debug

hwpang · hwpang · commit 1997ef94afe5 · 2024-03-21T17:51:25.000-04:00
diff --git a/.github/workflows/CI.yml b/.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 +24,13 @@ 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");'
+            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)'
+            julia -e 'using Pkg; Pkg.test("ReactionMechanismSimulator"; coverage=true)'
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v1
         with:
diff --git a/.github/workflows/Install.yml b/.github/workflows/Install.yml
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -16,15 +16,9 @@ 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();'
       - name: Build and deploy
         env:
diff --git a/Project.toml b/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"
@@ -43,7 +43,7 @@ YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 [compat]
 Calculus = "0.4,0.5"
 Colors = "0.11,0.12"
-Conda = "1"
+CondaPkg = "0"
 CSV = "0.10"
 DataFrames = "1"
 SciMLSensitivity = "^7"
@@ -57,8 +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"
diff --git a/deps/build.jl b/deps/build.jl
@@ -1,16 +1,12 @@
-using PyCall
-using Conda
-packages = Conda._installed_packages()
-if !("rmg" in packages) && !("rmgmolecule" in packages) && (PyCall.pyversion.major != 3 || !(PyCall.pyversion.minor in [7, 8, 9]))
+using CondaPkg
+using PythonCall
+packages = keys(CondaPkg.current_packages())
+if !("rmg" in packages) && !("rmgmolecule" in packages) || !(v"3.7" <= PythonCall.C.python_version() && PythonCall.C.python_version() <= v"3.9")
     const Pkg = Base.require(Base.PkgId(Base.UUID("44cfe95a-1eb2-52ea-b672-e2afdf69b78f"), "Pkg"))
-    Conda.add("python=3.8")
-    try
-        Conda.rm("numpy") #get around MKL problem
-    catch e
-    end
-    Conda.add("nomkl")
-    Conda.add("numpy")
-    Conda.add_channel("mjohnson541")
-    Conda.add("rmgmolecule")
-    Pkg.build("PyCall")
+    CondaPkg.add("python"; version="3.9")
+    CondaPkg.add("matplotlib")
+    CondaPkg.add("rdkit")
+    CondaPkg.add("pydot")
+    CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541")
+    Pkg.build("PythonCall")
 end
diff --git a/docs/src/Installation.md b/docs/src/Installation.md
@@ -37,9 +37,9 @@ The above instructions will automatically handle Julia-Python linking. However,
 
 ```
 import Pkg
-Pkg.add("PyCall")                              
+Pkg.add("PythonCall")                              
 ENV["CONDA_JL_HOME"] = PATH_TO_YOUR_ENV        
-Pkg.build("Conda")                             
+Pkg.build("CondaPkg")                             
 ENV["PYTHON"] = PATH_TO_PYTHON                 
-Pkg.build("PyCall")                            
+Pkg.build("PythonCall")                            
 ```
diff --git a/environment.yml b/environment.yml
diff --git a/iJulia/Automatic Mechanism Analysis Example.ipynb b/iJulia/Automatic Mechanism Analysis Example.ipynb
@@ -8,7 +8,7 @@
    "outputs": [],
    "source": [
     "using Sundials\n",
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "using ReactionMechanismSimulator"
    ]
   },
diff --git a/iJulia/ConstantPH2Combustion.ipynb b/iJulia/ConstantPH2Combustion.ipynb
@@ -29,7 +29,7 @@
    "outputs": [],
    "source": [
     "using DifferentialEquations\n",
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "using ReactionMechanismSimulator"
    ]
   },
diff --git a/iJulia/ConstantTPH2Combustion.ipynb b/iJulia/ConstantTPH2Combustion.ipynb
@@ -9,7 +9,7 @@
     "using DiffEqBase\n",
     "using Sundials\n",
     "using DiffEqSensitivity\n",
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "using ReactionMechanismSimulator"
    ]
   },
diff --git a/iJulia/ConstantTVOctaneOxidation.ipynb b/iJulia/ConstantTVOctaneOxidation.ipynb
@@ -7,7 +7,7 @@
    "outputs": [],
    "source": [
     "using DifferentialEquations\n",
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "using ReactionMechanismSimulator"
    ]
   },
