Merge pull request #268 from hwpang/fix_installation

Attempting to Fix the `juliacall` Overhaul on RMG

Author: JacksonBurns

.github/workflows/CI.yml

@@ -11,36 +11,19 @@ jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+
+      - name: Setup Juliaup
+        uses: julia-actions/install-juliaup@v2
         with:
-          version: 1.8
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ 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");'
-      - name: Run tests
+          channel: '1.10'
+
+      - name: Build and Test
         run: |
-            julia -e 'using Pkg; Pkg.test("ReactionMechanismSimulator";coverage=true)'
+            julia -e 'using Pkg; Pkg.develop(Pkg.PackageSpec(path="../ReactionMechanismSimulator.jl/")); Pkg.build("ReactionMechanismSimulator"); Pkg.test("ReactionMechanismSimulator"; coverage=true)'
+
       - uses: julia-actions/julia-processcoverage@v1
+
       - uses: codecov/codecov-action@v1
         with:
           file: lcov.info

.github/workflows/documentation.yml

@@ -13,21 +13,24 @@ jobs:
       contents: write
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@latest
-        with:
-          version: 1.8
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
+
+      - name: Setup Juliaup
+        uses: julia-actions/install-juliaup@v2
         with:
-          environment-file: environment.yml
-          python-version: 3.7
-          activate-environment: rms_env
-      - name: Install dependencies
+          channel: '1.10'
+
+      - uses: julia-actions/cache@v2
+
+      - uses: julia-actions/julia-buildpkg@v1
+
+      - name: Build
         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();'
-      - name: Build and deploy
+            julia -e 'using Pkg; Pkg.develop(Pkg.PackageSpec(path="../ReactionMechanismSimulator.jl/")); Pkg.build("ReactionMechanismSimulator"); Pkg.instantiate();'
+
+      - name: Build and deploy Documentation
         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: |
+          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 = ["mjohnson541", "rmg", "conda-forge", "cantera"]

Project.toml

@@ -6,7 +6,7 @@ version = "1.0.0"
 [deps]
 Calculus = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9"
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
-Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
+CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 FastGaussQuadrature = "442a2c76-b920-505d-bb47-c5924d526838"
@@ -21,8 +21,8 @@ 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"
@@ -39,12 +39,11 @@ 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]
 Calculus = "0.4,0.5"
 Colors = "0.11,0.12"
-Conda = "1"
+CondaPkg = "0"
 CSV = "0.10"
 DataFrames = "1"
 SciMLSensitivity = "^7"
@@ -58,8 +57,8 @@ ModelingToolkit = "8"
 OrdinaryDiffEq = "^6"
 Parameters = "0.12"
 PreallocationTools = "0.4"
-PyCall = "1"
-PyPlot = "2"
+PythonCall = "0"
+PythonPlot = "1"
 QuartzImageIO = "0.7"
 RecursiveArrayTools = "2.17"
 ReverseDiff = "1.9"
@@ -72,5 +71,4 @@ Symbolics = "4"
 Tracker = "0.2"
 Unitful = "^1.3"
 YAML = "0.4"
-Zygote = "0.5,0.6"
 julia = "^1.6"

deps/build.jl

@@ -1,21 +1,29 @@
-using PyCall
-using Conda
-packages = Conda._installed_packages()
-if !("rmg" in packages) && !("rmgmolecule" in packages) && (PyCall.pyversion.major != 3 || PyCall.pyversion.minor != 7)
-    const Pkg = Base.require(Base.PkgId(Base.UUID("44cfe95a-1eb2-52ea-b672-e2afdf69b78f"), "Pkg"))
-    Conda.rm("mamba")
-    Conda.add("conda=4")
-    Conda.add("mamba")
-    Conda.update()
-    Conda.add("python=3.7")
-    try
-        Conda.rm("numpy") #get around MKL problem
-    catch e 
+using CondaPkg
+using PythonCall
+
+has_rmgpy = true
+has_rmgmolecule = true
+try
+    PythonCall.pyimport("rmgpy")
+catch
+    has_rmgpy = false
+end
+try
+    PythonCall.pyimport("molecule")
+catch
+    has_rmgmolecule = false
+end
+
+if !has_rmgpy && !has_rmgmolecule
+
+    if !(v"3.7" <= PythonCall.C.python_version() && PythonCall.C.python_version() <= v"3.9")
+        CondaPkg.add("python"; version=">=3.9")
     end
-    Conda.add("nomkl")
-    Conda.add("numpy")
-    Conda.add_channel("mjohnson541")
-    Conda.add_channel("hwpang")
-    Conda.add("rmgmolecule")
-    Pkg.build("PyCall")
-end
+    CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541")
+    CondaPkg.add("matplotlib", channel="conda-forge")
+    CondaPkg.add("rdkit", channel="conda-forge")
+    CondaPkg.add("pydot", channel="conda-forge")
+end
+
+const Pkg = Base.require(Base.PkgId(Base.UUID("44cfe95a-1eb2-52ea-b672-e2afdf69b78f"), "Pkg"))
+Pkg.build("PythonCall")

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")
 ```

environment.yml

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

iJulia/Automatic Mechanism Analysis Example.ipynb

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

iJulia/ConstantPH2Combustion.ipynb

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

iJulia/ConstantTPH2Combustion.ipynb

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

iJulia/Gas-Catalyst Interface.ipynb

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

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

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

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

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

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

@@ -1037,8 +1037,10 @@ function selectobjects(react,edgereact,coreedgedomains,coreedgeinters,domains,in
         dydt,rts,frts,rrts,cs,corespeciesrates,charrate,edgespeciesrates,edgereactionrates,edgerxnradrateratios,
         corespeciesrateratios,edgespeciesrateratios,corereactionrates,corespeciesconcentrations,
         corespeciesproductionrates,corespeciesconsumptionrates = processfluxes(sim,corespcsinds,corerxninds,edgespcsinds,edgerxninds)
-        @inbounds ind = edgespcsinds[argmax(edgespeciesrates)]
-        @inbounds invalidobjects = [sim.species[ind]]
+        if !isempty(edgespeciesrates)
+            @inbounds ind = edgespcsinds[argmax(edgespeciesrates)]
+            @inbounds invalidobjects = [sim.species[ind]]
+        end        
         return (terminated,true,invalidobjects,unimolecularthreshold,
             bimolecularthreshold,trimolecularthreshold,maxedgespeciesrateratios,t,conversion)
     end

src/EdgeAnalysis.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)