Upgrading to Python 3.11/2

.github/workflows/CI.yml

@@ -52,6 +52,10 @@ env:
 jobs:
   build-osx:
     runs-on: macos-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12"]
     # skip scheduled runs from forks
     if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }}
     defaults:
@@ -62,13 +66,13 @@ jobs:
         uses: actions/checkout@v3
 
       # configures the mamba environment manager and builds the environment
-      - name: Setup Mambaforge Python 3.7
+      - name: Setup Mambaforge Python ${{ matrix.python-version }}
         uses: conda-incubator/setup-miniconda@v2
         with:
           environment-file: environment.yml
           miniforge-variant: Mambaforge
           miniforge-version: latest
-          python-version: 3.7
+          python-version: ${{ matrix.python-version }}
           activate-environment: rmg_env
           use-mamba: true
 
@@ -99,6 +103,10 @@ jobs:
 
   build-and-test-linux:
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12"]
     # skip scheduled runs from forks
     if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }}
     env: 
@@ -112,15 +120,13 @@ jobs:
         uses: actions/checkout@v3
 
       # configures the mamba environment manager and builds the environment
-      - name: Patch Environment File
-        run: sed -i 's/  - conda-forge::julia>=1.8.5,!=1.9.0/  - conda-forge::julia=1.9.1/' environment.yml
-      - name: Setup Mambaforge Python 3.7
+      - name: Setup Mambaforge Python ${{ matrix.python-version }}
         uses: conda-incubator/setup-miniconda@v2
         with:
           environment-file: environment.yml
           miniforge-variant: Mambaforge
           miniforge-version: latest
-          python-version: 3.7
+          python-version: ${{ matrix.python-version }}
           activate-environment: rmg_env
           use-mamba: true
 

environment.yml

@@ -16,6 +16,7 @@
 #   made dependency list more explicit (@JacksonBurns).
 # - October 16, 2023 Switched RDKit and descripatastorus to conda-forge,
 #   moved diffeqpy to pip and (temporarily) removed chemprop
+# - March 15, 2024 - started migration to Python 3.11/2
 #
 name: rmg_env
 channels:
@@ -53,7 +54,7 @@ dependencies:
   - conda-forge::pyjulia >=0.6
 
 # Python tools
-  - python >=3.7
+  - python =3.11,3.12
   - coverage
   - cython >=0.25.2
   - scikit-learn
@@ -68,13 +69,7 @@ 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