Stable test

.github/workflows/CI.yml

@@ -10,10 +10,10 @@ jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
-          version: 1.8
+          version: '1.10'
       - uses: actions/cache@v1
         env:
           cache-name: cache-artifacts
@@ -24,21 +24,17 @@ jobs:
             ${{ runner.os }}-test-${{ env.cache-name }}-
             ${{ runner.os }}-test-
             ${{ runner.os }}-
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          environment-file: environment.yml
-          python-version: 3.7
-          activate-environment: rms_env
-      - name: Fix PyCall linking
-        run: |
-            julia -e 'ENV["PYTHON"]=ENV["CONDA"] * "/envs/rms_env/bin/python"; using Pkg; Pkg.add("PyCall"); Pkg.build("PyCall")'
       - uses: julia-actions/julia-buildpkg@v1
       - name: Build
         run: |
-            julia -e 'using Pkg; Pkg.develop(PackageSpec(path="../ReactionMechanismSimulator.jl")); Pkg.build("ReactionMechanismSimulator");'
+            current_path=${{ github.workspace }}
+            export JULIA_CONDAPKG_ENV="$current_path/rms_env"
+            julia -e 'using Pkg; Pkg.develop(Pkg.PackageSpec(path="../ReactionMechanismSimulator.jl/")); Pkg.build("ReactionMechanismSimulator");'
       - name: Run tests
         run: |
-            julia -e 'using Pkg; Pkg.test("ReactionMechanismSimulator";coverage=true)'
+            current_path=${{ github.workspace }}
+            export JULIA_CONDAPKG_ENV="$current_path/rms_env"
+            julia -e 'using Pkg; Pkg.test("ReactionMechanismSimulator"; coverage=true)'
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v1
         with:

.github/workflows/documentation.yml

@@ -16,18 +16,17 @@ jobs:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@latest
         with:
-          version: 1.8
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          environment-file: environment.yml
-          python-version: 3.7
-          activate-environment: rms_env
+          version: '1.10'
       - 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.develop(PackageSpec(path=pwd())); Pkg.instantiate();'
+            current_path=${{ github.workspace }}
+            export JULIA_CONDAPKG_ENV="$current_path/rms_env"
+            julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.build("ReactionMechanismSimulator");'
       - name: Build and deploy
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
           DOCUMENTER_DEBUG: true
-        run: julia --color=yes --project=docs docs/make.jl
+        run: |
+          current_path=${{ github.workspace }}
+          export JULIA_CONDAPKG_ENV="$current_path/rms_env"
+          julia --color=yes --project=docs docs/make.jl

.gitignore

@@ -3,4 +3,8 @@
 *.dot
 docs/build/
 .DS_Store
-deps/build.log
+deps/build.log
+.CondaPkg/
+rms_env/
+*.cov
+Manifest.toml

CondaPkg.toml

@@ -0,0 +1 @@
+channels = ["defaults", "mjohnson541", "rmg", "conda-forge", "cantera"]

Project.toml

@@ -4,10 +4,10 @@ authors = ["Matt Johnson <[email protected]>", "Hao-Wei Pang <hao4wei3pang2@
 version = "1.0.0"
 
 [deps]
+CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 Calculus = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9"
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
-Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
-CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 FastGaussQuadrature = "442a2c76-b920-505d-bb47-c5924d526838"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
@@ -17,12 +17,13 @@ IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 LsqFit = "2fda8390-95c7-5789-9bda-21331edee243"
+MicroMamba = "0b3b1443-0f03-428d-bdfb-f27f9c1191ea"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 PreallocationTools = "d236fae5-4411-538c-8e31-a6e3d9e00b46"
-PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
-PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
+PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
+PythonPlot = "274fc56d-3b97-40fa-a1cd-1b4a50311bf9"
 QuartzImageIO = "dca85d43-d64c-5e67-8c65-017450d5d020"
 RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
@@ -39,31 +40,31 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
-Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [compat]
+CSV = "0.10"
 Calculus = "0.4,0.5"
 Colors = "0.11,0.12"
-Conda = "1"
-CSV = "0.10"
+CondaPkg = "0.2"
 DataFrames = "1"
-SciMLSensitivity = "^7"
 FastGaussQuadrature = "0.5"
 ForwardDiff = "0.10"
 Images = "0.24"
 IncompleteLU = "0.2"
 IterTools = "1.3"
 LsqFit = "0.12"
+MicroMamba = "0.1"
 ModelingToolkit = "8"
 OrdinaryDiffEq = "^6"
 Parameters = "0.12"
 PreallocationTools = "0.4"
-PyCall = "1"
-PyPlot = "2"
+PythonCall = "0.9"
+PythonPlot = "1"
 QuartzImageIO = "0.7"
 RecursiveArrayTools = "2.17"
 ReverseDiff = "1.9"
 SciMLBase = "^1"
+SciMLSensitivity = "^7"
 SmoothingSplines = "0.3"
 SpecialFunctions = "1"
 StaticArrays = "1"
@@ -72,5 +73,4 @@ Symbolics = "4"
 Tracker = "0.2"
 Unitful = "^1.3"
 YAML = "0.4"
-Zygote = "0.5,0.6"
 julia = "^1.6"

