Use PythonCall syntax in module

Author: hwpang

src/ReactionMechanismSimulator.jl

@@ -1,83 +1,79 @@
-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
+using CondaPkg
+packages = keys(CondaPkg.current_packages())
+const Chem = PythonCall.pynew()
+const Desc = PythonCall.pynew()
+const molecule = PythonCall.pynew()
+const chemkin = PythonCall.pynew()
+const species = PythonCall.pynew()
+const reaction = PythonCall.pynew()
+const nasa = PythonCall.pynew()
+const wilhoit = PythonCall.pynew()
+const arrhenius = PythonCall.pynew()
+const falloff = PythonCall.pynew()
+const chebyshev = PythonCall.pynew()
+const solvation = PythonCall.pynew()
+const fragment = PythonCall.pynew()
+const pydot = PythonCall.pynew()
+function __init__()
+    PythonCall.pycopy!(Chem, pyimport("rdkit.Chem"))
+    PythonCall.pycopy!(Desc, pyimport("rdkit.Chem.Descriptors"))
+    try
+        PythonCall.pycopy!(molecule, pyimport("rmgpy.molecule"))
+        PythonCall.pycopy!(chemkin, pyimport("rmgpy.chemkin"))
+        PythonCall.pycopy!(species, pyimport("rmgpy.species"))
+        PythonCall.pycopy!(reaction, pyimport("rmgpy.reaction"))
+        PythonCall.pycopy!(nasa, pyimport("rmgpy.thermo.nasa"))
+        PythonCall.pycopy!(wilhoit, pyimport("rmgpy.thermo.wilhoit"))
+        PythonCall.pycopy!(arrhenius, pyimport("rmgpy.kinetics.arrhenius"))
+        PythonCall.pycopy!(falloff, pyimport("rmgpy.kinetics.falloff"))
+        PythonCall.pycopy!(chebyshev, pyimport("rmgpy.kinetics.chebyshev"))
+        PythonCall.pycopy!(solvation, pyimport("rmgpy.data.solvation"))
+        PythonCall.pycopy!(fragment, pyimport("rmgpy.molecule.fragment"))
+    catch e
+        PythonCall.pycopy!(molecule, pyimport("molecule.molecule"))
+        PythonCall.pycopy!(chemkin, pyimport("molecule.chemkin"))
+        PythonCall.pycopy!(species, pyimport("molecule.species"))
+        PythonCall.pycopy!(reaction, pyimport("molecule.reaction"))
+        PythonCall.pycopy!(nasa, pyimport("molecule.thermo.nasa"))
+        PythonCall.pycopy!(wilhoit, pyimport("molecule.thermo.wilhoit"))
+        PythonCall.pycopy!(arrhenius, pyimport("molecule.kinetics.arrhenius"))
+        PythonCall.pycopy!(falloff, pyimport("molecule.kinetics.falloff"))
+        PythonCall.pycopy!(chebyshev, pyimport("molecule.kinetics.chebyshev"))
+        PythonCall.pycopy!(solvation, pyimport("molecule.data.solvation"))
+        PythonCall.pycopy!(fragment, 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")
+    PythonCall.pycopy!(pydot, pyimport("pydot"))
+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