Merge e1b3a00 into 59294a5

test/dsl/dsl_options.jl

@@ -488,12 +488,12 @@ let
     @test sol[:Y][end] ≈ 3.0
 
     # Tests that observables can be used for plot indexing.
-    @test_broken false # plot(sol; idxs=X).series_list[1].plotattributes[:y][end] ≈ 10.0
+    plot(sol; idxs=X).series_list[1].plotattributes[:y][end] ≈ 10.0
     @test plot(sol; idxs=rn.X).series_list[1].plotattributes[:y][end] ≈ 10.0
     @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 false # plot(sol; idxs=[:X, :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)
 end
 
 # Compares programmatic and DSL system with observables.

test/reactionsystem_core/coupled_equation_crn_systems.jl

@@ -293,7 +293,7 @@ end
 # Checks for both differential and algebraic equations.
 # Checks for problems, integrators, and solutions yielded by coupled systems.
 # Checks that metadata, types, and default values are carried through correctly.
-@test_broken let # SDEs are currently broken with structural simplify.
+@test_broken let # SDEs are currently broken with structural simplify (https://github.com/SciML/ModelingToolkit.jl/issues/2614).
     # Creates the model
     @parameters a1 [description="Parameter a1"] a2::Rational{Int64} a3=0.3 a4::Rational{Int64}=4//10 [description="Parameter a4"]
     @parameters b1 [description="Parameter b1"] b2::Int64 b3 = 3 b4::Int64=4 [description="Parameter b4"]
@@ -558,14 +558,12 @@ let
 
     # Checks that SteadyState simulation of the system achieves the correct steady state.
     # Currently broken due to MTK.
-    @test_broken begin
-        ssprob = SteadyStateProblem(coupled_rs, u0, ps; structural_simplify = true)
-        sssol = solve(oprob, DynamicSS(Vern7()); abstol = 1e-8, reltol = 1e-8)
-        @test osol[X][end] ≈ 2.0
-        @test osol[A][end] ≈ 0.0 atol = 1e-8
-        @test osol[D(A)][end] ≈ 0.0 atol = 1e-8
-        @test osol[B][end] ≈ 1.0
-    end
+    ssprob = SteadyStateProblem(coupled_rs, u0, ps; structural_simplify = true)
+    sssol = solve(ssprob, DynamicSS(Vern7()); abstol = 1e-8, reltol = 1e-8)
+    @test sssol[X][end] ≈ 2.0
+    @test sssol[A][end] ≈ 0.0 atol = 1e-8
+    @test sssol[D(A)][end] ≈ 0.0 atol = 1e-8
+    @test sssol[B][end] ≈ 1.0
 
     # Checks that the steady state can be found by solving a nonlinear problem.
     # Here `B => 0.1` has to be provided as well (and it shouldn't for the 2nd order ODE), hence the

test/reactionsystem_core/events.jl

@@ -362,9 +362,9 @@ let
     sol = solve(jprob, SSAStepper(); seed)
 
     # Checks that all `e` parameters have been updated properly.
-    # Note that periodic discrete events are currently broken for jump processes.
+    # Note that periodic discrete events are currently broken for jump processes (and unlikely to be fixed soon due to have events are implemented).
     @test sol.ps[:e1] == 1
-    @test_broken sol.ps[:e2] == 1
+    @test_broken sol.ps[:e2] == 1 # (https://github.com/SciML/JumpProcesses.jl/issues/417)
     @test sol.ps[:e3] == 1
 end
 
@@ -424,21 +424,22 @@ let
     osol_events = solve(oprob_events, Tsit5())
     @test osol == osol_events
 
-    # Checks for SDE simulations.
+    # Checks for SDE simulations (note, non-seed dependant test should be created instead).
     sprob = SDEProblem(rn, u0, tspan, ps)
     sprob_events = SDEProblem(rn_events, u0, tspan, ps)
     ssol = solve(sprob, ImplicitEM(); seed, callback)
     ssol_events = solve(sprob_events, ImplicitEM(); seed)
     @test ssol == ssol_events
 
-    # Checks for Jump simulations.
+    # Checks for Jump simulations. (note, non-seed dependant test should be created instead)
+    # Note that periodic discrete events are currently broken for jump processes (and unlikely to be fixed soon due to have events are implemented).
     callback = CallbackSet(cb_disc_1, cb_disc_2, cb_disc_3)
     dprob = DiscreteProblem(rn, u0, tspan, ps)
     dprob_events = DiscreteProblem(rn_dics_events, u0, tspan, ps)
     jprob = JumpProblem(rn, dprob, Direct(); rng)
     jprob_events = JumpProblem(rn_dics_events, dprob_events, Direct(); rng)
     sol = solve(jprob, SSAStepper(); seed, callback)
-    @test_broken let # Broken due to. Even if fixed, seeding might not work due to events.
+    @test_broken let # (https://github.com/SciML/JumpProcesses.jl/issues/417)
         sol_events = solve(jprob_events, SSAStepper(); seed)
         @test sol == sol_events
     end

test/reactionsystem_core/parameter_type_designation.jl

@@ -88,7 +88,7 @@ let
     nsol = solve(nprob, NewtonRaphson())
 
