Build a rmgmolecule Subpackage in Place, fix rmg conda recipe, initial SimulatorInterface Efforts

.conda/build.sh

@@ -1,6 +1,15 @@
-# Install RMG
+# conda build script
+#
+# conda executes this script during the build process to make the rmg
+# binary
 make install
 
-# lazy "install" of everything in our 'external' folder.
-# most of which should probably be elsewhere
-cp -R ${SRC_DIR}/external ${SP_DIR}
+# The below code does not work because the Julia programming langauge is a very interesting technical demo that is completely unfit for actual
+# deployment in any real world projects.
+# 
+# RMG will be shipped as a pure python package, and then RMS installed by the user.
+#
+# export PYTHON=$PREFIX/bin/python
+# export PYTHONPATH=$SRC_DIR:$PYTHONPATH
+# python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
+# julia -e 'using Pkg; Pkg.add(PackageSpec(name="Functors",version="0.4.3")); Pkg.pin("Functors"); Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="for_rmg")); using ReactionMechanismSimulator'

.conda/conda_build_config.yaml

@@ -3,6 +3,3 @@ python:
 numpy:
   - 1.15
 
-# Specifically for Travis build. Should change if building locally.
-CONDA_BUILD_SYSROOT:
-  - /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk # [osx] 

.conda/meta.yaml

@@ -11,77 +11,170 @@ build:
 
 requirements:
   build:
-    - {{ compiler('c') }} # [unix]
+    - {{ compiler('c') }}
   host:
+    - cairo
+    - cairocffi
+    - ffmpeg
+    - xlrd
+    - xlwt
+    - h5py
+    - graphviz
+    - markupsafe
+    - psutil
+    - ncurses
+    - suitesparse
+
+  # external software tools for chemistry
+    - coolprop
+    - cantera=2.6
+    - mopac
+    - cclib >=1.6.3,!=1.8.0
+    - openbabel >=3
+
+  # Python tools
+    - python >=3.7
+    - coverage
     - cython >=0.25.2
+    - scikit-learn
+    - scipy
+    - numpy >=1.10.0
+    - pydot
+    - jinja2
+    - jupyter
+    - pymongo
+    - pyparsing
+    - pyyaml
+    - networkx
+    - matplotlib >=1.5
+    - mpmath
+    - pandas
+
+  # packages we maintain
+    - rmgdatabase
+    - gprof2dot
     - lpsolve55
-    - numpy
-    - openbabel >=3
-    - pydas >=1.0.2
-    - pydqed >=1.0.1
+    - muq2
+    - numdifftools
+    - pydas >=1.0.3
+    - pydqed >=1.0.3
     - pyrdl
-    - python
     - quantities
-    - rdkit >=2018
-    - scipy
-    - setuptools
+    - symmetry
+    - chemprop==0.0.1
+    - rdkit >=2020.03.3.0
   run:
     - cairo
     - cairocffi
-    - cantera >=2.3.0
-    - cclib >=1.6.3
-    - chemprop
+    - ffmpeg
+    - xlrd
+    - xlwt
+    - h5py
+    - graphviz
+    - markupsafe
+    - psutil
+    - ncurses
+    - suitesparse
+
+  # external software tools for chemistry
     - coolprop
+    - cantera=2.6
+    - mopac
+    - cclib >=1.6.3,!=1.8.0
+    - openbabel >=3
+
+  # Python tools
+    - python >=3.7
     - coverage
     - cython >=0.25.2
-    - ffmpeg
-    - gprof2dot
-    - graphviz
-    - h5py
+    - scikit-learn
+    - scipy
+    - numpy >=1.10.0
+    - pydot
     - jinja2
     - jupyter
-    - lpsolve55
-    - markupsafe
+    - pymongo
+    - pyparsing
+    - pyyaml
+    - networkx
     - matplotlib >=1.5
-    - mopac
     - mpmath
+    - pandas
+
+  # packages we maintain
+    - rmgdatabase
+    - gprof2dot
+    - lpsolve55
     - muq2
-    - networkx
-    - nose
     - numdifftools
-    - {{ pin_compatible('numpy') }}
-    - openbabel >=3
-    - pandas
+    - pydas >=1.0.3
+    - pydqed >=1.0.3
+    - pyrdl
+    - quantities
+    - symmetry
+    - chemprop==0.0.1
+    - rdkit >=2020.03.3.0
+test:
+  requires:
+    - cairo
+    - cairocffi
+    - ffmpeg
+    - xlrd
+    - xlwt
+    - h5py
+    - graphviz
+    - markupsafe
     - psutil
-    - pydas >=1.0.2
+    - ncurses
+    - suitesparse
+
+  # external software tools for chemistry
+    - coolprop
+    - cantera=2.6
+    - mopac
+    - cclib >=1.6.3,!=1.8.0
+    - openbabel >=3
+
+  # Python tools
+    - python >=3.7
+    - coverage
+    - cython >=0.25.2
+    - scikit-learn
+    - scipy
+    - numpy >=1.10.0
     - pydot
-    - pydqed >=1.0.1
+    - jinja2
+    - jupyter
     - pymongo
     - pyparsing
-    - pyrdl
-    - python
     - pyyaml
-    - pyzmq
+    - networkx
+    - matplotlib >=1.5
+    - mpmath
+    - pandas
+
+  # packages we maintain
+    - rmgdatabase
+    - gprof2dot
+    - lpsolve55
+    - muq2
+    - numdifftools
+    - pydas >=1.0.3
+    - pydqed >=1.0.3
+    - pyrdl
     - quantities
-    - rdkit >=2018
-    - rmgdatabase >=3.2.0
-    - scikit-learn
-    - scipy
     - symmetry
-    - xlrd
-    - xlwt
-test:
+    - chemprop==0.0.1
+    - rdkit >=2020.03.3.0
   source_files:
     - 'examples/rmg/superminimal'
     - 'examples/arkane/networks/n-butanol'
   imports:
     - rmgpy
     - arkane
   commands:
-    - rmg.py examples/rmg/superminimal/input.py # [unix]
-    - Arkane.py examples/arkane/networks/n-butanol/input.py # [unix]
-    - python %SCRIPTS%\rmg.py examples\rmg\superminimal\input.py # [win]
-    - python %SCRIPTS\Arkane.py examples\arkane\networks\n-butanol\input.py # [win]
+    - rmg.py examples/rmg/superminimal/input.py
+    - Arkane.py examples/arkane/networks/n-butanol/input.py
 
