Overhaul RMG-RMS Python-Julia dependencies & Add tests for many testless Arkane network algorithms

.github/workflows/CI.yml

@@ -150,9 +150,11 @@ jobs:
       # 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: |
-          python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
-          julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator'
+          juliaup status
+          export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba
+          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
       - name: Install Q2DTor
         run: echo "" | make q2dtor
@@ -169,7 +171,7 @@ jobs:
         run: |
           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-jl rmg.py test/regression/"$regr_test"/input.py; then
+            if python rmg.py test/regression/"$regr_test"/input.py; then
               echo "$regr_test" "Executed Successfully"
             else
               echo "$regr_test" "Failed to Execute" | tee -a $GITHUB_STEP_SUMMARY
@@ -258,7 +260,7 @@ jobs:
 
             echo "<details>"
             # Compare the edge and core
-            if python-jl scripts/checkModels.py \
+            if python scripts/checkModels.py \
                 "$regr_test-core" \
                 $REFERENCE/"$regr_test"/chemkin/chem_annotated.inp \
                 $REFERENCE/"$regr_test"/chemkin/species_dictionary.txt \
@@ -275,7 +277,7 @@ jobs:
             cat "$regr_test-core.log"
             echo "</details>"
             echo "<details>"
-            if python-jl scripts/checkModels.py \
+            if python scripts/checkModels.py \
                 "$regr_test-edge" \
                 $REFERENCE/"$regr_test"/chemkin/chem_edge_annotated.inp \
                 $REFERENCE/"$regr_test"/chemkin/species_edge_dictionary.txt \
@@ -296,7 +298,7 @@ jobs:
             if [ -f test/regression/"$regr_test"/regression_input.py ];
             then
               echo "<details>"
-              if python-jl rmgpy/tools/regression.py \
+              if python rmgpy/tools/regression.py \
                 test/regression/"$regr_test"/regression_input.py \
                 $REFERENCE/"$regr_test"/chemkin \
                 test/regression/"$regr_test"/chemkin

.github/workflows/docs.yml

@@ -63,8 +63,9 @@ jobs:
       - name: Install and link Julia dependencies
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
-          python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
-          julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator'
+          which julia
+          export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba
+          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
       - name: Checkout gh-pages Branch
         uses: actions/checkout@v2

.gitignore

@@ -47,7 +47,7 @@ nbproject/*
 .vscode/*
 
 # Unit test files
-.coverage
+.coverage*
 testing/*
 htmlcov/*
 
@@ -117,3 +117,4 @@ examples/**/dictionary.txt
 examples/**/reactions.py
 examples/**/RMG_libraries
 examples/**/species
+examples/**/plots

Dockerfile

@@ -13,12 +13,12 @@ RUN ln -snf /bin/bash /bin/sh
 #  - libxrender1 required by RDKit
 RUN apt-get update && \
     apt-get install -y \
-    make \
-    gcc \
-    wget \
-    git \
-    g++ \
-    libxrender1 && \
+        make \
+        gcc \
+        wget \
+        git \
+        g++ \
+        libxrender1 && \
     apt-get autoremove -y && \
     apt-get clean -y
 
@@ -64,16 +64,15 @@ ENV PATH="$RUNNER_CWD/RMG-Py:$PATH"
 # setting this env variable fixes an issue with Julia precompilation on Windows
 ENV JULIA_CPU_TARGET="x86-64,haswell,skylake,broadwell,znver1,znver2,znver3,cascadelake,icelake-client,cooperlake,generic"
 RUN make && \
-    julia -e 'using Pkg; Pkg.add(PackageSpec(name="PyCall",rev="master")); Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator' && \
-    python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
+    julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
 # RMG-Py should now be installed and ready - trigger precompilation and test run
-RUN python-jl rmg.py examples/rmg/minimal/input.py
+RUN python rmg.py examples/rmg/minimal/input.py
 # delete the results, preserve input.py
 RUN mv examples/rmg/minimal/input.py . && \
     rm -rf examples/rmg/minimal/* && \
     mv input.py examples/rmg/minimal/
 
 # when running this image, open an interactive bash terminal inside the conda environment
-RUN echo "source activate rmg_env" > ~/.bashrc
+RUN echo "source activate rmg_env" >~/.bashrc
 ENTRYPOINT ["/bin/bash", "--login"]

Makefile

@@ -59,16 +59,16 @@ decython:
 	find . -name *.pyc -exec rm -f '{}' \;
 
 test-all:
-	python-jl -m pytest
+	python -m pytest
 
 test test-unittests:
-	python-jl -m pytest -m "not functional and not database"
+	python -m pytest -m "not functional and not database"
 
 test-functional:
-	python-jl -m pytest -m "functional"
+	python -m pytest -m "functional"
 
 test-database:
-	python-jl -m pytest -m "database"
+	python -m pytest -m "database"
 
 eg0: all
 	mkdir -p testing/eg0

documentation/Makefile

@@ -3,7 +3,7 @@
 
 # You can set these variables from the command line.
 SPHINXOPTS    =
-SPHINXBUILD   = python-jl $$(which sphinx-build)
+SPHINXBUILD   = python $$(which sphinx-build)
 PAPER         =
 BUILDDIR      = build
 

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

@@ -143,7 +143,7 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
 
 #. Finally, you can run RMG from any location by typing the following (given that you have prepared the input file as ``input.py`` in the current folder). ::
 
-    python-jl replace/with/path/to/rmg.py input.py
+    python replace/with/path/to/rmg.py input.py
 
 You may now use RMG-Py, Arkane, as well as any of the :ref:`Standalone Modules <modules>` included in the RMG-Py package.
 
@@ -158,15 +158,15 @@ You might have to edit them slightly to match your exact paths. Specifically,
 you will need ``/opt/miniconda3/envs/rmg_env`` to point to where your conda environment is located.
 
