Merge branch 'master' into doc_figure_update

Author: TorkelE

Project.toml

@@ -1,6 +1,6 @@
 name = "Catalyst"
 uuid = "479239e8-5488-4da2-87a7-35f2df7eef83"
-version = "13.5.1"
+version = "14.0.0-DEV"
 
 [deps]
 Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"

src/reactionsystem_conversions.jl

@@ -798,7 +798,7 @@ function _symbol_to_var(sys, sym)
     if hasproperty(sys, sym)
         var = getproperty(sys, sym, namespace = false)
     else
-        strs = split(String(sym), "₊")   # need to check if this should be split of not!!!
+        strs = split(String(sym), ModelingToolkit.NAMESPACE_SEPARATOR)   # need to check if this should be split of not!!!
         if length(strs) > 1
             var = getproperty(sys, Symbol(strs[1]), namespace = false)
             for str in view(strs, 2:length(strs))

test/dsl/dsl_options.jl

@@ -493,7 +493,7 @@ let
     @test plot(sol; idxs=:X).series_list[1].plotattributes[:y][end] ≈ 10.0
     @test plot(sol; idxs=[X, Y]).series_list[2].plotattributes[:y][end] ≈ 3.0
     @test plot(sol; idxs=[rn.X, rn.Y]).series_list[2].plotattributes[:y][end] ≈ 3.0
-    @test_broken plot(sol; idxs=[:X, :Y]).series_list[2].plotattributes[:y][end] ≈ 3.0 # (https://github.com/SciML/ModelingToolkit.jl/issues/2778)
+    @test plot(sol; idxs=[:X, :Y]).series_list[2].plotattributes[:y][end] ≈ 3.0 # (https://github.com/SciML/ModelingToolkit.jl/issues/2778)
 end
 
 # Compares programmatic and DSL system with observables.
@@ -950,4 +950,4 @@ let
     rl = oderatelaw(reactions(rn3)[1]; combinatoric_ratelaw)
     @unpack k1, A = rn3
     @test isequal(rl, k1*A^2)
-end
+end

test/upstream/mtk_structure_indexing.jl

@@ -64,7 +64,8 @@ end
 
 # Tests problem indexing and updating.
 let 
-    for prob in [deepcopy(problems); deepcopy(eproblems)]
+    @test_broken false # Currently does not work for nonlinearproblems and their ensemble problems (https://github.com/SciML/SciMLBase.jl/issues/720).
+    for prob in [deepcopy([oprob, sprob, dprob, jprob, ssprob]); deepcopy([eoprob, esprob, edprob, ejprob, essprob])]
         # Get u values (including observables).
         @test prob[X] == prob[model.X] == prob[:X] == 4
         @test prob[XY] == prob[model.XY] == prob[:XY] == 9
@@ -253,7 +254,8 @@ let
 
     # Handles nonlinear and steady state solutions differently.
     let
-        for sol in deepcopy([nsol, sssol])
+        @test_broken false # Currently a problem for nonlinear solutions and steady state solutions (https://github.com/SciML/SciMLBase.jl/issues/720).
+        for sol in deepcopy([])
             # Get u values.
             @test sol[X] == sol[model.X] == sol[:X]
             @test sol[XY] == sol[model.XY][1] == sol[:XY]