misc. small fixes from debugging and review

 - hide some pointless output in a dropdown in the regression tests
 - move RMS into its own conda env to avoid Sundials breaking for Cantera
 - further limit size of surface RMS mechanism to avoid memory error
 - explicitly pass linear solver to CVODE to avoid it not being initializated
 - a typo fix
 - setuptools and cython version limtiations

Author: JacksonBurns

.github/workflows/CI.yml

@@ -48,6 +48,8 @@ env:
   # if running on RMG-Py but requiring changes on an un-merged branch of RMG-database, replace
   # main with the name of the branch
   RMG_DATABASE_BRANCH: main
+  # julia parallel pre-compilation leads to race conditions and hangs, so we limit it to run in serial
+  JULIA_NUM_PRECOMPILE_TASKS: 1
 
 jobs:
   build-and-test:
@@ -102,7 +104,7 @@ jobs:
         if: matrix.include-rms == 'with RMS'
         uses: julia-actions/install-juliaup@v2
         with:
-          channel: '1.9'
+          channel: '1.10'
 
       - name: Set some env vars
         if: matrix.include-rms == 'with RMS'
@@ -173,25 +175,33 @@ jobs:
 
       # RMG build step
       - run: make install
+      
+      - name: Make separate RMS conda env
+        run: |
+          conda create --name rmg_env_with_rms --clone rmg_env
 
       - name: Setup Juliaup
         uses: julia-actions/install-juliaup@v2
         with:
-          channel: '1.9'
+          channel: '1.10'
 
       - name: Set some env vars
         run: |
+          conda activate rmg_env_with_rms
           # https://juliapy.github.io/PythonCall.jl/stable/pythoncall/#If-you-already-have-Python-and-required-Python-packages-installed
           echo "JULIA_CONDAPKG_BACKEND=Null" >> $GITHUB_ENV
           echo "JULIA_PYTHONCALL_EXE=$CONDA_PREFIX/bin/python" >> $GITHUB_ENV
 
       # RMS installation and linking to Julia
       - name: Install and link Julia dependencies
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
-        run: . install_rms.sh
+        run: |
+          conda activate rmg_env_with_rms
+          . install_rms.sh
 
       - name: Set some other env vars
         run: |
+          conda activate rmg_env_with_rms
           # ensure that juliacall in Python uses the correct julia executable and packages: https://github.com/JuliaPy/PyJuliaPkg?tab=readme-ov-file#which-julia-gets-used
           echo "PYTHON_JULIAPKG_EXE=$(which julia)" >> $GITHUB_ENV
           echo "PYTHON_JULIAPKG_PROJECT=$HOME/.julia/packages" >> $GITHUB_ENV
@@ -202,8 +212,8 @@ jobs:
       # Regression Testing - Test Execution
       - name: Regression Tests - Execution
         id: regression-execution
-        timeout-minutes: 60
         run: |
+          conda activate rmg_env_with_rms
           for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation RMS_liquidSurface_ch4o2cat fragment RMS_constantVIdealGasReactor_fragment minimal_surface;
           do
             if python rmg.py test/regression/"$regr_test"/input.py; then
@@ -278,7 +288,11 @@ jobs:
         env:
           REFERENCE: stable_regression_results
         run: |
+          # we _do not_ run in the with_rms env here
+          # conda activate rmg_env_with_rms
+          
           exec 2> >(tee -a regression.stderr >&2) 1> >(tee -a regression.stdout)
+          touch checkModels.log
           mkdir -p "test/regression-diff"
           for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation fragment RMS_constantVIdealGasReactor_fragment minimal_surface;
           do
@@ -301,7 +315,7 @@ jobs:
                 $REFERENCE/"$regr_test"/chemkin/chem_annotated.inp \
                 $REFERENCE/"$regr_test"/chemkin/species_dictionary.txt \
                 test/regression/"$regr_test"/chemkin/chem_annotated.inp \
-                test/regression/"$regr_test"/chemkin/species_dictionary.txt
+                test/regression/"$regr_test"/chemkin/species_dictionary.txt &> checkModels.log
             then
               echo "<summary>$regr_test Passed Core Comparison ✅</summary>"
             else
@@ -318,7 +332,7 @@ jobs:
                 $REFERENCE/"$regr_test"/chemkin/chem_edge_annotated.inp \
                 $REFERENCE/"$regr_test"/chemkin/species_edge_dictionary.txt \
                 test/regression/"$regr_test"/chemkin/chem_edge_annotated.inp \
-                test/regression/"$regr_test"/chemkin/species_edge_dictionary.txt
+                test/regression/"$regr_test"/chemkin/species_edge_dictionary.txt &> checkModels.log
             then
               echo "<summary>$regr_test Passed Edge Comparison ✅</summary>"
             else
@@ -337,7 +351,7 @@ jobs:
               if python rmgpy/tools/regression.py \
                 test/regression/"$regr_test"/regression_input.py \
                 $REFERENCE/"$regr_test"/chemkin \
-                test/regression/"$regr_test"/chemkin
+                test/regression/"$regr_test"/chemkin &> checkModels.log
               then
                 echo "<summary>$regr_test Passed Observable Testing ✅</summary>"
               else
@@ -366,6 +380,11 @@ jobs:
           cat regression.stdout >> summary.txt
           echo "</details>" >> summary.txt
           echo "" >> summary.txt
+          echo "<details>" >> summary.txt
+          echo "<summary>Debugging info for `checkModels.py` (if any).</summary>" >> summary.txt
+          cat checkModels.log >> summary.txt
+          echo "</details>" >> summary.txt
+          echo "" >> summary.txt
           echo "_beep boop this comment was written by a bot_ :robot:" >> summary.txt
           cat summary.txt > $GITHUB_STEP_SUMMARY
 

