formatting

src/ODE.jl

@@ -461,10 +461,18 @@ macro ODEmodel(ex::Expr...)
 
     logging_exprs = [
         :(StructuralIdentifiability.info_si("Summary of the model:")),
-        :(StructuralIdentifiability.info_si("State variables: " * $(join(map(string, collect(x_vars)), ", ")))),
-        :(StructuralIdentifiability.info_si("Parameters: " * $(join(map(string, collect(params)), ", ")))),
-        :(StructuralIdentifiability.info_si("Inputs: " * $(join(map(string, collect(u_vars)), ", ")))),
-        :(StructuralIdentifiability.info_si("Outputs: " * $(join(map(string, collect(y_vars)), ", ")))),
+        :(StructuralIdentifiability.info_si(
+            "State variables: " * $(join(map(string, collect(x_vars)), ", ")),
+        )),
+        :(StructuralIdentifiability.info_si(
+            "Parameters: " * $(join(map(string, collect(params)), ", ")),
+        )),
+        :(StructuralIdentifiability.info_si(
+            "Inputs: " * $(join(map(string, collect(u_vars)), ", ")),
+        )),
+        :(StructuralIdentifiability.info_si(
+            "Outputs: " * $(join(map(string, collect(y_vars)), ", ")),
+        )),
     ]
     # creating the ode object
     ode_expr = :(StructuralIdentifiability.ODE{StructuralIdentifiability.Nemo.fmpq_mpoly}(

src/RationalFunctionFields/IdealMQS.jl

@@ -86,7 +86,9 @@ mutable struct IdealMQS{T} <: AbstractBlackboxIdeal
             lcm,
             1:length(funcs_den_nums),
         )
-        debug_si("Rational functions common denominator is of degree $(total_degree(den_lcm)) and of length $(length(den_lcm))")
+        debug_si(
+            "Rational functions common denominator is of degree $(total_degree(den_lcm)) and of length $(length(den_lcm))",
+        )
         is_constant(den_lcm) &&
             (debug_si("Common denominator of the field generators is constant"))
         existing_varnames = map(String, symbols(ring))

src/RationalFunctionFields/RationalFunctionField.jl

@@ -255,7 +255,9 @@ function beautifuly_generators(
                 end
             end
         end
-        debug_si("Out of $(length(fracs)) simplified generators there are $(length(non_redundant)) non redundant")
+        debug_si(
+            "Out of $(length(fracs)) simplified generators there are $(length(non_redundant)) non redundant",
+        )
         fracs = fracs[non_redundant]
     end
     sort!(fracs, lt = rational_function_cmp)
@@ -356,7 +358,9 @@ function groebner_basis_coeffs(
         debug_si("Inclusion checked in $(runtime) seconds. Result: $two_sided_inclusion")
         current_degrees = current_degrees .* 2
     end
-    debug_si("The coefficients of the Groebner basis are presented by $(length(fracs)) rational functions")
+    debug_si(
+        "The coefficients of the Groebner basis are presented by $(length(fracs)) rational functions",
+    )
     new_rff.mqs.cached_groebner_bases[ordering, up_to_degree] = gb
     rff.mqs.cached_groebner_bases[ordering, up_to_degree] = gb
     return new_rff
@@ -382,7 +386,9 @@ function generating_sets_fan(
     time_start = time_ns()
     vars = gens(parent(rff.mqs))
     nbases = length(vars)
-    info_si("Computing $nbases Groebner bases for degrees $up_to_degree for block orderings")
+    info_si(
+        "Computing $nbases Groebner bases for degrees $up_to_degree for block orderings",
+    )
     ordering_to_generators = Dict()
     if code == 0
         return ordering_to_generators
@@ -552,9 +558,11 @@ function simplified_generating_set(
         append!(new_fracs, generators)
     end
     new_fracs_unique = unique(new_fracs)
-    debug_si("""
-    Final cleaning and simplification of generators. 
-    Out of $(length(new_fracs)) fractions $(length(new_fracs_unique)) are syntactically unique.""")
+    debug_si(
+        """
+Final cleaning and simplification of generators. 
+Out of $(length(new_fracs)) fractions $(length(new_fracs_unique)) are syntactically unique.""",
+    )
     runtime =
         @elapsed new_fracs = beautifuly_generators(RationalFunctionField(new_fracs_unique))
     debug_si("Checking inclusion with probability $p")
@@ -564,8 +572,12 @@ function simplified_generating_set(
         warn_si("Field membership check failed. Error will follow.")
         throw("The new subfield generators are not correct.")
     end
-    info_si("Inclusion checked with probability $p in $(_runtime_logger[:id_inclusion_check]) seconds")
-    debug_si("Out of $(length(rff.mqs.nums_qq)) initial generators there are $(length(new_fracs)) indepdendent")
+    info_si(
+        "Inclusion checked with probability $p in $(_runtime_logger[:id_inclusion_check]) seconds",
+    )
+    debug_si(
+        "Out of $(length(rff.mqs.nums_qq)) initial generators there are $(length(new_fracs)) indepdendent",
+    )
     ranking = generating_set_rank(new_fracs)
     _runtime_logger[:id_ranking] = ranking
     debug_si("The ranking of the new set of generators is $ranking")