     # Checks all stored parameters.
-    for mtk_struct in [oprob, sprob, dprob, jprob, nprob, oinit, sinit, jinit, osol, ssol, jsol, nsol]
+    for mtk_struct in [oprob, sprob, dprob, jprob, nprob, oinit, sinit, jinit, ninit, osol, ssol, jsol, nsol]
         # Checks that all parameters have the correct type.
         @test unwrap(mtk_struct.ps[p1]) isa Float64
         @test unwrap(mtk_struct.ps[d1]) isa Float64
@@ -114,8 +114,8 @@ let
         @test unwrap(mtk_struct.ps[d5]) == Float32(1.5)
     end
 
-    # Checks all stored variables.
-    for mtk_struct in [oprob, sprob, dprob, jprob, nprob, oinit, sinit, jinit]
+    # Checks all stored variables (these should always be `Float64`).
+    for mtk_struct in [oprob, sprob, dprob, jprob, nprob, oinit, sinit, jinit, ninit]
         # Checks that all variables have the correct type.
         @test unwrap(mtk_struct[X1]) isa Float64
         @test unwrap(mtk_struct[X2]) isa Float64
@@ -130,10 +130,4 @@ let
         @test unwrap(mtk_struct[X4]) == 0.4
         @test unwrap(mtk_struct[X5]) == 0.5
     end
-
-    # This test started working now, probably due to a MTK fix. Need to look at where to put it
-    # back into the test properly though.
-    @test_broken false 
-    # Indexing currently broken for NonlinearSystem integrators (MTK intend to support this though).
-    @test unwrap(ninit.ps[p1]) isa Float64
 end

test/simulation_and_solving/simulate_SDEs.jl

@@ -224,13 +224,14 @@ let
     @species X1(t) X2(t)
     p_syms = @parameters $(η_stored) k1 k2
 
-    r1 = Reaction(k1,[X1],[X2],[1],[1]; metadata = [:noise_scaling => η_stored])
-    r2 = Reaction(k2,[X2],[X1],[1],[1]; metadata = [:noise_scaling => η_stored])
+    r1 = Reaction(k1, [X1], [X2], [1], [1]; metadata = [:noise_scaling => p_syms[1]])
+    r2 = Reaction(k2, [X2], [X1], [1], [1]; metadata = [:noise_scaling => p_syms[1]])
     @named noise_scaling_network = ReactionSystem([r1, r2], t, [X1, X2], [k1, k2, p_syms[1]])
+    noise_scaling_network = complete(noise_scaling_network)
 
     u0 = [:X1 => 1100.0, :X2 => 3900.0]
     p = [:k1 => 2.0, :k2 => 0.5, :η => 0.0]
-    @test_broken SDEProblem(noise_scaling_network, u0, (0.0, 1000.0), p).ps[:η] == 0.0 # Broken due to SII/MTK stuff.
+    @test SDEProblem(noise_scaling_network, u0, (0.0, 1000.0), p).ps[:η] == 0.0
 end
 
 # Complicated test with many combinations of options.

test/spatial_modelling/lattice_reaction_systems.jl

@@ -280,6 +280,7 @@ end
 # Currently not supported. Won't be until the LatticeReactionSystem internal update is merged.
 
 # Checks that parameter types designated in the non-spatial `ReactionSystem` is handled correctly.
+# Broken lattice tests have local branches that fixes them.
 @test_broken let
     # Declares LatticeReactionSystem with designated parameter types.
     rs = @reaction_network begin

test/upstream/mtk_problem_inputs.jl

@@ -172,6 +172,11 @@ let
     @species X3(t)
     @parameters k3
 
+    # Creates systems (so these are not recreated in each problem call).
+    osys = convert(ODESystem, rn)
+    ssys = convert(SDESystem, rn)
+    nsys = convert(NonlinearSystem, rn)
+
     # Declares valid initial conditions and parameter values
     u0_valid = [X1 => 1, X2 => 2]
     ps_valid = [k1 => 0.5, k2 => 0.1]
@@ -218,25 +223,26 @@ let
     ]
 