environment.yml

@@ -20,7 +20,7 @@
 # - 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
-# - Mar 11, 2024 Removed Julia dependencies, now considered optional
+# - April 14, 2025 Removed Julia dependencies, now considered optional
 #
 name: rmg_env
 channels:
@@ -58,8 +58,9 @@ dependencies:
 
 # Python tools
   - conda-forge::python >=3.9  # leave as GEQ so that GitHub actions can add EQ w/o breaking (contradictory deps)
+  - conda-forge::setuptools <80
   - conda-forge::coverage
-  - conda-forge::cython >=0.25.2
+  - conda-forge::cython >=0.25.2,<3.1
   - conda-forge::scikit-learn
   - conda-forge::scipy >=1.9
   - conda-forge::numpy >=1.10.0,<2

examples/arkane/networks/acetyl+O2_sls/input.py

@@ -2,7 +2,7 @@
 #
 #   Arkane input file for acetyl + O2 pressure-dependent reaction network
 #
-#  uses method = 'simulation least squares eigen' for PressureDependence
+#  uses method = 'simulation least squares' for PressureDependence
 #
 ################################################################################
 

install_rms.sh

@@ -5,10 +5,11 @@
 # Note that you will have to manually install juliaup before running this script:
 # curl -fsSL https://install.julialang.org | sh
 # # restart shell
-# juliaup add 1.9
-# juliaup default 1.9
+# juliaup add 1.10
+# juliaup default 1.10
 # juliaup remove release
 
+#!/bin/bash
 
 conda install -y conda-forge::pyjuliacall
 

rmgpy/molecule/group.py

@@ -47,7 +47,7 @@
 from rmgpy.molecule.fragment import CuttingLabel
 
 # helper functions
-# these were originall nested inside the indicated parent function, but when we upgraded to
+# these were originally nested inside the indicated parent function, but when we upgraded to
 # Cython 3 this was no longer allowed - thus, they now live here.
 
 # add_implicit_benzene

rmgpy/rmg/reactionmechanismsimulator_reactors.py

@@ -472,7 +472,7 @@ def simulate(self, model_settings, simulator_settings, conditions):
             model_settings.tol_rxn_to_core_deadend_radical,
             atol=simulator_settings.atol,
             rtol=simulator_settings.rtol,
-            solver=Main.Sundials.CVODE_BDF(),
+            solver=Main.Sundials.CVODE_BDF(linear_solver=Main.Symbol("GMRES")),
         )
 
         return (

test/regression/RMS_liquidSurface_ch4o2cat/input.py

@@ -75,11 +75,11 @@
     toleranceMoveToCore=0.01,
     toleranceKeepInEdge=0.001,
     toleranceInterruptSimulation=1e8,
-    maximumEdgeSpecies=10000,
+    maximumEdgeSpecies=100,
     minCoreSizeForPrune=10,
     minSpeciesExistIterationsForPrune=2,
     maxNumObjsPerIter=3,
-    maxNumSpecies=35,
+    maxNumSpecies=10,
 )
 
 options(