SI updates

Author: TorkelE

ext/CatalystStructuralIdentifiabilityExtension.jl

@@ -2,6 +2,7 @@ module CatalystStructuralIdentifiabilityExtension
 
 # Fetch packages.
 using Catalyst
+import DataStructures.OrderedDict
 import StructuralIdentifiability as SI
 
 # Creates and exports hc_steady_states function.

ext/CatalystStructuralIdentifiabilityExtension/structural_identifiability_extension.jl

@@ -189,8 +189,8 @@ function make_measured_quantities(
         rs::ReactionSystem, measured_quantities::Vector{T}, known_p::Vector{S},
         conseqs; ignore_no_measured_warn = false) where {T, S}
     # Warning if the user didn't give any measured quantities.
-    if ignore_no_measured_warn || isempty(measured_quantities)
-        @warn "No measured quantity provided to the `measured_quantities` argument, any further identifiability analysis will likely fail. You can disable this warning by setting `ignore_no_measured_warn=true`."
+    if !ignore_no_measured_warn && isempty(measured_quantities)
+        @warn "No measured quantity provided to the `measured_quantities` argument, any further identifiability analysis will likely fail. You can disable this warning by setting `ignore_no_measured_warn = true`."
     end
 
     # Appends the known parameters to the measured_quantities vector. Converts any Symbols to symbolics.
@@ -220,9 +220,9 @@ end
 # Sorts the output according to their input order (defaults to the `[unknowns; parameters]` order).
 function make_output(out, funcs_to_check, conseqs)
     funcs_to_check = vector_subs(funcs_to_check, conseqs)
-    out = Dict(zip(vector_subs(keys(out), conseqs), values(out)))
+    out = OrderedDict(zip(vector_subs(keys(out), conseqs), values(out)))
     sortdict = Dict(ftc => i for (i, ftc) in enumerate(funcs_to_check))
-    return sort(out; by = x -> sortdict[x])
+    return sort!(out; by = x -> sortdict[x])
 end
 
 # For a vector of expressions and a conservation law, substitutes the law into every equation.

test/extensions/structural_identifiability.jl

@@ -178,13 +178,13 @@ let
     end
     @unpack M, E, P, pₑ, pₚ, pₘ = goodwind_oscillator_catalyst
     si_catalyst_ode = make_si_ode(goodwind_oscillator_catalyst; measured_quantities = [:M])
-    si_catalyst_ode = make_si_ode(goodwind_oscillator_catalyst; known_p = [:pₑ])
+    si_catalyst_ode = make_si_ode(goodwind_oscillator_catalyst; known_p = [:pₑ], ignore_no_measured_warn = true)
     si_catalyst_ode = make_si_ode(goodwind_oscillator_catalyst; measured_quantities = [:M], known_p = [:pₑ])
     si_catalyst_ode = make_si_ode(goodwind_oscillator_catalyst; measured_quantities = [:M, :E], known_p = [:pₑ])
     si_catalyst_ode = make_si_ode(goodwind_oscillator_catalyst; measured_quantities = [:M], known_p = [:pₑ, :pₚ])
     si_catalyst_ode = make_si_ode(goodwind_oscillator_catalyst; measured_quantities = [:M, :E], known_p = [:pₑ, :pₚ])
     si_catalyst_ode = make_si_ode(goodwind_oscillator_catalyst; measured_quantities = [M])
-    si_catalyst_ode = make_si_ode(goodwind_oscillator_catalyst; known_p = [pₑ])
+    si_catalyst_ode = make_si_ode(goodwind_oscillator_catalyst; known_p = [pₑ], ignore_no_measured_warn = true)
     si_catalyst_ode = make_si_ode(goodwind_oscillator_catalyst; measured_quantities = [M], known_p = [pₑ])
     si_catalyst_ode = make_si_ode(goodwind_oscillator_catalyst; measured_quantities = [M, E], known_p = [pₑ])
     si_catalyst_ode = make_si_ode(goodwind_oscillator_catalyst; measured_quantities = [M], known_p = [pₑ, pₚ])
@@ -196,7 +196,7 @@ let
     # Tests using model.component style (have to make system complete first).
     gw_osc_complt = complete(goodwind_oscillator_catalyst)
     @test make_si_ode(gw_osc_complt; measured_quantities = [gw_osc_complt.M]) isa ODE
-    @test make_si_ode(gw_osc_complt; known_p = [gw_osc_complt.pₑ]) isa ODE
+    @test make_si_ode(gw_osc_complt; known_p = [gw_osc_complt.pₑ], ignore_no_measured_warn = true) isa ODE
     @test make_si_ode(gw_osc_complt; measured_quantities = [gw_osc_complt.M], known_p = [gw_osc_complt.pₑ]) isa ODE
     @test make_si_ode(gw_osc_complt; measured_quantities = [gw_osc_complt.M, gw_osc_complt.E], known_p = [gw_osc_complt.pₑ]) isa ODE
     @test make_si_ode(gw_osc_complt; measured_quantities = [gw_osc_complt.M], known_p = [gw_osc_complt.pₑ, gw_osc_complt.pₚ]) isa ODE
@@ -288,7 +288,7 @@ let
         b, A0 --> 2A2
         c, A0 --> A1 + A2
     end
-    id_report = assess_identifiability(rs, measured_quantities = [:A0, :A1, :A2])
+    id_report = assess_identifiability(rs; measured_quantities = [:A0, :A1, :A2], loglevel)
     @test sym_dict(id_report) == Dict(
         :A0 => :globally,
         :A1 => :globally,
@@ -358,6 +358,6 @@ let
 
     # Computes bifurcation diagram.
     @test_throws Exception assess_identifiability(incomplete_network; measured_quantities, loglevel)
-    @test_throws Exception assess_local_identifiability(incomplete_network; measured_quantities, loglevels)
+    @test_throws Exception assess_local_identifiability(incomplete_network; measured_quantities, loglevel)
     @test_throws Exception find_identifiable_functions(incomplete_network; measured_quantities, loglevel)
 end