 This configuration will allow you to debug the rms_constant_V example, running through
-python-jl. ::
+python. ::
 
         {
             "name": "Python: rmg.py rms_constant_V",
             "type": "python",
             "request": "launch",
             "cwd": "${workspaceFolder}/",
             "program": "rmg.py",
-            "python": "/opt/miniconda3/envs/rmg_env/bin/python-jl",
+            "python": "/opt/miniconda3/envs/rmg_env/bin/python",
             "args": [
                 "examples/rmg/rms_constant_V/input.py",
             ],
@@ -185,7 +185,7 @@ Open one of the many test files named ``*Test.py`` in ``test/rmgpy`` before you
             "type": "python",
             "request": "launch",
             "program": "/opt/miniconda3/envs/rmg_env/bin/pytest",
-            "python": "/opt/miniconda3/envs/rmg_env/bin/python-jl",
+            "python": "/opt/miniconda3/envs/rmg_env/bin/python",
             "args": [
                 "--capture=no",
                 "--verbose",
@@ -205,7 +205,7 @@ This configuration will allow you to debug running all the database tests.::
             "type": "python",
             "request": "launch",
             "program": "/opt/miniconda3/envs/rmg_env/bin/pytest",
-            "python": "/opt/miniconda3/envs/rmg_env/bin/python-jl",
+            "python": "/opt/miniconda3/envs/rmg_env/bin/python",
             "args": [
                 "--capture=no",
                 "--verbose",
@@ -226,7 +226,7 @@ This configuration will allow you to use the debugger breakpoints inside unit te
             "request": "launch",
             "program": "${file}",
             "purpose": ["debug-test"],
-            "python": "/opt/miniconda3/envs/rmg_env/bin/python-jl",
+            "python": "/opt/miniconda3/envs/rmg_env/bin/python",
             "console": "integratedTerminal",
             "justMyCode": false,
             "env": {"PYTEST_ADDOPTS": "--no-cov",} // without disabling coverage VS Code doesn't stop at breakpoints while debugging because pytest-cov is using the same technique to access the source code being run
@@ -274,7 +274,7 @@ To configure the rest of the settings, find the ``settings.json`` file in your `
 You can use the following settings to configure the pytest framework::
 
     "python.testing.pytestEnabled": true,
-    "python.testing.pytestPath": "python-jl -m pytest",
+    "python.testing.pytestPath": "python -m pytest",
     "python.testing.pytestArgs": [
         "-p", "julia.pytestplugin",
         "--julia-compiled-modules=no",

documentation/source/users/rmg/running.rst

@@ -10,7 +10,7 @@ Running a basic RMG job is straightforward, as shown in the example below. Howev
 
 Basic run::
 
-	python-jl rmg.py input.py
+	python rmg.py input.py
 
 .. _inputflags:
 
@@ -19,7 +19,7 @@ Input flags
 
 The options for input flags can be found in ``/RMG-Py/rmgpy/util.py``. Running ::
 
- 	python-jl rmg.py -h
+ 	python rmg.py -h
 
 at the command line will print the documentation from ``util.py``, which is reproduced below for convenience::
 
@@ -63,23 +63,23 @@ Some representative example usages are shown below.
 
 Run by restarting from a seed mechanism::
 
-    python-jl rmg.py -r path/to/seed/ input.py
+    python rmg.py -r path/to/seed/ input.py
 
 Run with CPU time profiling::
 
-    python-jl rmg.py -p input.py
+    python rmg.py -p input.py
 
 Run with multiprocessing for reaction generation and QMTP::
 
-    python-jl rmg.py -n <Max number of processes allowed> input.py 
+    python rmg.py -n <Max number of processes allowed> input.py 
 
 Run with setting a limit on the maximum execution time::
 
-	python-jl rmg.py -t <DD:HH:MM:SS> input.py
+	python rmg.py -t <DD:HH:MM:SS> input.py
 
 Run with setting a limit on the maximum number of iterations::
 
-	python-jl rmg.py -i <Max number of desired iterations> input.py
+	python rmg.py -i <Max number of desired iterations> input.py
 
 
 Details on the multiprocessing implementation

environment.yml

@@ -16,7 +16,8 @@
 #   made dependency list more explicit (@JacksonBurns).
 # - October 16, 2023 Switched RDKit and descripatastorus to conda-forge,
 #   moved diffeqpy to pip and (temporarily) removed chemprop
-#
+# - May 14, 2024 Removed diffeqpy by switching to call SciMLBase and Sundials using JuliaCall
+
 name: rmg_env
 channels:
   - defaults
@@ -49,8 +50,8 @@ dependencies:
   - conda-forge::rdkit >=2022.09.1
 
 # general-purpose external software tools
-  - conda-forge::julia=1.9.1
-  - conda-forge::pyjulia >=0.6
+  - conda-forge::juliaup
+  - conda-forge::pyjuliacall # for calling julia packages
 
 # Python tools
   - python >=3.7
@@ -88,18 +89,8 @@ dependencies:
   - rmg::pydas >=1.0.3
   - rmg::pydqed >=1.0.3
   - rmg::pyrdl
-  - rmg::pyrms
   - rmg::symmetry
 
-# packages we would like to stop maintaining (and why)
-  - rmg::diffeqpy
-  # we should use the official verison https://github.com/SciML/diffeqpy),
-  # rather than ours (which is only made so that we can get it from conda)
-  # It is only on pip, so we will need to do something like:
-  # https://stackoverflow.com/a/35245610
-  # Note that _some other_ dep. in this list requires diffeqpy in its recipe
-  # which will cause it to be downloaded from the rmg conda channel
-
 # conda mutex metapackage
   - nomkl