cont_int.yml

name: CI

on: 
    pull_request:
        branches:
            - main
        types: [opened, synchronize, reopened, ready_for_review, review_requested]

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
          id: cache-rmg
          uses: actions/cache@v2
          with:
            path: RMG-Py
            key: ${{ runner.os }}-rmg-main
            restore-keys: |
              ${{ runner.os }}-rmg-
        - name: Debug RMG Cache
          run: |  
            echo "cache hit: ${{ steps.cache-rmg.outputs.cache-hit }}"
        - name: Checkout RMG
          if: steps.cache-rmg.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: main
            fetch-depth: 1

        - name: Cache Conda Packages
          uses: actions/cache@v2
          env:
            CACHE_NUMBER: 0
          with:
            path: ~/conda_pkgs_dir
            key:
                ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}-t3


        - name: Setup RMG-Py Env
          uses: conda-incubator/setup-miniconda@v2
          with:
              miniforge-variant: Mambaforge
              miniforge-version: latest
              activate-environment: rmg_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: 1
          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
            make clean
            make
            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: Cache RMS
          id: cache-rms
          uses: actions/cache@v2
          env:
            CACHE_NUMBER: 0
          with:
            path: | 
                /usr/share/miniconda3/envs/rmg_env/share/julia/artifacts/
                /usr/share/miniconda3/envs/rmg_env/share/julia/packages/
                /usr/share/miniconda3/envs/rmg_env/share/julia/registries/
                /usr/share/miniconda3/envs/rmg_env/share/julia/compiled/
            key:
                ${{ runner.os }}-julia-${{ env.CACHE_NUMBER }}-rms

        - name: Install RMS Julia
          run: julia -e 'using Pkg; Pkg.add(PackageSpec(name="PyCall",rev="master"));Pkg.build("PyCall");Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator;'

        - name: Install PyCall RMG_ENV
          run: python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"

        - name: Install ARC ENV
          run: |
            cd ARC
            mamba env create -f environment.yml
            conda activate arc_env
            echo "export arc_path=$(pwd)" >> $GITHUB_ENV
            echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> $GITHUB_ENV
            echo "PATH=$(pwd):$PATH" >> $GITHUB_ENV
            echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> ~/.bashrc
            echo "PATH=$(pwd):$PATH" >> ~/.bashrc
            echo "export arc_path=$(pwd)" >> ~/.bashrc
            cd ..

        - 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