format

benchmarking/IdentifiableFunctions/experiments.jl

@@ -995,8 +995,8 @@ begin
 end
 
 begin
-    StructuralIdentifiability.find_identifiable_functions(Pivastatin);
-    StructuralIdentifiability.print_timings_table();
+    StructuralIdentifiability.find_identifiable_functions(Pivastatin)
+    StructuralIdentifiability.print_timings_table()
 end
 
 fracs = StructuralIdentifiability.dennums_to_fractions(dennums);

src/ODE.jl

@@ -460,13 +460,13 @@ macro ODEmodel(ex::Expr...)
     end
 
     logging_exprs = [
-       # :(with_logger(StructuralIdentifiability._si_logger[]) do),
+        # :(with_logger(StructuralIdentifiability._si_logger[]) do),
         :(@info "Summary of the model:"),
         :(@info "State variables: " * $(join(map(string, collect(x_vars)), ", "))),
         :(@info "Parameters: " * $(join(map(string, collect(params)), ", "))),
         :(@info "Inputs: " * $(join(map(string, collect(u_vars)), ", "))),
         :(@info "Outputs: " * $(join(map(string, collect(y_vars)), ", "))),
-       # :(end),
+        # :(end),
     ]
     # creating the ode object
     ode_expr = :(StructuralIdentifiability.ODE{StructuralIdentifiability.Nemo.fmpq_mpoly}(

src/StructuralIdentifiability.jl

@@ -96,10 +96,7 @@ function assess_identifiability(
     restart_logging(loglevel = loglevel)
     reset_timings()
     with_logger(_si_logger[]) do
-        return _assess_identifiability(ode,
-            funcs_to_check = funcs_to_check,
-            p = p
-        )
+        return _assess_identifiability(ode, funcs_to_check = funcs_to_check, p = p)
     end
 end
 
@@ -108,7 +105,6 @@ function _assess_identifiability(
     funcs_to_check = Vector(),
     p::Float64 = 0.99,
 ) where {P <: MPolyElem{fmpq}}
-
     p_glob = 1 - (1 - p) * 0.9
     p_loc = 1 - (1 - p) * 0.1
 
@@ -182,7 +178,8 @@ function assess_identifiability(
 )
     restart_logging(loglevel = loglevel)
     with_logger(_si_logger[]) do
-        return _assess_identifiability(ode,
+        return _assess_identifiability(
+            ode,
             measured_quantities = measured_quantities,
             funcs_to_check = funcs_to_check,
             p = p,
@@ -207,11 +204,7 @@ function _assess_identifiability(
     end
     funcs_to_check_ = [eval_at_nemo(each, conversion) for each in funcs_to_check]
 
-    result = _assess_identifiability(
-        ode,
-        funcs_to_check = funcs_to_check_,
-        p = p,
-    )
+    result = _assess_identifiability(ode, funcs_to_check = funcs_to_check_, p = p)
     nemo2mtk = Dict(funcs_to_check_ .=> funcs_to_check)
     out_dict = Dict(nemo2mtk[param] => result[param] for param in funcs_to_check_)
     return out_dict

src/identifiable_functions.jl

@@ -54,7 +54,8 @@ function find_identifiable_functions(
     restart_logging(loglevel = loglevel)
     reset_timings()
     with_logger(_si_logger[]) do
-        return _find_identifiable_functions(ode,
+        return _find_identifiable_functions(
+            ode,
             p = p,
             seed = seed,
             with_states = with_states,
@@ -71,7 +72,7 @@ function _find_identifiable_functions(
     with_states = false,
     simplify = :standard,
     rational_interpolator = :VanDerHoevenLecerf,
-) where {T <: MPolyElem{fmpq}} 
+) where {T <: MPolyElem{fmpq}}
     Random.seed!(seed)
     @assert simplify in (:standard, :weak, :strong, :absent)
     runtime_start = time_ns()
@@ -112,7 +113,7 @@ function _find_identifiable_functions(
     _runtime_logger[:id_total] = (time_ns() - runtime_start) / 1e9
     _runtime_logger[:are_id_funcs_polynomial] = all(isone ∘ denominator, id_funcs_fracs)
     @info "The search for identifiable functions concluded in $(_runtime_logger[:id_total]) seconds"
-    
+
     return id_funcs_fracs
 end
 
@@ -166,7 +167,8 @@ function find_identifiable_functions(
     restart_logging(loglevel = loglevel)
     reset_timings()
     with_logger(_si_logger[]) do
-        return _find_identifiable_functions(ode,
+        return _find_identifiable_functions(
+            ode,
             measured_quantities = measured_quantities,
             p = p,
             seed = seed,

src/lincomp.jl

@@ -29,7 +29,7 @@ function linear_compartment_model(
     graph::Vector{Vector{Int}},
     inputs::Vector{Int},
     outputs::Vector{Int},
-    leaks::Vector{Int}
+    leaks::Vector{Int},
 )
     n = length(graph)
     x_vars_names = ["x$i" for i in 1:n]

src/local_identifiability.jl

@@ -173,7 +173,8 @@ function assess_local_identifiability(
 )
     restart_logging(loglevel = loglevel)
     with_logger(_si_logger[]) do
-        return _assess_local_identifiability(ode,
+        return _assess_local_identifiability(
+            ode,
             measured_quantities = measured_quantities,
             funcs_to_check = funcs_to_check,
             p = p,
@@ -260,7 +261,8 @@ function assess_local_identifiability(
     restart_logging(loglevel = loglevel)
     reset_timings()
     with_logger(_si_logger[]) do
-        return _assess_local_identifiability(ode,
+        return _assess_local_identifiability(
+            ode,
             funcs_to_check = funcs_to_check,
             p = p,
             type = type,
@@ -276,7 +278,6 @@ function _assess_local_identifiability(
     type = :SE,
     trbasis = nothing,
 ) where {P <: MPolyElem{Nemo.fmpq}}
-
     if isempty(funcs_to_check)
         funcs_to_check = ode.parameters
         if type == :SE