Merge pull request #156 from ReactionMechanismGenerator/py_v

Updated CI and env

.github/workflows/cont_int.yml

@@ -1,181 +1,181 @@
 name: CI
 
 on:
-    pull_request:
-        branches:
-            - main
-        types: [opened, synchronize, reopened, ready_for_review, review_requested]
+  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
-          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
+  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: 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/[email protected]
-          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: 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
-            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: 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
+    - 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