Merge PR #2456 to fix Continous Integration testing

Closes #2455.
The problem is conda-forge upgraded from
libstdcxx-ng              12.3.0               h0f45ef3_0
to
libstdcxx-ng              13.1.0               hfd8a6a1_0
which is incompatible with something in our stack (maybe julia, though perhaps not).
The solution is, until this is fixed, patch the environment.yml to require libstdcxx-ng = 12.

This PR adds a matrix build to the CI so that we continue to test ubuntu-latest with version 13
so we'll notice if it starts to work again. Then we can remove this hackery.

.github/workflows/CI.yml

@@ -13,12 +13,11 @@
 # a push is made to a non-main branch. The new proposed changes are referred to as "Dynamic".
 #
 # Changelog:
-# April 2023 - Jackson Burns - Added this header, regression tests, cleanup of action in 
-# in general, and documentation throughout the file.
-#
-# May 2023 - added Docker build steps
-#
-# May 12 2023 - added changes to allow running on forks
+# 2023-04    - Jackson Burns - Added this header, regression tests, cleanup of action in 
+#              in general, and documentation throughout the file.
+# 2023-05    - added Docker build steps
+# 2023-05-12 - added changes to allow running on forks
+# 2023-06-06 - added matrix build for libstdcxx-ng versions 12 and 13 on ubuntu. Only expect 12 to work.
 name: Constant Integration
 
 on:
@@ -41,8 +40,17 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
+        libstdcxx-ng: [null, 12, 13]
+        exclude:
+          - os: macos-latest
+            libstdcxx-ng: 12
+          - os: macos-latest
+            libstdcxx-ng: 13
+          - os: ubuntu-latest
+            libstdcxx-ng: null
     runs-on: ${{ matrix.os }}
-    # skip scheduled runs on main from forks
+    continue-on-error: ${{ matrix.libstdcxx-ng == 13 }} # allow (expect) this to fail
+    # skip scheduled runs from forks
     if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }}
     env: # update this if needed to match a pull request on the RMG-database
       RMG_DATABASE_BRANCH: main
@@ -51,7 +59,11 @@ jobs:
         shell: bash -l {0}
     steps:
       - uses: actions/checkout@v3
-
+      - name: Patch the environment file
+        if: ${{ matrix.libstdcxx-ng }}
+        run: |
+          echo -e "\n  - libstdcxx-ng = ${{ matrix.libstdcxx-ng }}\n" >> environment.yml
+          cat environment.yml
       # configures the mamba environment manager and builds the environment
       - name: Setup Mambaforge Python 3.7
         uses: conda-incubator/setup-miniconda@v2

.github/workflows/docs.yml

@@ -16,6 +16,10 @@ jobs:
         shell: bash -l {0}
     steps:
       - uses: actions/checkout@v2
+      - name: Patch the environment file
+        run: |
+          echo -e "\n  - libstdcxx-ng < 13\n" >> environment.yml
+          cat environment.yml
       - name: Setup Mambaforge Python 3.7
         uses: conda-incubator/setup-miniconda@v2
         with:

documentation/source/users/rmg/installation/anacondaDeveloper.rst

@@ -90,7 +90,17 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
     conda config --env --set subdir osx-64
     conda env update -f environment.yml
 
-#. Create the conda environment for RMG-Py ::
+#. Modify the environment file for Linux (eg. Ubuntu). If you are using MacOS, you should skip this step.::
+
+    echo -e "\n  - libstdcxx-ng<13\n" >> environment.yml
+
+   Details: Recently (June 2023) conda-forge have a GNU C++ library version 13,
+   which is incompatible with some of the other binaries in the environment.
+   By specifying that we want a version of the library less than 13, we ensure
+   compatibility. MacOS does not use the conda-forge g++ libraries, so this line 
+   would fail if we included it in the environment.yml file for everyone.
+
+#. Create the conda environment for RMG-Py::
 
     conda env create -f environment.yml
 

environment.yml

@@ -13,7 +13,7 @@
 #
 # Changelog:
 # - May 15, 2023 Added this changelog, added inline documentation,
-#   made depdency list more explicit (@JacksonBurns).
+#   made dependency list more explicit (@JacksonBurns).
 #
 name: rmg_env
 channels:
@@ -106,4 +106,4 @@ dependencies:
   # it here the environment creation would fail on Mac. The way it ends up working behind
   # the scenes is that conda will find a different package for Mac that provides gfortran,
   # but because we cannot specify per-platform requirements in this file we simply leave
-  # it out.
+  # it out.