     # Loops through all potential parameter sets, checking their inputs yield errors.
+    # Broken tests are due to this issue: https://github.com/SciML/ModelingToolkit.jl/issues/2779
     for ps in [ps_valid; ps_invalid], u0 in [u0_valid; u0s_invalid]
         # Handles problems with/without tspan separately. Special check ensuring that valid inputs passes.
-        for XProblem in [ODEProblem, SDEProblem, DiscreteProblem]
+        for (xsys, XProblem) in zip([osys, ssys, rn], [ODEProblem, SDEProblem, DiscreteProblem])
             if (ps == ps_valid) && (u0 == u0_valid)
-                XProblem(rn, u0, (0.0, 1.0), ps); @test true;
+                XProblem(xsys, u0, (0.0, 1.0), ps); @test true;
             else
                 # Several of these cases do not throw errors (https://github.com/SciML/ModelingToolkit.jl/issues/2624).
                 @test_broken false
                 continue
-                @test_throws Exception XProblem(rn, u0, (0.0, 1.0), ps)
+                @test_throws Exception XProblem(xsys, u0, (0.0, 1.0), ps)
             end
         end
-        for XProblem in [NonlinearProblem, SteadyStateProblem]
+        for (xsys, XProblem) in zip([nsys, osys], [NonlinearProblem, SteadyStateProblem])
             if (ps == ps_valid) && (u0 == u0_valid)
-                XProblem(rn, u0, ps); @test true;
+                XProblem(xsys, u0, ps); @test true;
             else
                 @test_broken false
                 continue
-                @test_throws Exception XProblem(rn, u0, ps)
+                @test_throws Exception XProblem(xsys, u0, ps)
             end
         end
     end

test/upstream/mtk_structure_indexing.jl

@@ -50,7 +50,7 @@ begin
     sint = init(sprob, ImplicitEM(); save_everystep=false)
     jint = init(jprob, SSAStepper())
     nint = init(nprob, NewtonRaphson(); save_everystep=false)
-    @test_broken ssint = init(ssprob, DynamicSS(Tsit5()); save_everystep=false) # https://github.com/SciML/SciMLBase.jl/issues/660
+    @test_broken ssint = init(ssprob, DynamicSS(Tsit5()); save_everystep=false) # https://github.com/SciML/SteadyStateDiffEq.jl/issues/79
     integrators = [oint, sint, jint, nint]
 
     # Creates solutions.
@@ -64,14 +64,12 @@ end
 
 # Tests problem indexing and updating.
 let 
-    @test_broken false # A few cases fails for SteadyStateProblem: https://github.com/SciML/SciMLBase.jl/issues/660
-    @test_broken false # Most cases broken for Ensemble problems: https://github.com/SciML/SciMLBase.jl/issues/661
-    for prob in deepcopy(problems[1:end-1])
+    for prob in [deepcopy(problems); deepcopy(eproblems)]
         # Get u values (including observables).
         @test prob[X] == prob[model.X] == prob[:X] == 4
         @test prob[XY] == prob[model.XY] == prob[:XY] == 9
         @test prob[[XY,Y]] == prob[[model.XY,model.Y]] == prob[[:XY,:Y]] == [9, 5]
-        @test_broken prob[(XY,Y)] == prob[(model.XY,model.Y)] == prob[(:XY,:Y)] == (9, 5)
+        @test_broken prob[(XY,Y)] == prob[(model.XY,model.Y)] == prob[(:XY,:Y)] == (9, 5) # https://github.com/SciML/SciMLBase.jl/issues/709
         @test getu(prob, X)(prob) == getu(prob, model.X)(prob) == getu(prob, :X)(prob) == 4
         @test getu(prob, XY)(prob) == getu(prob, model.XY)(prob) == getu(prob, :XY)(prob) == 9 
         @test getu(prob, [XY,Y])(prob) == getu(prob, [model.XY,model.Y])(prob) == getu(prob, [:XY,:Y])(prob) == [9, 5]  
@@ -117,8 +115,7 @@ end
 
 # Test remake function.
 let 
-    @test_broken false # Currently cannot be run for Ensemble problems: https://github.com/SciML/SciMLBase.jl/issues/661 (as indexing cannot be used to check values).
-    for prob in deepcopy(problems)
+    for prob in [deepcopy(problems); deepcopy(eproblems)]
         # Remake for all u0s.
         rp = remake(prob; u0 = [X => 1, Y => 2])
         @test rp[[X, Y]] == [1, 2]
@@ -156,9 +153,7 @@ end
 # Test integrator indexing.
 let 
     @test_broken false # NOTE: Multiple problems for `nint` (https://github.com/SciML/SciMLBase.jl/issues/662).
-    @test_broken false # NOTE: Multiple problems for `jint` (https://github.com/SciML/SciMLBase.jl/issues/654).
-    @test_broken false # NOTE: Cannot even create a `ssint` (https://github.com/SciML/SciMLBase.jl/issues/660).
-    for int in deepcopy([oint, sint])
+    for int in deepcopy([oint, sint, jint])
         # Get u values.
         @test int[X] == int[model.X] == int[:X] == 4
         @test int[XY] == int[model.XY] == int[:XY] == 9
@@ -208,6 +203,7 @@ let
 end
 
