Fix Python 3.9 julia Overhaul

.github/workflows/CI.yml

@@ -73,7 +73,9 @@ jobs:
 
       - name: Compel Arm-based Mac to use x86
         if: matrix.os == 'macos-latest'
-        run: echo "CONDA_SUBDIR=osx-64" >> $GITHUB_ENV
+        run: |
+          echo "CONDA_SUBDIR=osx-64" >> $GITHUB_ENV
+          # softwareupdate --install-rosetta --agree-to-license   # did not help with encodings issue
 
       - name: Setup Miniforge Python ${{ matrix.python-version }}
         uses: conda-incubator/setup-miniconda@v3
@@ -83,64 +85,90 @@ jobs:
           miniforge-version: latest
           python-version: ${{ matrix.python-version }}
           activate-environment: rmg_env
-          use-mamba: true
+          auto-update-conda: true
           show-channel-urls: true
           channels: conda-forge,cantera,rmg
+          conda-remove-defaults: "true"
+
+      # - name: Continue to Coerce Arm-Mac  # pure python mode works without this, so it isn't required
+      #   if: matrix.os == 'macos-latest'
+      #   run: |
+      #     conda config --env --set subdir osx-64
 
       # list the environment for debugging purposes
-      - name: mamba info
+      - name: conda info
         run: |
-          mamba info
-          mamba list
+          conda info
+          conda 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" >> $GITHUB_PATH
+      # # modify env variables as directed in the RMG installation instructions
+      # - name: Set Environment Variables
+      #   run: |
+      #     RUNNER_CWD=$(pwd)
+      #     echo "$RUNNER_CWD/RMG-Py" >> $GITHUB_PATH  # I don't think this actually accomplishes anything
 
       # RMG build step
       - name: make RMG
         run: |
-          make clean
-          make
+          make install
 
-      # Setup Juliaup
-      - name: Set Julia paths
+      - name: PRE-JULIA ENVIRONMENT
         run: |
-          # echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
-          # echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
-          # echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
-          # echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
-          # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
-          # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH
-          # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
-          # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH
-          echo "JULIA_CONDAPKG_BACKEND=Current" >> $GITHUB_ENV
-          # echo "JULIA_CONDAPKG_BACKEND=Current" >> $GITHUB_PATH
+          printenv | sort
+          conda list
 
       - name: Setup Juliaup
         uses: julia-actions/install-juliaup@v2
         with:
           channel: '1.9'
 
-      - name: Check Julia version
-        run: julia --version
+      - name: POST JULIAUP
+        run: |
+          printenv | sort
+          conda list
+
+      # - name: Try and Make Julia stop ruining the Compilers
+      #   run: |
+      #     echo "LD_LIBRARY_PATH=$CONDA_PREFIX/lib" >> $GITHUB_ENV
+
+      # - name: POST LIBRARY PATH UPDATE
+      #   run: |
+      #     printenv | sort
+      #     conda list
+
+      - name: Set some env vars
+        run: |
+          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).
-        # JULIA_CONDAPKG_EXE points to the existing conda/mamba to avoid JuliaCall from installing their own. See https://juliapy.github.io/PythonCall.jl/stable/pythoncall/#If-you-already-have-a-Conda-environment.
+        run: . install_rms.sh
+
+      - name: Where is RMS?
+        run: julia -E "using ReactionMechanismSimulator; pathof(ReactionMechanismSimulator)"
+
+      - name: Set some other env vars
         run: |
-          mamba install conda-forge::pyjuliacall
-          julia -e 'using Pkg; Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
+          echo "PYTHON_JULIAPKG_EXE=$(which julia)" >> $GITHUB_ENV
+          echo "PYTHON_JULIAPKG_PROJECT=$HOME/.julia/packages" >> $GITHUB_ENV
+
+      - name: POST-JULIA ENVIRONMENT
+        run: |
+          printenv | sort
+          conda list
+
+      # - name: Rebuild RMG
+      #   run: |
+      #     make clean
+      #     make
 
