Merge pull request #218 from hwpang/rmgmolecule

Fixing dependency conflicts

Author: mjohnson541

.github/workflows/documentation.yml

@@ -9,6 +9,8 @@ on:
 
 jobs:
   build:
+    permissions:
+      contents: write
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
@@ -23,7 +25,7 @@ jobs:
       - name: Install dependencies
         run: |
             julia -e 'ENV["PYTHON"]=ENV["CONDA"] * "/envs/rms_env/bin/python"; using Pkg; Pkg.add("PyCall"); Pkg.build("PyCall")'
-            julia --project=docs/ -e 'using Pkg; Pkg.add(PackageSpec(name="StochasticDiffEq",version="6.36.0")); Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate();'
+            julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate();'
       - name: Build and deploy
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token

Project.toml

@@ -1,6 +1,6 @@
 name = "ReactionMechanismSimulator"
 uuid = "c2d78dd2-25c4-5b79-bebc-be6c69dd440f"
-authors = ["Matt Johnson <mjohnson541@gmail.com>"]
+authors = ["Matt Johnson <mjohnson541@gmail.com>", "Hao-Wei Pang <hao4wei3pang2@gmail.com>"]
 version = "0.4.0"
 
 [deps]

deps/build.jl

@@ -9,7 +9,7 @@ if PyCall.pyversion.major != 3 || PyCall.pyversion.minor != 7
     end
     Conda.add("nomkl")
     Conda.add("numpy")
-    Conda.add_channel("rmg")
-    Conda.add("rmg")
+    Conda.add_channel("hwpang")
+    Conda.add("rmgmolecule")
     Pkg.build("PyCall")
 end

environment.yml

@@ -1,9 +1,11 @@
 name: rms_env
 channels:
   - defaults
+  - hwpang
   - rmg
+  - conda-forge
 dependencies:
   - rdkit
-  - rmg
+  - hwpang::rmgmolecule
   - pydot
-  - yaml
+  - matplotlib

src/ReactionMechanismSimulator.jl

@@ -14,23 +14,21 @@ module ReactionMechanismSimulator
     const falloff = PyNULL()
     const chebyshev = PyNULL()
     const solvation = PyNULL()
-    const yaml = PyNULL()
     const os = PyNULL()
     function __init__()
         copy!(Chem,pyimport_conda("rdkit.Chem","rdkit","rmg"))
         copy!(Desc,pyimport_conda("rdkit.Chem.Descriptors","rdkit","rmg"))
-        copy!(molecule,pyimport_conda("rmgpy.molecule","rmg","rmg"))
+        copy!(molecule,pyimport_conda("molecule.molecule","rmgmolecule","hwpang"))
         copy!(pydot,pyimport_conda("pydot","pydot"))
-        copy!(chemkin,pyimport_conda("rmgpy.chemkin","rmg","rmg"))
-        copy!(species,pyimport_conda("rmgpy.species","rmg","rmg"))
-        copy!(reaction,pyimport_conda("rmgpy.reaction","rmg","rmg"))
-        copy!(nasa,pyimport_conda("rmgpy.thermo.nasa","rmg","rmg"))
-        copy!(wilhoit,pyimport_conda("rmgpy.thermo.wilhoit","rmg","rmg"))
-        copy!(arrhenius,pyimport_conda("rmgpy.kinetics.arrhenius","rmg","rmg"))
-        copy!(falloff,pyimport_conda("rmgpy.kinetics.falloff","rmg","rmg"))
-        copy!(chebyshev,pyimport_conda("rmgpy.kinetics.chebyshev","rmg","rmg"))
-        copy!(solvation,pyimport_conda("rmgpy.data.solvation","rmg","rmg"))
-        copy!(yaml,pyimport_conda("yaml","yaml"))
+        copy!(chemkin,pyimport_conda("molecule.chemkin","rmgmolecule","hwpang"))
+        copy!(species,pyimport_conda("molecule.species","rmgmolecule","hwpang"))
+        copy!(reaction,pyimport_conda("molecule.reaction","rmgmolecule","hwpang"))
+        copy!(nasa,pyimport_conda("molecule.thermo.nasa","rmgmolecule","hwpang"))
+        copy!(wilhoit,pyimport_conda("molecule.thermo.wilhoit","rmgmolecule","hwpang"))
+        copy!(arrhenius,pyimport_conda("molecule.kinetics.arrhenius","rmgmolecule","hwpang"))
+        copy!(falloff,pyimport_conda("molecule.kinetics.falloff","rmgmolecule","hwpang"))
+        copy!(chebyshev,pyimport_conda("molecule.kinetics.chebyshev","rmgmolecule","hwpang"))
+        copy!(solvation,pyimport_conda("molecule.data.solvation","rmgmolecule","hwpang"))
         copy!(os,pyimport_conda("os","os"))
     end
     include("Constants.jl")

src/rmstest.jl

@@ -3,7 +3,7 @@ const Chem = PyNULL()
 const molecule = PyNULL()
 const pydot = PyNULL()
 copy!(Chem,pyimport_conda("rdkit.Chem","rdkit","rmg"))
-copy!(molecule,pyimport_conda("rmgpy.molecule","rmgpy","rmg"))
+copy!(molecule, pyimport_conda("molecule.molecule", "rmgmolecule", "hwpang"))
 copy!(pydot,pyimport_conda("pydot","pydot","rmg"))