save progress

Author: TorkelE

ext/CatalystBifurcationKitExtension/bifurcation_kit_extension.jl

@@ -4,7 +4,7 @@
 function BK.BifurcationProblem(rs::ReactionSystem, u0_bif, ps, bif_par, args...;
         plot_var = nothing, record_from_solution = BK.record_sol_default, jac = true, u0 = [], kwargs...)
     if !isautonomous(rs)
-        error("Attempting to create a `BifurcationProblem` for a non-autonomous system (e.g. where some rate depend on $(rs.iv)). This is not possible.")
+        error("Attempting to create a `BifurcationProblem` for a non-autonomous system (e.g. where some rate depend on $(get_iv(rs))). This is not possible.")
     end
 
     # Converts symbols to symbolics.

ext/CatalystHomotopyContinuationExtension/homotopy_continuation_extension.jl

@@ -38,7 +38,7 @@ Notes:
 function Catalyst.hc_steady_states(rs::ReactionSystem, ps; filter_negative = true,
         neg_thres = -1e-20, u0 = [], kwargs...)
     if !isautonomous(rs)
-        error("Attempting to compute steady state for a non-autonomous system (e.g. where some rate depend on $(rs.iv)). This is not possible.")
+        error("Attempting to compute steady state for a non-autonomous system (e.g. where some rate depend on $(get_iv(rs))). This is not possible.")
     end
     ss_poly = steady_state_polynomial(rs, ps, u0)
     sols = HC.real_solutions(HC.solve(ss_poly; kwargs...))

src/reactionsystem_conversions.jl

@@ -520,7 +520,7 @@ function Base.convert(::Type{<:NonlinearSystem}, rs::ReactionSystem; name = name
     iscomplete(rs) || error(COMPLETENESS_ERROR)
     spatial_convert_err(rs::ReactionSystem, NonlinearSystem)
     if !isautonomous(rs)
-        error("Attempting to convert a non-autonomous `ReactionSystem` (e.g. where some rate depend on $(rs.iv)) to a `NonlinearSystem`. This is not possible. if you are intending to compute system steady states, consider creating and solving a `SteadyStateProblem.")
+        error("Attempting to convert a non-autonomous `ReactionSystem` (e.g. where some rate depend on $(get_iv(rs))) to a `NonlinearSystem`. This is not possible. if you are intending to compute system steady states, consider creating and solving a `SteadyStateProblem.")
     end
 
     # Generates system equations.

src/reactionsystem_serialisation/serialise_reactionsystem.jl

@@ -147,13 +147,13 @@ function make_reaction_system_call(
     has_connection_type && (@string_append! reaction_system_string ", connection_type")
 
     # Potentially appends a combinatoric_ratelaws statement.
-    if !Symbolics.unwrap(rs.combinatoric_ratelaws)
+    if !Symbolics.unwrap(combinatoric_ratelaws(rs))
         @string_append! reaction_system_string ", combinatoric_ratelaws = false"
     end
 
     # Potentially appends `ReactionSystem` metadata value(s). Weird composite types are not supported.
-    if !isnothing(rs.metadata)
-        @string_append! reaction_system_string ", metadata = $(x_2_string(rs.metadata))"
+    if !isnothing(MT.get_metadata(rs))
+        @string_append! reaction_system_string ", metadata = $(x_2_string(MT.get_metadata(rs)))"
     end
 
     # Finalises the call. Appends potential annotation. If the system is complete, add a call for this. 

src/steady_state_stability.jl

@@ -48,7 +48,7 @@ function steady_state_stability(u::Vector, rs::ReactionSystem, ps;
         tol = 10 * sqrt(eps(ss_val_type(u))), ss_jac = steady_state_jac(rs; u0 = u))
     # Warning checks.
     if !isautonomous(rs)
-        error("Attempting to compute stability for a non-autonomous system (e.g. where some rate depend on $(rs.iv)). This is not possible.")
+        error("Attempting to compute stability for a non-autonomous system (e.g. where some rate depend on $(get_iv(rs))). This is not possible.")
     end
 
     # If `u` is a vector of values, we convert it to a map. Also, if there are conservation laws,

test/dsl/dsl_options.jl

@@ -574,8 +574,8 @@ let
         end
     end
     V,W = getfield.(observed(rn), :lhs)
-    @test isequal(arguments(ModelingToolkit.unwrap(V)), Any[rn.iv, rn.sivs[1], rn.sivs[2]])
-    @test isequal(arguments(ModelingToolkit.unwrap(W)), Any[rn.iv, rn.sivs[2]])
+    @test isequal(arguments(ModelingToolkit.unwrap(V)), Any[Catalyst.get_iv(rs), Catalyst.get_sivs(rn)[1], Catalyst.get_sivs(rn)[2]])
+    @test isequal(arguments(ModelingToolkit.unwrap(W)), Any[Catalyst.get_iv(rs), Catalyst.get_sivs(rn)[2]])
 end
 
 # Checks that metadata is written properly.

test/extensions/structural_identifiability.jl

@@ -29,7 +29,7 @@ let
               :d => 0.5 + rand(rng))
 
         # Computes stability using various jacobian options.
-        sss = hc_steady_states(rn, ps)
+        sss = hc_steady_states(rn, ps; show_progress=false)
         stabs_1 = [steady_state_stability(ss, rn, ps) for ss in sss]
         stabs_2 = [steady_state_stability(ss, rn, ps; ss_jac = ss_jac) for ss in sss]
 
@@ -71,7 +71,7 @@ let
     ps_3 = [rn.k1 => 8.0, rn.k2 => 2.0, rn.k3 => 1.0, rn.k4 => 1.5, rn.kD1 => 0.5, rn.kD2 => 4.0]
 
     # Computes stability using various input forms, and checks that the output is correct. 
-    sss = hc_steady_states(rn, ps_1; u0 = u0_1)
+    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]
         stab_1 =  [steady_state_stability(ss, rn, ps) for ss in sss]
         ss_jac = steady_state_jac(rn; u0 = u0)

test/miscellaneous_tests/stability_computation.jl

@@ -64,7 +64,7 @@ let
     for p in p_alts
         oprob = ODEProblem(rs, u0, (0.0, 1000.0), p; abstol = 1e-10, reltol = 1e-10)
         sol = solve(oprob, Tsit5())
-        @test all(sol[end] .≈ 1.0)
+        @test all(sol.u[end] .≈ 1.0)
     end
 end