 about:
   home: https://github.com/ReactionMechanismGenerator/RMG-Py

.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 --override-channels julia>=1.8.5,!=1.9.0 pyjulia>=0.6 
+          conda install -c rmg --override-channels numdifftools pyrms diffeqpy
+
       # list the environment for debugging purposes
       - name: mamba info
         run: |

.github/workflows/docs.yml

@@ -31,11 +31,6 @@ jobs:
         run: |
           mamba info
           mamba list
-      - name: Install and link Julia dependencies 
-        run: |
-          julia -e "using Pkg; Pkg.add(PackageSpec(url=\"https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl\", rev=\"main\"))"
-          julia -e "using Pkg; Pkg.add(\"PyCall\"); Pkg.add(\"DifferentialEquations\")"
-          python -c "import julia; julia.install()"
       - name: Install and compile RMG
         run: |
           cd ..

.rmgmolecule_conda/build.sh

@@ -0,0 +1,2 @@
+# Install rmgmolecule
+python rmgmolecule_setup.py install

.rmgmolecule_conda/conda_build_config.yaml

@@ -0,0 +1,2 @@
+numpy:
+  - 1.19

.rmgmolecule_conda/meta.yaml

@@ -0,0 +1,48 @@
+# meta.yaml - package specification for rmgmolecule subpackage
+package:
+  name: rmgmolecule
+  version: 1.0.0
+
+source:
+  path: ../
+
+build:
+  number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }}
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+  host:
+    - cairo
+    - cairocffi
+    - cython >=0.25.2
+    - lpsolve55
+    - numpy
+    - openbabel >=3
+    - pydot
+    - pyrdl
+    - python==3.7
+    - quantities
+    - rdkit >=2018
+  run:
+    - cairo
+    - cairocffi
+    - cython >=0.25.2
+    - lpsolve55
+    - numpy
+    - openbabel >=3
+    - pydot
+    - pyrdl
+    - python==3.7
+    - quantities
+    - rdkit >=2018
+test:
+  imports:
+    - rmgpy.molecule
+  commands:
+    - python -c 'from rmgpy.molecule import Molecule; mol=Molecule().from_smiles("CC")'
+
+about:
+  home: https://github.com/ReactionMechanismGenerator/RMG-Py
+  license: MIT
+  summary: "The ReactionMechanismGenerator Molecule Subpackage"

Dockerfile

@@ -45,6 +45,8 @@ RUN git clone --single-branch --branch main --depth 1 https://github.com/Reactio
 # build the conda environment
 WORKDIR /rmg/RMG-Py
 RUN conda env create --file environment.yml && \
+    conda install -c conda-forge julia>=1.8.5,!=1.9.0 pyjulia>=0.6 && \
+    conda install -c rmg numdifftools pyrms diffeqpy && \
     conda clean --all --yes
 
 # This runs all subsequent commands inside the rmg_env conda environment

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