clean up conda installs

avoid use of PythonCall
resolve all conda changes at once

Project.toml

@@ -4,10 +4,10 @@ authors = ["Matt Johnson <mjohnson541@gmail.com>", "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"
 CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
-CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 FastGaussQuadrature = "442a2c76-b920-505d-bb47-c5924d526838"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
@@ -17,6 +17,7 @@ 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"
@@ -41,18 +42,18 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 
 [compat]
+CSV = "0.10"
 Calculus = "0.4,0.5"
 Colors = "0.11,0.12"
 CondaPkg = "0.2"
-CSV = "0.10"
 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"
@@ -63,6 +64,7 @@ QuartzImageIO = "0.7"
 RecursiveArrayTools = "2.17"
 ReverseDiff = "1.9"
 SciMLBase = "^1"
+SciMLSensitivity = "^7"
 SmoothingSplines = "0.3"
 SpecialFunctions = "1"
 StaticArrays = "1"

src/ReactionMechanismSimulator.jl

@@ -1,7 +1,34 @@
 module ReactionMechanismSimulator
-using PythonCall
+ENV["JULIA_CONDAPKG_BACKEND"] = "MicroMamba"
 using CondaPkg
 using Logging
+packages = keys(CondaPkg.current_packages())
+
+if !("rmg" in packages) && !("rmgmolecule" in packages)
+    @info "missing rmg and rmgmolecule installing rmgmolecule..."
+    if "python" in packages
+        py_version = VersionNumber(CondaPkg.current_packages()["python"][:version])
+    else
+        py_version = nothing
+    end
+    if py_version === nothing || !(v"3.7" <= py_version && py_version <= v"3.9")
+        @info "python version was not in 3.7-3.9 changing python version"
+        CondaPkg.add("python"; version="3.9",resolve=false)
+        CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541",resolve=false)
+        CondaPkg.add("matplotlib", channel="conda-forge",resolve=false)
+        CondaPkg.add("rdkit", channel="conda-forge",resolve=false)
+        CondaPkg.add("pydot", channel="conda-forge",resolve=false)
+        CondaPkg.resolve()
+    else
+        CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541",resolve=false)
+        CondaPkg.add("matplotlib", channel="conda-forge",resolve=false)
+        CondaPkg.add("rdkit", channel="conda-forge",resolve=false)
+        CondaPkg.add("pydot", channel="conda-forge",resolve=false)
+        CondaPkg.resolve()
+    end
+end
+
+using PythonCall
 const Chem = PythonCall.pynew()
 const Desc = PythonCall.pynew()
 const molecule = PythonCall.pynew()
@@ -17,24 +44,6 @@ const solvation = PythonCall.pynew()
 const fragment = PythonCall.pynew()
 const pydot = PythonCall.pynew()
 
-packages = keys(CondaPkg.current_packages())
-
-if !("rmg" in packages) && !("rmgmolecule" in packages)
-    @info "missing rmg and rmgmolecule installing rmgmolecule..."
-    if !(v"3.7" <= PythonCall.C.python_version() && PythonCall.C.python_version() <= v"3.9")
-        @info "python version was not in 3.7-3.9 changing python version"
-        CondaPkg.add("python"; version="3.9")
-    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")
-
-    Pkgc = Base.require(Base.PkgId(Base.UUID("44cfe95a-1eb2-52ea-b672-e2afdf69b78f"), "Pkg"))
-    Pkgc.build("PythonCall")
-end
-
-
 function __init__()
     PythonCall.pycopy!(Chem, pyimport("rdkit.Chem"))
     PythonCall.pycopy!(Desc, pyimport("rdkit.Chem.Descriptors"))

src/rmstest.jl

@@ -1,30 +1,41 @@
 import Logging
 Logging.disable_logging(Logging.Warn)
-
-using PythonCall
-using CondaPkg
-const Chem = PythonCall.pynew()
-const molecule = PythonCall.pynew()
-const fragment = PythonCall.pynew()
-const pydot = PythonCall.pynew()
+ENV["JULIA_CONDAPKG_BACKEND"] = "MicroMamba"
+using CondaPkg 
 
 packages = keys(CondaPkg.current_packages())
 
 if !("rmg" in packages) && !("rmgmolecule" in packages)
     @info "missing rmg and rmgmolecule installing rmgmolecule..."
-    if !(v"3.7" <= PythonCall.C.python_version() && PythonCall.C.python_version() <= v"3.9")
+    if "python" in packages
+        py_version = VersionNumber(CondaPkg.current_packages()["python"][:version])
+    else
+        py_version = nothing
+    end
+    if py_version === nothing || !(v"3.7" <= py_version && py_version <= v"3.9")
         @info "python version was not in 3.7-3.9 changing python version"
-        CondaPkg.add("python"; version="3.9")
+        CondaPkg.add("python"; version="3.9",resolve=false)
+        CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541",resolve=false)
+        CondaPkg.add("matplotlib", channel="conda-forge",resolve=false)
+        CondaPkg.add("rdkit", channel="conda-forge",resolve=false)
+        CondaPkg.add("pydot", channel="conda-forge",resolve=false)
+        CondaPkg.resolve()
+    else
+        CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541",resolve=false)
+        CondaPkg.add("matplotlib", channel="conda-forge",resolve=false)
+        CondaPkg.add("rdkit", channel="conda-forge",resolve=false)
+        CondaPkg.add("pydot", channel="conda-forge",resolve=false)
+        CondaPkg.resolve()
     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")
-
-    Pkgc = Base.require(Base.PkgId(Base.UUID("44cfe95a-1eb2-52ea-b672-e2afdf69b78f"), "Pkg"))
-    Pkgc.build("PythonCall")
 end
 
+using PythonCall
+
+const Chem = PythonCall.pynew()
+const molecule = PythonCall.pynew()
+const fragment = PythonCall.pynew()
+const pydot = PythonCall.pynew()
+
 PythonCall.pycopy!(Chem, pyimport("rdkit.Chem"))
 try
     PythonCall.pycopy!(molecule, pyimport("rmgpy.molecule"))