JWB initial increase to Python 3.9

These were the first commits to change to Python 3.9, and they do not work on their own but instead open the door to finding issues to make the rest of the changes

Author: JacksonBurns

.github/workflows/CI.yml

@@ -51,66 +51,14 @@ env:
 
 
 jobs:
-  build-osx:
-    runs-on: macos-13
-    # skip scheduled runs from forks
-    if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }}
-    defaults:
-      run:
-        shell: bash -l {0}
-    steps:
-      - name: Checkout RMG-Py
-        uses: actions/checkout@v4
-
-      # Step to create a custom condarc.yml before setting up conda
-      - name: Create custom conda config file
-        run: |
-          RUNNER_CWD=$(pwd)
-          echo "channels:" > $RUNNER_CWD/condarc.yml
-          echo "  - conda-forge" >> $RUNNER_CWD/condarc.yml
-          echo "  - rmg" >> $RUNNER_CWD/condarc.yml
-          echo "  - cantera" >> $RUNNER_CWD/condarc.yml
-          echo "show_channel_urls: true" >> $RUNNER_CWD/condarc.yml
-
-      # configures the mamba environment manager and builds the environment
-      - name: Setup Miniforge Python 3.7
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-          environment-file: environment.yml
-          miniforge-variant: Miniforge3
-          miniforge-version: latest
-          python-version: 3.7
-          condarc-file: condarc.yml
-          activate-environment: rmg_env
-          use-mamba: true
-
-      # list the environment for debugging purposes
-      - name: mamba info
-        run: |
-          mamba info
-          mamba list
-
-      # Clone RMG-database
-      - name: Clone RMG-database
-        run: |
-          cd ..
-          git clone -b $RMG_DATABASE_BRANCH https://github.com/ReactionMechanismGenerator/RMG-database.git
-
-      # modify env variables as directed in the RMG installation instructions
-      - name: Set Environment Variables
-        run: |
-          RUNNER_CWD=$(pwd)
-          echo "PYTHONPATH=$RUNNER_CWD/RMG-Py:$PYTHONPATH" >> $GITHUB_ENV
-          echo "$RUNNER_CWD/RMG-Py" >> $GITHUB_PATH
-
-      # RMG build step
-      - name: make RMG
-        run: |
-          make clean
-          make
-
-  build-and-test-linux:
-    runs-on: ubuntu-latest
+  build-and-test:
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9"]
+        os: [macos-13, macos-latest, ubuntu-latest]
+    runs-on: ${{ matrix.os }}
+    name: ${{ matrix.os }} Build and Test Python ${{ matrix.python-version }}
     # skip scheduled runs from forks
     if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }}
     env: 
@@ -123,27 +71,17 @@ jobs:
       - name: Checkout RMG-Py
         uses: actions/checkout@v4
 
-      # Step to create a custom condarc.yml before setting up conda
-      - name: Create custom condarc.yml
-        run: |
-          RUNNER_CWD=$(pwd)
-          echo "channels:" > $RUNNER_CWD/condarc.yml
-          echo "  - conda-forge" >> $RUNNER_CWD/condarc.yml
-          echo "  - rmg" >> $RUNNER_CWD/condarc.yml
-          echo "  - cantera" >> $RUNNER_CWD/condarc.yml
-          echo "show_channel_urls: true" >> $RUNNER_CWD/condarc.yml
-
-      # configures the mamba environment manager and builds the environment
-      - name: Setup Miniforge Python 3.7
+      - name: Setup Miniforge Python ${{ matrix.python-version }}
         uses: conda-incubator/setup-miniconda@v3
         with:
           environment-file: environment.yml
           miniforge-variant: Miniforge3
           miniforge-version: latest
-          python-version: 3.7
-          condarc-file: condarc.yml
+          python-version: ${{ matrix.python-version }}
           activate-environment: rmg_env
           use-mamba: true
+          show-channel-urls: true
+          channels: conda-forge,cantera,rmg
 
       # list the environment for debugging purposes
       - name: mamba info
@@ -386,7 +324,7 @@ jobs:
     # who knows ¯\_(ツ)_/¯
     #
     # taken from https://github.com/docker/build-push-action
-    needs: build-and-test-linux
+    needs: build-and-test
     runs-on: ubuntu-latest
     if: github.ref == 'refs/heads/main' && github.repository == 'ReactionMechanismGenerator/RMG-Py'
     steps:

.github/workflows/docs.yml

@@ -26,15 +26,17 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Setup Mambaforge Python 3.7
+      - name: Setup Miniforge Python 3.9
         uses: conda-incubator/setup-miniconda@v3
         with:
           environment-file: environment.yml
           miniforge-variant: Miniforge3
           miniforge-version: latest
-          python-version: 3.7
+          python-version: 3.9
           activate-environment: rmg_env
           use-mamba: true
+          show-channel-urls: true
+          channels: conda-forge,cantera,rmg
 
       - name: Make libtiff Symlink to Avoid Runner Bug
         run: | # This action may need to be removed/adjusted in future runs.

environment.yml

@@ -19,7 +19,8 @@
 # - April 17, 2024 Limit versions of cclib at advice of maintainers.
 # - August 4, 2024 Restricted pyrms to <2
 # - May 14, 2024 Removed diffeqpy by switching to call SciMLBase and Sundials using JuliaCall
-
+# - March 15, 2024 - started migration to Python 3.9
+#
 name: rmg_env
 channels:
   - rmg
@@ -45,7 +46,7 @@ dependencies:
 
 # external software tools for chemistry
   - coolprop
-  - cantera::cantera=2.6
+  - cantera::cantera >=3
   - conda-forge::mopac
   # see https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2639#issuecomment-2050292972
   - conda-forge::cclib >=1.6.3,<1.9
@@ -57,11 +58,11 @@ dependencies:
   - conda-forge::pyjuliacall # for calling julia packages
 
 # Python tools
-  - python >=3.7
+  - python >=3.9  # leave as GEQ so that GitHub actions can add EQ w/o breaking (contradictory deps)
   - coverage
   - cython >=0.25.2
   - scikit-learn
-  - scipy <1.11
+  - scipy
   - numpy >=1.10.0
   - pydot
   - jinja2
@@ -72,13 +73,7 @@ dependencies:
   - networkx
   - pytest
   - pytest-cov
-  # we use a the pytest-check plugin, which is on Conda and PyPI, but the
-  # version compatible with Python 3.7 is only on PyPI
-  # switch to the conda version after upgrading to 3.11
-  # - conda-forge::pytest-check
-  - pip
-  - pip:
-    - pytest-check
+  - conda-forge::pytest-check
   - matplotlib >=1.5
   - mpmath
   - pandas