src/RationalFunctionFields/normalforms.jl

@@ -365,9 +365,11 @@ function linear_relations_between_normal_forms(
                 push!(zeroed_relations_inds, i)
             end
         end
-        debug_si("""
-        Relations in the previous intersection: $(length(complete_intersection_relations_ff))
-        Vanished at the current point: $(length(zeroed_relations_inds))""")
+        debug_si(
+            """
+   Relations in the previous intersection: $(length(complete_intersection_relations_ff))
+   Vanished at the current point: $(length(zeroed_relations_inds))""",
+        )
         non_zeroed_relations_inds =
             setdiff(collect(1:n_relations_ff), zeroed_relations_inds)
         zeroed_relations_from_complete_intersection =
@@ -383,7 +385,9 @@ function linear_relations_between_normal_forms(
             non_zeroed_relations_from_complete_intersection,
             zeroed_relations_from_complete_intersection,
         )
-        debug_si("There are $(length(complete_intersection_relations_ff)) relations in the intersection")
+        debug_si(
+            "There are $(length(complete_intersection_relations_ff)) relations in the intersection",
+        )
         m_relations_ff = length(complete_intersection_relations_ff)
         if n_relations_ff == m_relations_ff || isempty(complete_intersection_relations_ff)
             break
@@ -412,6 +416,8 @@ function linear_relations_between_normal_forms(
         )
         relations_qq[i] = relation_qq_param // one(relation_qq_param)
     end
-    info_si("Used $iters specializations in $((time_ns() - time_start) / 1e9) seconds, found $(length(complete_intersection_relations_ff)) relations")
+    info_si(
+        "Used $iters specializations in $((time_ns() - time_start) / 1e9) seconds, found $(length(complete_intersection_relations_ff)) relations",
+    )
     relations_qq
 end

src/StructuralIdentifiability.jl

@@ -176,7 +176,12 @@ 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, loglevel = loglevel)
+    result = assess_identifiability(
+        ode,
+        funcs_to_check = funcs_to_check_,
+        p = p,
+        loglevel = loglevel,
+    )
     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/discrete.jl

@@ -314,7 +314,9 @@ function assess_local_identifiability(
 )
     if length(measured_quantities) == 0
         if any(ModelingToolkit.isoutput(eq.lhs) for eq in ModelingToolkit.equations(dds))
-            info_si("Measured quantities are not provided, trying to find the outputs in input dynamical system.")
+            info_si(
+                "Measured quantities are not provided, trying to find the outputs in input dynamical system.",
+            )
             measured_quantities = filter(
                 eq -> (ModelingToolkit.isoutput(eq.lhs)),
                 ModelingToolkit.equations(dds),
@@ -342,7 +344,9 @@ function assess_local_identifiability(
     nemo2mtk = Dict(funcs_to_check_ .=> funcs_to_check)
     out_dict = Dict(nemo2mtk[param] => result[param] for param in funcs_to_check_)
     if length(known_ic) > 0
-        warn_si("Since known initial conditions were provided, identifiability of states (e.g., `x(t)`) is at t = 0 only !")
+        warn_si(
+            "Since known initial conditions were provided, identifiability of states (e.g., `x(t)`) is at t = 0 only !",
+        )
     end
     return out_dict
 end

src/global_identifiability.jl

@@ -130,7 +130,9 @@ function initial_identifiable_functions(
         _runtime_logger[:rank_time] = rank_times
 
         if any([dim != rk + 1 for (dim, rk) in zip(dims, wranks)])
-            warn_si("One of the Wronskians has corank greater than one, so the results of the algorithm will be valid only for multiexperiment identifiability. If you still would like to assess single-experiment identifiability, we recommend using SIAN (https://github.com/alexeyovchinnikov/SIAN-Julia) or transforming all the parameters to states with zero derivative")
+            warn_si(
+                "One of the Wronskians has corank greater than one, so the results of the algorithm will be valid only for multiexperiment identifiability. If you still would like to assess single-experiment identifiability, we recommend using SIAN (https://github.com/alexeyovchinnikov/SIAN-Julia) or transforming all the parameters to states with zero derivative",
+            )
         end
     end
 