 # Test solve's save_idxs argument.
+# Currently, `save_idxs` is broken with symbolic stuff (https://github.com/SciML/ModelingToolkit.jl/issues/1761).
 let 
     for (prob, solver) in zip(deepcopy([oprob, sprob, jprob]), [Tsit5(), ImplicitEM(), SSAStepper()])
         # Save single variable
@@ -241,10 +237,10 @@ let
         @test getu(sol, (XY,Y))(sol)[1] == getu(sol, (model.XY,model.Y))(sol)[1] == getu(sol, (:XY,:Y))(sol)[1] == (9, 5)       
 
         # Get u values via idxs and functional call.
-        @test osol(0.0; idxs=X) == osol(0.0; idxs=X) == osol(0.0; idxs=X) == 4
-        @test osol(0.0; idxs=XY) == osol(0.0; idxs=XY) == osol(0.0; idxs=XY) == 9
-        @test_broken osol(0.0; idxs=[model.Y,model.XY]) == osol(0.0; idxs=[model.Y,model.XY]) == osol(0.0; idxs=[model.XY,model.X]) == [9, 5]
-        @test_broken osol(0.0; idxs=(:Y,:XY)) == osol(0.0; idxs=(:Y,:XY)) == osol(0.0; idxs=(:XY,:Y)) == (9, 5)
+        @test osol(0.0; idxs=X) == osol(0.0; idxs=model.X) == osol(0.0; idxs=:X) == 4
+        @test osol(0.0; idxs=XY) == osol(0.0; idxs=model.XY) == osol(0.0; idxs=:XY) == 9
+        @test osol(0.0; idxs = [XY,Y]) == osol(0.0; idxs = [model.XY,model.Y]) == osol(0.0; idxs = [:XY,:Y]) == [9, 5]
+        @test_broken osol(0.0; idxs = (XY,Y)) == osol(0.0; idxs = (model.XY,model.Y)) == osol(0.0; idxs = (:XY,:Y)) == (9, 5) # https://github.com/SciML/SciMLBase.jl/issues/711
 
         # Get p values.
         @test sol.ps[kp] == sol.ps[model.kp] == sol.ps[:kp] == 1.0    
@@ -262,11 +258,11 @@ let
             @test sol[X] == sol[model.X] == sol[:X]
             @test sol[XY] == sol[model.XY][1] == sol[:XY]
             @test sol[[XY,Y]] == sol[[model.XY,model.Y]] == sol[[:XY,:Y]]
-            @test_broken sol[(XY,Y)] == sol[(model.XY,model.Y)] == sol[(:XY,:Y)]
+            @test_broken sol[(XY,Y)] == sol[(model.XY,model.Y)] == sol[(:XY,:Y)] # https://github.com/SciML/SciMLBase.jl/issues/710
             @test getu(sol, X)(sol) == getu(sol, model.X)(sol)[1] == getu(sol, :X)(sol)
             @test getu(sol, XY)(sol) == getu(sol, model.XY)(sol)[1] == getu(sol, :XY)(sol)
             @test getu(sol, [XY,Y])(sol) == getu(sol, [model.XY,model.Y])(sol) == getu(sol, [:XY,:Y])(sol)
-            @test_broken getu(sol, (XY,Y))(sol) == getu(sol, (model.XY,model.Y))(sol) == getu(sol, (:XY,:Y))(sol)[1]   
+            @test_broken getu(sol, (XY,Y))(sol) == getu(sol, (model.XY,model.Y))(sol) == getu(sol, (:XY,:Y))(sol)[1] # https://github.com/SciML/SciMLBase.jl/issues/710
 
             # Get p values.
             @test sol.ps[kp] == sol.ps[model.kp] == sol.ps[:kp]
@@ -281,8 +277,7 @@ end
 
 # Tests plotting.
 let 
-    @test_broken false # Currently broken for `ssol` (https://github.com/SciML/SciMLBase.jl/issues/580) 
-    for sol in deepcopy([osol, jsol])
+    for sol in deepcopy([osol, ssol, jsol])
         # Single variable.
         @test length(plot(sol; idxs = X).series_list) == 1
         @test length(plot(sol; idxs = XY).series_list) == 1
@@ -386,4 +381,5 @@ let
     @test jint.cb.condition.ma_jumps.scaled_rates[1] == 16.0
     reset_aggregated_jumps!(jint)
     @test jint.cb.condition.ma_jumps.scaled_rates[1] == 6.0
-end
+end
+