docs/src/Installation.md

@@ -37,9 +37,10 @@ The above instructions will automatically handle Julia-Python linking. However,
 
 ```
 import Pkg
-Pkg.add("PyCall")                              
-ENV["CONDA_JL_HOME"] = PATH_TO_YOUR_ENV        
-Pkg.build("Conda")                             
-ENV["PYTHON"] = PATH_TO_PYTHON                 
-Pkg.build("PyCall")                            
+ENV["JULIA_CONDAPKG_BACKEND"] = "Null"
+ENV["JULIA_PYTHONCALL_EXE"] = "/path/to/python"
+Pkg.add("CondaPkg")
+Pkg.build("CondaPkg")
+Pkg.add("PythonCall")                                    
+Pkg.build("PythonCall")
 ```

iJulia/Automatic Mechanism Analysis Example.ipynb

@@ -8,7 +8,7 @@
    "outputs": [],
    "source": [
     "using Sundials\n",
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "using ReactionMechanismSimulator"
    ]
   },

iJulia/ConstantPH2Combustion.ipynb

@@ -29,7 +29,7 @@
    "outputs": [],
    "source": [
     "using DifferentialEquations\n",
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "using ReactionMechanismSimulator"
    ]
   },

iJulia/ConstantTPH2Combustion.ipynb

@@ -9,7 +9,7 @@
     "using DiffEqBase\n",
     "using Sundials\n",
     "using DiffEqSensitivity\n",
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "using ReactionMechanismSimulator"
    ]
   },

iJulia/ConstantTVOctaneOxidation.ipynb

@@ -7,7 +7,7 @@
    "outputs": [],
    "source": [
     "using DifferentialEquations\n",
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "using ReactionMechanismSimulator"
    ]
   },

iJulia/ConstantVH2Combustion.ipynb

@@ -7,7 +7,7 @@
    "outputs": [],
    "source": [
     "using DifferentialEquations\n",
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "using ReactionMechanismSimulator"
    ]
   },

iJulia/Gas-Catalyst Interface.ipynb

@@ -7,7 +7,7 @@
    "outputs": [],
    "source": [
     "using ReactionMechanismSimulator\n",
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "using DifferentialEquations\n",
     "using Sundials"
    ]

iJulia/ParametrizedTConstantVOctaneOxidation.ipynb

@@ -7,7 +7,7 @@
    "outputs": [],
    "source": [
     "using DifferentialEquations\n",
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "using ReactionMechanismSimulator"
    ]
   },

iJulia/ParametrizedTPH2Combustion.ipynb

@@ -7,7 +7,7 @@
    "outputs": [],
    "source": [
     "using DifferentialEquations\n",
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "using ReactionMechanismSimulator"
    ]
   },

iJulia/ParametrizedVH2Combustion.ipynb

@@ -7,7 +7,7 @@
    "outputs": [],
    "source": [
     "using DifferentialEquations\n",
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "using ReactionMechanismSimulator"
    ]
   },

iJulia/Quasi-Steady State Assumptions and Isomer Lumping.ipynb

@@ -9,7 +9,7 @@
    "source": [
     "using ReactionMechanismSimulator\n",
     "using ReactionMechanismSimulator.Sundials\n",
-    "using ReactionMechanismSimulator.PyPlot"
+    "using ReactionMechanismSimulator.PythonPlot"
    ]
   },
   {

