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SciML · Jan 8, 2024 · 8c30f65 · 8c30f65
1 parent 9d6a27a
commit 8c30f65
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Showing 4 changed files with 39 additions and 10 deletions.
diff --git a/src/RationalFunctionFields/RationalFunctionField.jl b/src/RationalFunctionFields/RationalFunctionField.jl
@@ -158,18 +158,30 @@ function field_contains(
     return field_contains(field, fractions_to_dennums(ratfuncs), prob_threshold)
 end
 
-function field_contains(field::RationalFunctionField{T}, polys::Vector{T}, prob_threshold) where {T}
+function field_contains(
+    field::RationalFunctionField{T},
+    polys::Vector{T},
+    prob_threshold,
+) where {T}
     id = one(parent(first(polys)))
     return field_contains(field, [[id, p] for p in polys], prob_threshold)
 end
 
 # ------------------------------------------------------------------------------
 
-function issubfield(F::RationalFunctionField{T}, E::RationalFunctionField{T}, prob_threshold) where {T}
+function issubfield(
+    F::RationalFunctionField{T},
+    E::RationalFunctionField{T},
+    prob_threshold,
+) where {T}
     return all(field_contains(E, F.dennums, prob_threshold))
 end
 
-function fields_equal(F::RationalFunctionField{T}, E::RationalFunctionField{T}, prob_threshold) where {T}
+function fields_equal(
+    F::RationalFunctionField{T},
+    E::RationalFunctionField{T},
+    prob_threshold,
+) where {T}
     new_p = 1 - (1 - prob_threshold) / 2
     return issubfield(F, E, new_p) && issubfield(E, F, new_p)
 end
@@ -558,7 +570,8 @@ Out of $(length(new_fracs)) fractions $(length(new_fracs_unique)) are syntactica
     runtime =
         @elapsed new_fracs = beautifuly_generators(RationalFunctionField(new_fracs_unique))
     @debug "Checking inclusion with probability $prob_threshold"
-    runtime = @elapsed result = issubfield(rff, RationalFunctionField(new_fracs), prob_threshold)
+    runtime =
+        @elapsed result = issubfield(rff, RationalFunctionField(new_fracs), prob_threshold)
     _runtime_logger[:id_inclusion_check] = runtime
     if !result
         @warn "Field membership check failed. Error will follow."

diff --git a/src/StructuralIdentifiability.jl b/src/StructuralIdentifiability.jl
@@ -105,7 +105,11 @@ function assess_identifiability(
     restart_logging(loglevel = loglevel)
     reset_timings()
     with_logger(_si_logger[]) do
-        return _assess_identifiability(ode, funcs_to_check = funcs_to_check, prob_threshold = prob_threshold)
+        return _assess_identifiability(
+            ode,
+            funcs_to_check = funcs_to_check,
+            prob_threshold = prob_threshold,
+        )
     end
 end
 
@@ -214,7 +218,11 @@ 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_, prob_threshold = prob_threshold)
+    result = _assess_identifiability(
+        ode,
+        funcs_to_check = funcs_to_check_,
+        prob_threshold = prob_threshold,
+    )
     nemo2mtk = Dict(funcs_to_check_ .=> funcs_to_check)
     out_dict = OrderedDict(nemo2mtk[param] => result[param] for param in funcs_to_check_)
     return out_dict

diff --git a/src/discrete.jl b/src/discrete.jl
@@ -373,8 +373,12 @@ function _assess_local_identifiability(
     funcs_to_check_ = [eval_at_nemo(x, conversion) for x in funcs_to_check]
     known_ic_ = [eval_at_nemo(x, conversion) for x in known_ic]
 
-    result =
-        _assess_local_identifiability_discrete_aux(dds_aux, funcs_to_check_, known_ic_, prob_threshold)
+    result = _assess_local_identifiability_discrete_aux(
+        dds_aux,
+        funcs_to_check_,
+        known_ic_,
+        prob_threshold,
+    )
     nemo2mtk = Dict(funcs_to_check_ .=> funcs_to_check)
     out_dict = OrderedDict(nemo2mtk[param] => result[param] for param in funcs_to_check_)
     if length(known_ic) > 0

diff --git a/src/parametrizations.jl b/src/parametrizations.jl
@@ -483,8 +483,12 @@ end
 
 function _reparametrize_global(ode::ODE{P}; prob_threshold = 0.99, seed = 42) where {P}
     Random.seed!(seed)
-    id_funcs =
-        find_identifiable_functions(ode, with_states = true, simplify = :strong, prob_threshold = prob_threshold)
+    id_funcs = find_identifiable_functions(
+        ode,
+        with_states = true,
+        simplify = :strong,
+        prob_threshold = prob_threshold,
+    )
     ode_ring = parent(ode)
     @assert base_ring(parent(first(id_funcs))) == ode_ring
     @info "Constructing a new parametrization"