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

Author: JacksonBurns

.github/workflows/CI.yml

@@ -112,8 +112,6 @@ jobs:
         uses: actions/checkout@v3
 
       # configures the mamba environment manager and builds the environment
-      - name: Patch Environment File
-        run: sed -i 's/  - conda-forge::julia>=1.8.5,!=1.9.0/  - conda-forge::julia=1.9.1/' environment.yml
       - name: Setup Mambaforge Python 3.7
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -124,6 +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

@@ -14,6 +14,7 @@
 # Changelog:
 # - May 15, 2023 Added this changelog, added inline documentation,
 #   made dependency list more explicit (@JacksonBurns).
+# - Mar 11, 2024 Removed Julia dependencies, now considered optional
 #
 name: rmg_env
 channels:
@@ -45,10 +46,6 @@ dependencies:
   - conda-forge::cclib >=1.6.3,!=1.8.0
   - conda-forge::openbabel >= 3
 
-# general-purpose external software tools
-  - conda-forge::julia=1.9.1
-  - conda-forge::pyjulia >=0.6
-
 # Python tools
   - python >=3.7
   - coverage
@@ -85,16 +82,9 @@ 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
-
   - rmg::chemprop
   # Our build of this is version 0.0.1 (!!) and we are using parts
   # of the API that are now gone. Need a serious PR to fix this.
@@ -106,6 +96,19 @@ dependencies:
 # 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