update environment file, CI, Dockerfile to install optional Julia deps

Author: JacksonBurns

.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: |
+          conda install -c conda-forge julia=1.9.1 pyjulia>=0.6 
+          conda 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: |
+          conda install -c conda-forge julia=1.9.1 pyjulia>=0.6 
+          conda install -c rmg pyrms diffeqpy
+
       - name: Install sphinx
         run: mamba install -y sphinx
 

Dockerfile

@@ -45,6 +45,8 @@ 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 install -c conda-forge julia=1.9.1 pyjulia>=0.6 && \
+    conda install -c rmg pyrms diffeqpy && \
     conda clean --all --yes
 
 # This runs all subsequent commands inside the rmg_env conda environment

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:
   - 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
 
+# 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