Avoid Unnecessary Julia Operations + Optional RMS Installation

.github/workflows/CI.yml

@@ -122,6 +122,12 @@ jobs:
           activate-environment: rmg_env
           use-mamba: true
 
+      # installs the extra RMS conda dependencies
+      - name: Add RMS dependencies
+        run: |
+          mamba install -c conda-forge julia=1.9.1 pyjulia>=0.6 
+          mamba install -c rmg pyrms diffeqpy
+
       # list the environment for debugging purposes
       - name: mamba info
         run: |

.github/workflows/docs.yml

@@ -36,6 +36,12 @@ jobs:
           activate-environment: rmg_env
           use-mamba: true
 
+      # installs the extra RMS conda dependencies
+      - name: Add RMS dependencies
+        run: |
+          mamba install -c conda-forge julia=1.9.1 pyjulia>=0.6 
+          mamba install -c rmg pyrms diffeqpy
+
       - name: Install sphinx
         run: mamba install -y sphinx
 

Dockerfile

@@ -28,10 +28,6 @@ RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh &
     rm Miniconda3-latest-Linux-x86_64.sh
 ENV PATH="$PATH:/miniconda/bin"
 
-# Set solver backend to mamba for speed
-RUN conda install -n base conda-libmamba-solver && \
-    conda config --set solver libmamba
-
 # Set Bash as the default shell for following commands
 SHELL ["/bin/bash", "-c"]
 
@@ -44,8 +40,7 @@ RUN git clone --single-branch --branch main --depth 1 https://github.com/Reactio
 
 WORKDIR /rmg/RMG-Py
 # build the conda environment
-RUN conda env create --file environment.yml && \
-    conda clean --all --yes
+RUN conda env create --file environment.yml
 
 # This runs all subsequent commands inside the rmg_env conda environment
 #
@@ -54,6 +49,10 @@ RUN conda env create --file environment.yml && \
 # in a Dockerfile build script)
 SHELL ["conda", "run", "--no-capture-output", "-n", "rmg_env", "/bin/bash", "-c"]
 
+RUN conda install -c conda-forge julia=1.9.1 pyjulia>=0.6 && \
+    conda install -c rmg pyrms diffeqpy && \
+    conda clean --all --yes
+
 # Set environment variables as directed in the RMG installation instructions
 ENV RUNNER_CWD=/rmg
 ENV PYTHONPATH="$RUNNER_CWD/RMG-Py:$PYTHONPATH"

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

@@ -25,6 +25,11 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
 
       Note that you should reinitialize or restart your terminal in order for the changes to take effect, as the installer will tell you.
 
+#. If your `conda` version is older than 23.10.0, switch the solver backend to `libmamba` ::
+
+    conda install -n base conda-libmamba-solver
+    conda config --set solver libmamba
+
 #. There are a few system-level dependencies which are required and should not be installed via Conda. These include
    `Git <https://git-scm.com/>`_ for version control, `GNU Make <https://www.gnu.org/software/make/>`_, and the C and C++ compilers from the `GNU Compiler Collection (GCC) <https://gcc.gnu.org/>`_ for compiling RMG.
 
@@ -71,11 +76,6 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
 
    For information on using ``ssh`` with GitHub see the `Connecting to GitHub with SSH <https://docs.github.com/en/authentication/connecting-to-github-with-ssh>`_
 
-#. Switch the conda solver backend to speed up creation of the RMG environment ::
-
-    conda install -n base conda-libmamba-solver
-    conda config --set solver libmamba
-
 #. Navigate to the RMG-Py directory ::
 
     cd RMG-Py
@@ -110,16 +110,11 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
 
     conda activate rmg_env
 
-#. Switch the conda solver to libmamba again, to accelerate any changes you might make to this conda environment in the future::
-
-    conda config --set solver libmamba
-
 #. Compile RMG-Py after activating the conda environment ::
 
     make
 
 #. Modify environment variables. Add RMG-Py to the PYTHONPATH to ensure that you can access RMG modules from any folder.
-   *This is important before the next step in which julia dependencies are installed.*
    Also, add your RMG-Py folder to PATH to launch ``rmg.py`` from any folder.
 
    In general, these commands should be placed in the appropriate shell initialization file.
@@ -134,16 +129,21 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
 
    Be sure to either close and reopen your terminal to refresh your environment variables (``source ~/.bashrc`` or ``source ~/.zshrc``).
 