       - name: Install Q2DTor
         run: echo "" | make q2dtor
@@ -322,14 +350,14 @@ jobs:
 
       - name: Upload regression summary artifact
        # the annotate workflow uses this artifact to add a comment to the PR
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if : ${{ github.event_name == 'pull_request' }}
         with:
           name: regression_summary
           path: summary.txt
 
       - name: Upload Comparison Results
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: regression_test_comparison_results
           path: |
@@ -339,7 +367,7 @@ jobs:
       - name: Code coverage install and run
         if: success() || ( failure() && steps.regression-execution.conclusion == 'success' )
         run: |
-          mamba install -y -c conda-forge codecov
+          conda install -y -c conda-forge codecov
           codecov
 
   build-and-push-docker:

.github/workflows/pure_python_ci.yml

@@ -55,29 +55,23 @@ jobs:
           miniforge-version: latest
           python-version: ${{ matrix.python-version }}
           activate-environment: rmg_env
-          use-mamba: true
+          auto-update-conda: true
           show-channel-urls: true
           channels: conda-forge,cantera,rmg
+          conda-remove-defaults: "true"
 
       # list the environment for debugging purposes
-      - name: mamba info
+      - name: conda info
         run: |
-          mamba info
-          mamba list
+          conda info
+          conda 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: |

.gitignore

@@ -4,13 +4,18 @@
 #
 ################################################################################
 
+# build dir
+reactionmechanismgenerator.egg-info/
+
 # MacOS files
 .DS_Store
 
 # Compiled Python modules
 *.pyc
 *.so
 *.pyd
+# and intermediate source files
+*.c
 
 # Image files generated by RMG
 *.png

Makefile

@@ -7,28 +7,14 @@
 CC=gcc
 CXX=g++
 
-.PHONY : all minimal main solver check pycheck arkane clean install decython documentation test q2dtor
+.PHONY : all check clean install decython documentation test q2dtor
 
-all: pycheck main solver check
-
-minimal:
-	python setup.py build_ext minimal --inplace --build-temp .
-
-main:
-	python setup.py build_ext main --inplace --build-temp .
-
-solver:
-	@ python utilities.py check-pydas
-	python setup.py build_ext solver --inplace --build-temp .
-
-arkane:
-	python setup.py build_ext arkane --inplace --build-temp .
+all: check install check
 
 check:
 	@ python utilities.py check-dependencies
-
-pycheck:
 	@ python utilities.py check-python
+	@ python utilities.py check-pydas
 
 documentation:
 	$(MAKE) -C documentation html
@@ -42,7 +28,7 @@ clean-solver:
 
 install:
 	@ python utilities.py check-pydas
-	python setup.py install
+	python -m pip install -vv --no-cache-dir -e .
 
 q2dtor:
 	@ echo -e "\nInstalling Q2DTor...\n"

arkane/encorr/data.py

@@ -54,6 +54,8 @@
 from arkane.exceptions import BondAdditivityCorrectionError
 from arkane.modelchem import LevelOfTheory, CompositeLevelOfTheory
 
+pybel.ob.obErrorLog.SetOutputLevel(0)
+
 # ######## Database loading ##########
 quantum_corrections_path = os.path.join(settings['database.directory'], 'quantum_corrections', 'data.py')
 spec = importlib.util.spec_from_file_location("quantum_calculations", quantum_corrections_path)

