try upper bounding SciMLBase

Author: isaacsas

Project.toml

@@ -62,7 +62,7 @@ Parameters = "0.12"
 Reexport = "0.2, 1.0"
 Requires = "1.0"
 RuntimeGeneratedFunctions = "0.5.12"
-SciMLBase = "2.46"
+SciMLBase = "<=2.57.1"
 Setfield = "1"
 # StructuralIdentifiability = "0.5.8"
 SymbolicUtils = "2.1.2, 3.3.0"

src/steady_state_stability.jl

@@ -60,9 +60,6 @@ function steady_state_stability(u::Vector, rs::ReactionSystem, ps;
 
     # Generates the Jacobian at the steady state (technically, `ss_jac` is an `ODEProblem` with dummy values for `u0` and `p`).
     J = zeros(length(u), length(u))
-    @show u
-    @show ps
-    @show parameters(ss_jac)
     ss_jac = remake(ss_jac; u0 = u, p = ps)
     ss_jac.f.jac(J, ss_jac.u0, ss_jac.p, Inf)
 

test/extensions/stability_computation.jl

@@ -73,7 +73,6 @@ let
     # Computes stability using various input forms, and checks that the output is correct. 
     sss = hc_steady_states(rn, ps_1; u0 = u0_1, show_progress = false)
     for u0 in [u0_1, u0_2, u0_3, u0_4], ps in [ps_1, ps_2, ps_3]
-        @show eltype(first(u0)),eltype(first(ps))
         stab_1 =  [steady_state_stability(ss, rn, ps) for ss in sss]
         ss_jac = steady_state_jac(rn; u0 = u0)
         stab_2 =  [steady_state_stability(ss, rn, ps; ss_jac = ss_jac) for ss in sss]

test/upstream/mtk_problem_inputs.jl

@@ -64,35 +64,35 @@ begin
         # Vectors not providing default values.
         [kp => 1.0, kd => 0.1, k1 => 0.25, Z0 => 10],
         [model.kp => 1.0, model.kd => 0.1, model.k1 => 0.25, model.Z0 => 10],
-        #[:kp => 1.0, :kd => 0.1, :k1 => 0.25, :Z0 => 10],
+        [:kp => 1.0, :kd => 0.1, :k1 => 0.25, :Z0 => 10],
         # Vectors providing default values.
         [kp => 1.0, kd => 0.1, k1 => 0.25, k2 => 0.5, Z0 => 10],
         [model.kp => 1.0, model.kd => 0.1, model.k1 => 0.25, model.k2 => 0.5, model.Z0 => 10],
-        #[:kp => 1.0, :kd => 0.1, :k1 => 0.25, :k2 => 0.5, :Z0 => 10],
+        [:kp => 1.0, :kd => 0.1, :k1 => 0.25, :k2 => 0.5, :Z0 => 10],
         # Static vectors not providing default values.
         SA[kp => 1.0, kd => 0.1, k1 => 0.25, Z0 => 10],
         SA[model.kp => 1.0, model.kd => 0.1, model.k1 => 0.25, model.Z0 => 10],
-        #SA[:kp => 1.0, :kd => 0.1, :k1 => 0.25, :Z0 => 10],
+        SA[:kp => 1.0, :kd => 0.1, :k1 => 0.25, :Z0 => 10],
         # Static vectors providing default values.
         SA[kp => 1.0, kd => 0.1, k1 => 0.25, k2 => 0.5, Z0 => 10],
         SA[model.kp => 1.0, model.kd => 0.1, model.k1 => 0.25, model.k2 => 0.5, model.Z0 => 10],
-        #SA[:kp => 1.0, :kd => 0.1, :k1 => 0.25, :k2 => 0.5, :Z0 => 10],
+        SA[:kp => 1.0, :kd => 0.1, :k1 => 0.25, :k2 => 0.5, :Z0 => 10],
         # Dicts not providing default values.
         Dict([kp => 1.0, kd => 0.1, k1 => 0.25, Z0 => 10]),
         Dict([model.kp => 1.0, model.kd => 0.1, model.k1 => 0.25, model.Z0 => 10]),
-        #Dict([:kp => 1.0, :kd => 0.1, :k1 => 0.25, :Z0 => 10]),
+        Dict([:kp => 1.0, :kd => 0.1, :k1 => 0.25, :Z0 => 10]),
         # Dicts providing default values.
         Dict([kp => 1.0, kd => 0.1, k1 => 0.25, k2 => 0.5, Z0 => 10]),
         Dict([model.kp => 1.0, model.kd => 0.1, model.k1 => 0.25, model.k2 => 0.5, model.Z0 => 10]),
-        #Dict([:kp => 1.0, :kd => 0.1, :k1 => 0.25, :k2 => 0.5, :Z0 => 10]),
+        Dict([:kp => 1.0, :kd => 0.1, :k1 => 0.25, :k2 => 0.5, :Z0 => 10]),
         # Tuples not providing default values.
         (kp => 1.0, kd => 0.1, k1 => 0.25, Z0 => 10),
         (model.kp => 1.0, model.kd => 0.1, model.k1 => 0.25, model.Z0 => 10),
-        #(:kp => 1.0, :kd => 0.1, :k1 => 0.25, :Z0 => 10),
+        (:kp => 1.0, :kd => 0.1, :k1 => 0.25, :Z0 => 10),
         # Tuples providing default values.
         (kp => 1.0, kd => 0.1, k1 => 0.25, k2 => 0.5, Z0 => 10),
         (model.kp => 1.0, model.kd => 0.1, model.k1 => 0.25, model.k2 => 0.5, model.Z0 => 10),
-        #(:kp => 1.0, :kd => 0.1, :k1 => 0.25, :k2 => 0.5, :Z0 => 10),
+        (:kp => 1.0, :kd => 0.1, :k1 => 0.25, :k2 => 0.5, :Z0 => 10),
     ]
 end