diff --git a/iJulia/ConstantVH2Combustion.ipynb b/iJulia/ConstantVH2Combustion.ipynb
@@ -7,7 +7,7 @@
    "outputs": [],
    "source": [
     "using DifferentialEquations\n",
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "using ReactionMechanismSimulator"
    ]
   },
diff --git a/iJulia/Gas-Catalyst Interface.ipynb b/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"
    ]
diff --git a/iJulia/ParametrizedTConstantVOctaneOxidation.ipynb b/iJulia/ParametrizedTConstantVOctaneOxidation.ipynb
@@ -7,7 +7,7 @@
    "outputs": [],
    "source": [
     "using DifferentialEquations\n",
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "using ReactionMechanismSimulator"
    ]
   },
diff --git a/iJulia/ParametrizedTPH2Combustion.ipynb b/iJulia/ParametrizedTPH2Combustion.ipynb
@@ -7,7 +7,7 @@
    "outputs": [],
    "source": [
     "using DifferentialEquations\n",
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "using ReactionMechanismSimulator"
    ]
   },
diff --git a/iJulia/ParametrizedVH2Combustion.ipynb b/iJulia/ParametrizedVH2Combustion.ipynb
@@ -7,7 +7,7 @@
    "outputs": [],
    "source": [
     "using DifferentialEquations\n",
-    "using PyPlot\n",
+    "using PythonPlot\n",
     "using ReactionMechanismSimulator"
    ]
   },
diff --git a/iJulia/Quasi-Steady State Assumptions and Isomer Lumping.ipynb b/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"
    ]
   },
   {
diff --git a/iJulia/Vapor-Liquid Two-Phase Low-Temperature Pyrolysis.ipynb b/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"
    ]
   },
   {
diff --git a/src/Parse.jl b/src/Parse.jl
@@ -1,6 +1,6 @@
 using Unitful
 using YAML
-using PyCall
+using PythonCall
 using StaticArrays
 
 module Calc
diff --git a/src/Plotting.jl b/src/Plotting.jl
@@ -1,4 +1,4 @@
-using PyPlot
+using PythonPlot
 
 """
 Plot the mole fractions of the simulation bsol from t0 to tf
@@ -484,7 +484,7 @@ function plottimescales(Jy;taumax=1e6,taumin=1e-18,taures=10.0^0.5,usediag=true)
     else
         taus = 1.0./abs.(eigvals(Jy))
     end
-    PyPlot.hist([x==Inf ? 0.0 : x for x in taus],bins=10.0.^(log10(taumin):log10(taures):log10(taumax)))
+    PythonPlot.hist([x == Inf ? 0.0 : x for x in taus], bins=10.0 .^ (log10(taumin):log10(taures):log10(taumax)))
     xscale("log")
     xlabel("Species Time Scale [sec]")
     ylabel("Counts")
diff --git a/src/ReactionMechanismSimulator.jl b/src/ReactionMechanismSimulator.jl
@@ -1,54 +1,53 @@
+module ReactionMechanismSimulator
 import Logging
 Logging.disable_logging(Logging.Warn)
-
-module ReactionMechanismSimulator
-using PyCall
-push!(PyVector(pyimport("sys")["path"]), "")
-const Chem = PyNULL()
-const Desc = PyNULL()
-const molecule = PyNULL()
-const fragment = PyNULL()
-const pydot = PyNULL()
-const chemkin = PyNULL()
-const species = PyNULL()
-const reaction = PyNULL()
-const nasa = PyNULL()
-const wilhoit = PyNULL()
-const arrhenius = PyNULL()
-const falloff = PyNULL()
-const chebyshev = PyNULL()
-const solvation = PyNULL()
-const os = PyNULL()
+using PythonCall
+pyimport("sys").path.append("")
+const Chem = Ref{Py}()
+const Desc = Ref{Py}()
+const molecule = Ref{Py}()
+const chemkin = Ref{Py}()
+const species = Ref{Py}()
+const reaction = Ref{Py}()
+const nasa = Ref{Py}()
+const wilhoit = Ref{Py}()
+const arrhenius = Ref{Py}()
+const falloff = Ref{Py}()
+const chebyshev = Ref{Py}()
+const solvation = Ref{Py}()
+const fragment = Ref{Py}()
+const pydot = Ref{Py}()
+const os = Ref{Py}()
 function __init__()
-    copy!(Chem, pyimport_conda("rdkit.Chem", "rdkit", "rmg"))
-    copy!(Desc, pyimport_conda("rdkit.Chem.Descriptors", "rdkit", "rmg"))
+    Chem[] = pyimport("rdkit.Chem")
+    Desc[] = pyimport("rdkit.Chem.Descriptors")
     try
-        copy!(molecule, pyimport("rmgpy.molecule"))
-        copy!(chemkin, pyimport("rmgpy.chemkin"))
-        copy!(species, pyimport("rmgpy.species"))
-        copy!(reaction, pyimport("rmgpy.reaction"))
-        copy!(nasa, pyimport("rmgpy.thermo.nasa"))
-        copy!(wilhoit, pyimport("rmgpy.thermo.wilhoit"))
-        copy!(arrhenius, pyimport("rmgpy.kinetics.arrhenius"))
-        copy!(falloff, pyimport("rmgpy.kinetics.falloff"))
-        copy!(chebyshev, pyimport("rmgpy.kinetics.chebyshev"))
-        copy!(solvation, pyimport("rmgpy.data.solvation"))
-        copy!(fragment, pyimport("rmgpy.molecule.fragment"))
+        molecule[] = pyimport("rmgpy.molecule")
+        chemkin[] = pyimport("rmgpy.chemkin")
+        species[] = pyimport("rmgpy.species")
+        reaction[] = pyimport("rmgpy.reaction")
+        nasa[] = pyimport("rmgpy.thermo.nasa")
+        wilhoit[] = pyimport("rmgpy.thermo.wilhoit")
+        arrhenius[] = pyimport("rmgpy.kinetics.arrhenius")
+        falloff[] = pyimport("rmgpy.kinetics.falloff")
+        chebyshev[] = pyimport("rmgpy.kinetics.chebyshev")
+        solvation[] = pyimport("rmgpy.data.solvation")
+        fragment[] = pyimport("rmgpy.molecule.fragment")
     catch e
-        copy!(molecule, pyimport_conda("molecule.molecule", "rmgmolecule", "mjohnson541"))
-        copy!(chemkin, pyimport_conda("molecule.chemkin", "rmgmolecule", "mjohnson541"))
-        copy!(species, pyimport_conda("molecule.species", "rmgmolecule", "mjohnson541"))
-        copy!(reaction, pyimport_conda("molecule.reaction", "rmgmolecule", "mjohnson541"))
-        copy!(nasa, pyimport_conda("molecule.thermo.nasa", "rmgmolecule", "mjohnson541"))
-        copy!(wilhoit, pyimport_conda("molecule.thermo.wilhoit", "rmgmolecule", "mjohnson541"))
-        copy!(arrhenius, pyimport_conda("molecule.kinetics.arrhenius", "rmgmolecule", "mjohnson541"))
-        copy!(falloff, pyimport_conda("molecule.kinetics.falloff", "rmgmolecule", "mjohnson541"))
-        copy!(chebyshev, pyimport_conda("molecule.kinetics.chebyshev", "rmgmolecule", "mjohnson541"))
-        copy!(solvation, pyimport_conda("molecule.data.solvation", "rmgmolecule", "mjohnson541"))
-        copy!(fragment, pyimport_conda("molecule.molecule.fragment", "rmgmolecule", "mjohnson541"))
+        molecule[] = pyimport("molecule.molecule")
+        chemkin[] = pyimport("molecule.chemkin")
+        species[] = pyimport("molecule.species")
+        reaction[] = pyimport("molecule.reaction")
+        nasa[] = pyimport("molecule.thermo.nasa")
+        wilhoit[] = pyimport("molecule.thermo.wilhoit")
+        arrhenius[] = pyimport("molecule.kinetics.arrhenius")
+        falloff[] = pyimport("molecule.kinetics.falloff")
+        chebyshev[] = pyimport("molecule.kinetics.chebyshev")
+        solvation[] = pyimport("molecule.data.solvation")
+        fragment[] = pyimport("molecule.molecule.fragment")
     end
-    copy!(pydot, pyimport_conda("pydot", "pydot"))
-    copy!(os, pyimport_conda("os", "os"))
+    pydot[] = pyimport("pydot")
+    os[] = pyimport("os")
 end
 include("Constants.jl")
 include("Tools.jl")
diff --git a/src/fluxdiagrams.jl b/src/fluxdiagrams.jl
diff --git a/src/rmstest.jl b/src/rmstest.jl

Original file line number	Diff line number	Diff line change
`@@ -8,7 +8,7 @@`
`8`	`8`	`"outputs": [],`
`9`	`9`	`"source": [`
`10`	`10`	`"using Sundials\n",`
`11`		`- "using PyPlot\n",`
	`11`	`+ "using PythonPlot\n",`
`12`	`12`	`"using ReactionMechanismSimulator"`
`13`	`13`	`]`
`14`	`14`	`},`
Original file line number	Diff line number	Diff line change
`@@ -29,7 +29,7 @@`
`29`	`29`	`"outputs": [],`
`30`	`30`	`"source": [`
`31`	`31`	`"using DifferentialEquations\n",`
`32`		`- "using PyPlot\n",`
	`32`	`+ "using PythonPlot\n",`
`33`	`33`	`"using ReactionMechanismSimulator"`
`34`	`34`	`]`
`35`	`35`	`},`
Original file line number	Diff line number	Diff line change
`@@ -9,7 +9,7 @@`
`9`	`9`	`"using DiffEqBase\n",`
`10`	`10`	`"using Sundials\n",`
`11`	`11`	`"using DiffEqSensitivity\n",`
`12`		`- "using PyPlot\n",`
	`12`	`+ "using PythonPlot\n",`
`13`	`13`	`"using ReactionMechanismSimulator"`
`14`	`14`	`]`
`15`	`15`	`},`