install_rms.sh

@@ -0,0 +1,24 @@
+# manual installation steps
+# start by installing juliaup on your system globally
+# curl -fsSL https://install.julialang.org | sh
+# # restart shell
+# juliaup add 1.9
+# juliaup default 1.9
+# juliaup remove release
+
+# actual steps
+conda install -y conda-forge::pyjuliacall  # conda-forge::pyside2
+# export JULIA_CONDAPKG_BACKEND=Current
+# export JULIA_CONDAPKG_EXE=$CONDA_EXE
+# export JULIA_PYTHONCALL_EXE=$CONDA_PREFIX/bin/python
+
+# https://juliapy.github.io/PythonCall.jl/stable/pythoncall/#If-you-already-have-Python-and-required-Python-packages-installed
+export JULIA_CONDAPKG_BACKEND=Null
+export JULIA_PYTHONCALL_EXE=$CONDA_PREFIX/bin/python
+# export MPLBACKEND=tkagg  # supported backend for PythonPlot.jl, needed by RMS
+
+julia -e 'using Pkg; Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator; Pkg.instantiate()' | echo "RMS install error - continuing anyway ¯\_(ツ)_/¯"
+
+# ensure that juliacall in Python uses the correct julia executable and packages: https://github.com/JuliaPy/PyJuliaPkg?tab=readme-ov-file#which-julia-gets-used
+export PYTHON_JULIAPKG_EXE=$(which julia)
+export PYTHON_JULIAPKG_PROJECT=$HOME/.julia/packages

rmgpy/rmg/reactionmechanismsimulator_reactors.py

@@ -32,40 +32,20 @@
 """
 import itertools
 import logging
-import sys
 
 import numpy as np
 
-import rmgpy.constants as constants
-
-NO_JULIA = True
-try:
-    import juliacall
-    from juliacall import Main
-    Main.seval("using PythonCall")
-    Main.seval("using ReactionMechanismSimulator")
-    Main.seval("using ReactionMechanismSimulator.Sundials")
-    NO_JULIA = False
-except:
-    logging.warning("Julia import failed, RMS reactors not available.")
-
-from rmgpy import constants
-from rmgpy.data.kinetics.depository import DepositoryReaction
-from rmgpy.data.kinetics.family import TemplateReaction
 from rmgpy.data.solvation import SolventData
 from rmgpy.kinetics.arrhenius import (
     Arrhenius,
-    ArrheniusBM,
     ArrheniusChargeTransfer,
-    ArrheniusEP,
     Marcus,
     MultiArrhenius,
     MultiPDepArrhenius,
     PDepArrhenius,
 )
 from rmgpy.kinetics.chebyshev import Chebyshev
 from rmgpy.kinetics.falloff import Lindemann, ThirdBody, Troe
-from rmgpy.kinetics.kineticsdata import KineticsData
 from rmgpy.kinetics.surface import StickingCoefficient, SurfaceChargeTransfer
 from rmgpy.molecule.fragment import Fragment
 from rmgpy.reaction import Reaction
@@ -77,7 +57,17 @@
 from rmgpy.species import Species
 from rmgpy.thermo.nasa import NASA, NASAPolynomial
 from rmgpy.thermo.thermodata import ThermoData
-from rmgpy.thermo.wilhoit import Wilhoit
+
+
+NO_JULIA = True
+try:
+    from juliacall import Main
+    Main.seval("using PythonCall")
+    Main.seval("using ReactionMechanismSimulator")
+    Main.seval("using ReactionMechanismSimulator.Sundials")
+    NO_JULIA = False
+except Exception as e:
+    logging.warning(f"Julia import failed, RMS reactors not available.\nException: {str(e)}\nStacktrace:\n{e.__traceback__}")
 
 
 def to_julia(obj):
@@ -104,21 +94,6 @@ def to_julia(obj):
     else: # Other native Python project does not need special conversion.
         return obj
 
-NO_JULIA = False
-try:
-    if __debug__:
-        from os.path import abspath, dirname, exists, join
-
-        from julia.api import Julia
-        path_rms = dirname(dirname(dirname(abspath(__file__))))
-        jl = Julia(sysimage=join(path_rms, "rms.so")) if exists(join(path_rms, "rms.so")) else Julia(compiled_modules=False)
-    from diffeqpy import de
-    from julia import Main
-    from pyrms import rms
-except Exception as e:
-    logging.info("Unable to import Julia dependencies, original error: " + str(e) + ". RMS features will not be available on this execution.")
-    NO_JULIA = True
-
 
 class PhaseSystem:
     """