@@ -142,7 +144,9 @@ function initial_identifiable_functions(
     )
 
     if with_states && !isempty(ode.parameters)
-        debug_si("Generators of identifiable functions involve states, the parameter-only part is getting simplified")
+        debug_si(
+            "Generators of identifiable functions involve states, the parameter-only part is getting simplified",
+        )
         # NOTE: switching to a ring without states for a moment
         param_ring, _ = PolynomialRing(
             base_ring(bring),
@@ -305,7 +309,9 @@ function assess_global_identifiability(
 ) where {P <: MPolyElem{fmpq}}
     submodels = find_submodels(ode)
     if length(submodels) > 0
-        info_si("Note: the input model has nontrivial submodels. If the computation for the full model will be too heavy, you may want to try to first analyze one of the submodels. They can be produced using function `find_submodels`")
+        info_si(
+            "Note: the input model has nontrivial submodels. If the computation for the full model will be too heavy, you may want to try to first analyze one of the submodels. They can be produced using function `find_submodels`",
+        )
     end
 
     result = check_identifiability(

src/identifiable_functions.jl

@@ -51,7 +51,7 @@ function find_identifiable_functions(
     rational_interpolator = :VanDerHoevenLecerf,
     loglevel = Logging.Info,
 ) where {T <: MPolyElem{fmpq}}
-    restart_logging(loglevel=loglevel) 
+    restart_logging(loglevel = loglevel)
     Random.seed!(seed)
     @assert simplify in (:standard, :weak, :strong, :absent)
     runtime_start = time_ns()
@@ -91,7 +91,9 @@ function find_identifiable_functions(
     id_funcs_fracs = [parent_ring_change(f, parent(ode)) for f in id_funcs_fracs]
     _runtime_logger[:id_total] = (time_ns() - runtime_start) / 1e9
     _runtime_logger[:are_id_funcs_polynomial] = all(isone ∘ denominator, id_funcs_fracs)
-    info_si("The search for identifiable functions concluded in $(_runtime_logger[:id_total]) seconds")
+    info_si(
+        "The search for identifiable functions concluded in $(_runtime_logger[:id_total]) seconds",
+    )
     return id_funcs_fracs
 end
 

src/io_equation.jl

@@ -215,7 +215,9 @@ function find_ioprojections(
                     A, B = simplify_frac(A, B)
                     if isempty(filter!(v -> (v in keys(x_equations)), vars(A))) && (B != 0) # && (length(coeffs(A))==1)
                         # variable change x_i' --> x_i' - (B/A)', x_i --> x_i - B/A
-                        debug_si("\t Applying variable change: $(x) --> $(x) - ( $B )/( $A )")
+                        debug_si(
+                            "\t Applying variable change: $(x) --> $(x) - ( $B )/( $A )",
+                        )
                         dB = diff_poly(B, derivation)
                         dA = diff_poly(A, derivation)
                         numer_d, denom_d = simplify_frac(A * dB - dA * B, A * A)
@@ -339,7 +341,7 @@ Output:
 function find_ioequations(
     ode::ODE{P};
     var_change_policy = :default,
-    loglevel = Logging.Info
+    loglevel = Logging.Info,
 ) where {P <: MPolyElem{<:FieldElem}}
     # Setting the var_change policy
     if (var_change_policy == :yes) ||
@@ -358,13 +360,17 @@ function find_ioequations(
 
     debug_si("Check whether the original projections are enough")
     if length(io_projections) == 1 || check_primality(io_projections)
-        debug_si("The projections generate an ideal with a single components of highest dimension, returning")
+        debug_si(
+            "The projections generate an ideal with a single components of highest dimension, returning",
+        )
         return io_projections
     end
 
     sampling_range = 5
     while true
-        debug_si("There are several components of the highest dimension, trying to isolate one")
+        debug_si(
+            "There are several components of the highest dimension, trying to isolate one",
+        )
         extra_projection = sum(rand(1:sampling_range) * v for v in keys(io_projections))
         debug_si("Extra projections: $extra_projection")
         new_projections, _, projection_equation =

src/local_identifiability.jl

@@ -174,7 +174,9 @@ function assess_local_identifiability(
     restart_logging(loglevel = loglevel)
     if length(measured_quantities) == 0
         if any(ModelingToolkit.isoutput(eq.lhs) for eq in ModelingToolkit.equations(ode))
-            info_si("Measured quantities are not provided, trying to find the outputs in input ODE.")
+            info_si(
+                "Measured quantities are not provided, trying to find the outputs in input ODE.",
+            )
             measured_quantities = filter(
                 eq -> (ModelingToolkit.isoutput(eq.lhs)),
                 ModelingToolkit.equations(ode),
@@ -202,7 +204,7 @@ function assess_local_identifiability(
             funcs_to_check = funcs_to_check_,
             p = p,
             type = type,
-            loglevel = loglevel
+            loglevel = loglevel,
         )
         nemo2mtk = Dict(funcs_to_check_ .=> funcs_to_check)
         out_dict = Dict(nemo2mtk[param] => result[param] for param in funcs_to_check_)
@@ -238,7 +240,7 @@ function assess_local_identifiability(
     p::Float64 = 0.99,
     type = :SE,
     trbasis = nothing,
-    loglevel = Logging.Info
+    loglevel = Logging.Info,
 ) where {P <: MPolyElem{Nemo.fmpq}}
     restart_logging(loglevel = loglevel)
     if isempty(funcs_to_check)
@@ -254,7 +256,9 @@ function assess_local_identifiability(
             num, den = unpack_fraction(f)
             for v in vcat(vars(num), vars(den))
                 if !(v in ode.parameters)
-                    error_si("Multi-experiment identifiability is not properly defined for the states")
+                    error_si(
+                        "Multi-experiment identifiability is not properly defined for the states",
+                    )
                     throw(ArgumentError("State variable $v appears in $f"))
                 end
             end

src/logging.jl

@@ -8,8 +8,8 @@
 
 # not the exhaustive list, just the ones to be initialized
 const _runtime_rubrics = (
-    :id_calls_to_gb, 
-    :id_groebner_time, 
+    :id_calls_to_gb,
+    :id_groebner_time,
     :id_inclusion_check_mod_p,
     :id_npoints_degree,
     :id_npoints_interpolation,
@@ -25,12 +25,8 @@ const _runtime_logger = Dict(
     :id_beautifulization => 0,
 )
 
-const _si_logger = Ref{Logging.ConsoleLogger}(
-    Logging.ConsoleLogger(
-        Logging.Info,
-        show_limited = false,
-    )
-)
+const _si_logger =
+    Ref{Logging.ConsoleLogger}(Logging.ConsoleLogger(Logging.Info, show_limited = false))
 
 function restart_logging(; loglevel = Logging.Info)
     _si_logger[] = Logging.ConsoleLogger(loglevel, show_limited = false)

src/parametrizations.jl

@@ -168,12 +168,14 @@ function check_constructive_field_membership(
         gen_tag_names(length(fracs_gen), "Tag")
     end
     sat_string = gen_tag_name("Sat")
-    debug_si("""
-    Tags:
-    $(join(map(x -> string(x[1]) * " -> " * string(x[2]),  zip(fracs_gen, tag_strings)), "\t\n"))
-    Saturation tag:
-    $sat_string
-    """)
+    debug_si(
+        """
+Tags:
+$(join(map(x -> string(x[1]) * " -> " * string(x[2]),  zip(fracs_gen, tag_strings)), "\t\n"))
+Saturation tag:
+$sat_string
+""",
+    )
     poly_ring_tag, vars_tag = PolynomialRing(K, vcat(sat_string, orig_strings, tag_strings))
     sat_var = vars_tag[1]
     orig_vars = vars_tag[2:(nvars(poly_ring) + 1)]
@@ -225,10 +227,12 @@ function check_constructive_field_membership(
     ring_of_tags, tags = PolynomialRing(K, tag_strings)
     tag_to_gen = Dict(tags[i] => fracs_gen[i] for i in 1:length(fracs_gen))
     if !isempty(intersect(tag_strings, orig_strings))
-        warn_si("""
-        There is an intersection between the names of the tag variables and the original variables.
-        Tags: $tag_strings
-        Original vars: $orig_strings""")
+        warn_si(
+            """
+    There is an intersection between the names of the tag variables and the original variables.
+    Tags: $tag_strings
+    Original vars: $orig_strings""",
+        )
     end
     parametric_ring, _ =
         PolynomialRing(FractionField(ring_of_tags), orig_strings, ordering = :degrevlex)
@@ -464,7 +468,12 @@ Dict{Nemo.QQMPolyRingElem, AbstractAlgebra.Generic.Frac{Nemo.QQMPolyRingElem}} w
 Notice that the `new_ode` is fully identifiabile, and has `1` less parameter
 compared to the original one.
 """
-function reparametrize_global(ode::ODE{P}; p = 0.99, seed = 42, loglevel = Logging.Info) where {P}
+function reparametrize_global(
+    ode::ODE{P};
+    p = 0.99,
+    seed = 42,
+    loglevel = Logging.Info,
+) where {P}
     restart_logging(loglevel = loglevel)
     Random.seed!(seed)
     id_funcs =

src/precompile.jl

@@ -22,7 +22,11 @@
             )
             assess_identifiability(ode, loglevel = Logging.Warn)
             assess_identifiability(de; measured_quantities = [x0], loglevel = Logging.Warn)
-            assess_identifiability(de; measured_quantities = [y ~ x0], loglevel = Logging.Warn)
+            assess_identifiability(
+                de;
+                measured_quantities = [y ~ x0],
+                loglevel = Logging.Warn,
+            )
             find_identifiable_functions(ode, with_states = true, loglevel = Logging.Warn)
             restart_logging(loglevel = Logging.Info)
         end