cache if etc/example-environment.yml has not changed
        CACHE_NUMBER: 3
      id: cache-rmgpy-env
    - name: Update environment
      run: mamba env update -n rmg_env -f RMG-Py/environment.yml
      if: steps.cache-rmgpy-env.outputs.cache-hit != 'true'

    - name: Cythonize RMG-Py
      run: |
        cd RMG-Py
        conda activate rmg_env
        git fetch origin no_qm
        git checkout no_qm
        make clean
        make
        julia -e 'using Pkg; Pkg.add("PyCall");Pkg.build("PyCall");Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator;'
        python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
        echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> $GITHUB_ENV
        echo "PATH=$(pwd):$PATH" >> $GITHUB_ENV
        echo "export rmgpy_path=$(pwd)" >> $GITHUB_ENV
        echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> ~/.bashrc
        echo "PATH=$(pwd):$PATH" >> ~/.bashrc
        echo "export rmgpy_path=$(pwd)" >> ~/.bashrc

    - name: Install xtb
      run: |
        mamba create -n xtb_env python=3.7  -c conda-forge -y
        conda activate xtb_env
        mamba install -c conda-forge xtb=6.3.3 -y
        mamba install -c anaconda pyyaml -y

    - name: Install T3
      run: |
        mamba env create -f environment.yml

    - name: Install CodeCov
      run: |
        conda activate t3_env
        mamba install -c conda-forge codecov
        mamba install -c conda-forge pytest-cov

    - name: Run T3 Tests
      shell: bash -el {0}
      run: |
        source ~/.bashrc
        conda activate t3_env
        make test
        codecov --token=${{ secrets.CODECOV_TOKEN }}

    - name: Code Coverage
      uses: codecov/codecov-action@v3
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: ./coverage.xml
        flags: unittests
        name: codecov-umbrella
        verbose: true
        fail_ci_if_error: true