-#. Install and Link Julia dependencies: ::
+#. **Optional (Recommended)**: Install and Link Julia dependencies. Ensure that you have modified your environment variables as described above, and then run the following: ::
 
      julia -e 'using Pkg; Pkg.add("PyCall");Pkg.build("PyCall");Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator;'
 
      python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
 
+    Installing these dependencies will allow using ``method='ode'`` when solving the Master Equation with Arkane and using ``ReactionMechanismSimulator.jl``-based reactors in RMG.
 
 #. 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-jl rmg.py input.py
+
+    or, if the Julia dependencies are not installed: ::
+
+     python 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.
 

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
+# - Mar 11, 2024 Removed Julia dependencies, now considered optional
 #
 name: rmg_env
 channels:
@@ -48,10 +49,6 @@ dependencies:
   - conda-forge::openbabel >= 3
   - conda-forge::rdkit >=2022.09.1
 
-# general-purpose external software tools
-  - conda-forge::julia=1.9.1
-  - conda-forge::pyjulia >=0.6
-
 # Python tools
   - python >=3.7
   - coverage
@@ -88,21 +85,24 @@ dependencies:
 # packages we maintain
   - rmg::pydas >=1.0.3
   - rmg::pydqed >=1.0.3
-  - 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
 
+# optional dependencies for using ReactionMechanismSimulator
+# remove the leading '#' to install the required dependencies
+  # - conda-forge::julia=1.9.1
+  # - conda-forge::pyjulia >=0.6
+  # - rmg::pyrms
+  # - rmg::diffeqpy
+
+# Note about 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
+
 # additional packages that are required, but not specified here (and why)
   # pydqed, pydas, mopac, and likely others require a fortran compiler (specifically gfortran)
   # in the environment. Normally we would add this to the environment file with

rmgpy/pdep/sls.py

@@ -32,9 +32,8 @@
 and implementing the SLS master equation reduction method
 """
 import sys
+import logging
 
-from diffeqpy import de
-from julia import Main
 import scipy.sparse as sparse
 import numpy as np
 import scipy.linalg
@@ -46,6 +45,17 @@
 from rmgpy.pdep.me import generate_full_me_matrix, states_to_configurations
 from rmgpy.statmech.translation import IdealGasTranslation
 
+NO_JULIA = False
+try:
+    from diffeqpy import de
+    from julia import Main
+except Exception as e:
+    logging.info(
+        f"Unable to import Julia dependencies, original error: {str(e)}"
+        ". Master equation method 'ode' will not be available on this execution."
+    )
+    NO_JULIA = True
+
 
 def get_initial_condition(network, x0, indices):
     """
@@ -150,6 +160,11 @@ def get_rate_coefficients_SLS(network, T, P, method="mexp", neglect_high_energy_
     tau = np.abs(1.0 / fastest_reaction)
 
     if method == "ode":
+        if NO_JULIA:
+            raise RuntimeError(
+                "Required Julia dependencies for method 'ode' are not installed.\n"
+                "Please follow the steps to install Julia dependencies at https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/anacondaDeveloper.html."
+            )
         f = Main.eval(
             """
 function f(u,M,t)

rmgpy/rmg/input.py

@@ -48,9 +48,10 @@
 from rmgpy.solver.surface import SurfaceReactor
 from rmgpy.util import as_list
 from rmgpy.data.surface import MetalDatabase
-from rmgpy.rmg.reactors import Reactor, ConstantVIdealGasReactor, ConstantTLiquidSurfaceReactor, ConstantTVLiquidReactor, ConstantTPIdealGasReactor
 from rmgpy.data.vaporLiquidMassTransfer import liquidVolumetricMassTransferCoefficientPowerLaw
 from rmgpy.molecule.fragment import Fragment
+from rmgpy.rmg.reactionmechanismsimulator_reactors import Reactor, ConstantVIdealGasReactor, ConstantTLiquidSurfaceReactor, ConstantTVLiquidReactor, ConstantTPIdealGasReactor, NO_JULIA
+
 
 ################################################################################
 
@@ -1558,6 +1559,11 @@ def read_input_file(path, rmg0):
         exec(f.read(), global_context, local_context)
     except (NameError, TypeError, SyntaxError) as e:
         logging.error('The input file "{0}" was invalid:'.format(full_path))
+        if NO_JULIA:
+            logging.error(
+                "During runtime, import of Julia dependencies failed. To use phase systems and RMS reactors, install RMG-Py with RMS."
+                " (https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/anacondaDeveloper.html)"
+            )
         logging.exception(e)
         raise
     finally: