debug

Author: hwpang

.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:

.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:

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 +1,12 @@
-using PyCall
-using Conda
-packages = Conda._installed_packages()
-if !("rmg" in packages) && !("rmgmolecule" in packages) && (PyCall.pyversion.major != 3 || PyCall.pyversion.minor != 7)
+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.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 
-    end
-    Conda.add("nomkl")
-    Conda.add("numpy")
-    Conda.add_channel("mjohnson541")
-    Conda.add_channel("hwpang")
-    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

environment.yml

@@ -1,83 +1,67 @@
+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()
-    function __init__()
-        copy!(Chem,pyimport_conda("rdkit.Chem","rdkit","rmg"))
-        copy!(Desc,pyimport_conda("rdkit.Chem.Descriptors","rdkit","rmg"))
-        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"))
-        catch e
-            copy!(molecule,pyimport_conda("molecule.molecule","rmgmolecule","hwpang"))
-            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!(fragment,pyimport_conda("molecule.molecule.fragment","rmgmolecule","hwpang"))
-        end
-        copy!(pydot,pyimport_conda("pydot","pydot"))
-        copy!(os,pyimport_conda("os","os"))
+using PythonCall
+pyimport("sys").path.append("")
+function __init__()
+    Chem = @pyconst(pyimport("rdkit.Chem"))
+    Desc = @pyconst(pyimport("rdkit.Chem.Descriptors"))
+    try
+        molecule = @pyconst(pyimport("rmgpy.molecule"))
+        chemkin = @pyconst(pyimport("rmgpy.chemkin"))
+        species = @pyconst(pyimport("rmgpy.species"))
+        reaction = @pyconst(pyimport("rmgpy.reaction"))
+        nasa = @pyconst(pyimport("rmgpy.thermo.nasa"))
+        wilhoit = @pyconst(pyimport("rmgpy.thermo.wilhoit"))
+        arrhenius = @pyconst(pyimport("rmgpy.kinetics.arrhenius"))
+        falloff = @pyconst(pyimport("rmgpy.kinetics.falloff"))
+        chebyshev = @pyconst(pyimport("rmgpy.kinetics.chebyshev"))
+        solvation = @pyconst(pyimport("rmgpy.data.solvation"))
+        fragment = @pyconst(pyimport("rmgpy.molecule.fragment"))
+    catch e
+        molecule = @pyconst(pyimport("molecule.molecule"))
+        chemkin = @pyconst(pyimport("molecule.chemkin"))
+        species = @pyconst(pyimport("molecule.species"))
+        reaction = @pyconst(pyimport("molecule.reaction"))
+        nasa = @pyconst(pyimport("molecule.thermo.nasa"))
+        wilhoit = @pyconst(pyimport("molecule.thermo.wilhoit"))
+        arrhenius = @pyconst(pyimport("molecule.kinetics.arrhenius"))
+        falloff = @pyconst(pyimport("molecule.kinetics.falloff"))
+        chebyshev = @pyconst(pyimport("molecule.kinetics.chebyshev"))
+        solvation = @pyconst(pyimport("molecule.data.solvation"))
+        fragment = @pyconst(pyimport("molecule.molecule.fragment"))
     end
-    include("Constants.jl")
-    include("Tools.jl")
-    include("Calculators/RateUncertainty.jl")
-    include("Calculators/ThermoUncertainty.jl")
-    include("Calculators/Thermo.jl")
-    include("Calculators/Diffusion.jl")
-    include("Calculators/Rate.jl")
-    include("Calculators/Viscosity.jl")
-    include("Calculators/Thermovec.jl")
-    include("Calculators/Ratevec.jl")
-    include("Calculators/kLAkH.jl")
-    include("Species.jl")
-    include("Solvent.jl")
-    include("Reaction.jl")
-    include("Phase.jl")
-    include("PhaseState.jl")
-    include("Interface.jl")
-    include("Domain.jl")
-    include("yml.jl")
-    include("Parse.jl")
-    include("ModelReduction.jl")
-    include("Reactor.jl")
-    include("ThreadedSensitivities.jl")
-    include("Simulation.jl")
-    include("TransitorySensitivities.jl")
-    include("AutomaticMechanismAnalysis.jl")
-    include("EdgeAnalysis.jl")
-    include("Debugging.jl")
-    include("Plotting.jl")
-    include("fluxdiagrams.jl")
+    pydot = @pyconst(pyimport("pydot"))
+    os = @pyconst(pyimport("os"))
+end
+include("Constants.jl")
+include("Tools.jl")
+include("Calculators/RateUncertainty.jl")
+include("Calculators/ThermoUncertainty.jl")
+include("Calculators/Thermo.jl")
+include("Calculators/Diffusion.jl")
+include("Calculators/Rate.jl")
+include("Calculators/Viscosity.jl")
+include("Calculators/Thermovec.jl")
+include("Calculators/Ratevec.jl")
+include("Calculators/kLAkH.jl")
+include("Species.jl")
+include("Solvent.jl")
+include("Reaction.jl")
+include("Phase.jl")
+include("PhaseState.jl")
+include("Interface.jl")
+include("Domain.jl")
+include("yml.jl")
+include("Parse.jl")
+include("ModelReduction.jl")
+include("Reactor.jl")
+include("ThreadedSensitivities.jl")
+include("Simulation.jl")
+include("TransitorySensitivities.jl")
+include("AutomaticMechanismAnalysis.jl")
+include("EdgeAnalysis.jl")
+include("Debugging.jl")
+include("Plotting.jl")
+include("fluxdiagrams.jl")
 end