iJulia/Vapor-Liquid Two-Phase Low-Temperature Pyrolysis.ipynb

@@ -1429,7 +1429,7 @@
    "source": [
     "using ReactionMechanismSimulator\n",
     "using ReactionMechanismSimulator.Sundials\n",
-    "using ReactionMechanismSimulator.PyPlot"
+    "using ReactionMechanismSimulator.PythonPlot"
    ]
   },
   {

src/AutomaticMechanismAnalysis.jl

@@ -665,16 +665,28 @@ function getrxnanalysisstring(sim,ra;branchingcutoff=1e-2,branchfract=0.01)
             s *= "Associated key reaction path in $spname loss direction \n"
             for i = 1:length(rp.rxninds)
                 rstr = getrxnstr(sim.reactions[rp.rxninds[i]])
+                sgn = rp.spcsinds[i+1] in sim.reactions[rp.rxninds[i]].productinds
+                if sgn
+                    sn = "+"
+                else
+                    sn = "-"
+                end
                 br = round(rp.branchfracts[i],sigdigits=6)
-                s *= "$rstr at path branching of $br \n"
+                s *= "$rstr ($sn) at path branching of $br \n"
             end
         else
             s *= "Associated key reaction path in $spname production direction \n"
             revinds = reverse(rp.rxninds)
             for i = 1:length(rp.rxninds)
                 rstr = getrxnstr(sim.reactions[revinds[i]])
+                sgn = rp.spcsinds[i+1] in sim.reactions[rp.rxninds[i]].productinds
+                if sgn
+                    sn = "+"
+                else
+                    sn = "-"
+                end
                 br = round(rp.branchfracts[i],sigdigits=6)
-                s *= "$rstr at path step branching of $br \n"
+                s *= "$rstr ($sn) at path step branching of $br \n"
             end
         end
         s *= "\n"
@@ -684,7 +696,7 @@ function getrxnanalysisstring(sim,ra;branchingcutoff=1e-2,branchfract=0.01)
     for i = 1:length(ra.clusterprodlossfracts)
         if abs(ra.clusterprodlossfracts[i]) > branchfract
             cluster = ra.clusternames[i]
-            fract = abs(ra.clusterprodlossfracts[i])
+            fract = round(abs(ra.clusterprodlossfracts[i]),sigdigits=6)
             if ra.clusterprodlossfracts[i] > 0
                 s *= "Reaction accounts for $fract of the net production for cluster $cluster \n"
             else

src/Parse.jl

@@ -1,6 +1,6 @@
 using Unitful
 using YAML
-using PyCall
+using PythonCall
 using StaticArrays
 
 module Calc
@@ -131,7 +131,7 @@ function getatomdictfromrdkit(mol)
     atmD = Dict{String,Int64}()
     molecularweight = 0.0
     for atm in mol.GetAtoms()
-        v = elementdict[atm.GetAtomicNum()]
+        v = elementdict[PythonCall.pyconvert(Int64, atm.GetAtomicNum())]
         if v in keys(atmD)
             atmD[v] += 1
         else
@@ -140,9 +140,9 @@ function getatomdictfromrdkit(mol)
     end
     nbonds = length(mol.GetBonds())
     try
-        molecularweight = Desc.MolWt(mol)/1000.0
-    catch
-        @warn("unable to compute molecular weight")
+        molecularweight = PythonCall.pyconvert(Float64, Desc.MolWt(mol)) / 1000.0
+    catch e
+        @warn("unable to compute molecular weight: $e")
     end
     return atmD,nbonds,molecularweight
 end
@@ -151,15 +151,15 @@ export getatomdictfromrdkit
 function getatomdictfromrmg(mol)
     atmD = Dict{String,Int64}()
     for atm in mol.atoms
-        v = elementdict[atm.element.number]
+        v = elementdict[PythonCall.pyconvert(Int64, atm.element.number)]
         if v in keys(atmD)
             atmD[v] += 1
         else
             atmD[v] = 1
         end
     end
     nbonds = length(mol.get_all_edges())
-    molecularweight = mol.get_molecular_weight()
+    molecularweight = PythonCall.pyconvert(Float64, mol.get_molecular_weight())
     return atmD,nbonds,molecularweight
 end
 function getatomdictsmiles(smiles)