round 2

Author: TorkelE

ext/CatalystBifurcationKitExtension/bifurcation_kit_extension.jl

@@ -26,6 +26,6 @@ function BK.BifurcationProblem(rs::ReactionSystem, u0_bif, ps, bif_par, args...;
     nsys = complete(nsys)
 
     # Makes BifurcationProblem (this call goes through the ModelingToolkit-based BifurcationKit extension).
-    return BK.BifurcationProblem(nsys, u0_bif, ps, bif_par, args...; plot_var, 
+    return BK.BifurcationProblem(nsys, u0_bif, ps, bif_par, args...; plot_var,
         record_from_solution, jac, kwargs...)
 end

ext/CatalystHomotopyContinuationExtension/homotopy_continuation_extension.jl

@@ -52,7 +52,7 @@ function steady_state_polynomial(rs::ReactionSystem, ps, u0)
     ns = complete(convert(NonlinearSystem, rs; remove_conserved = true))
     pre_varmap = [symmap_to_varmap(rs, u0)..., symmap_to_varmap(rs, ps)...]
     Catalyst.conservationlaw_errorcheck(rs, pre_varmap)
-    p_vals = ModelingToolkit.varmap_to_vars(pre_varmap, parameters(ns); 
+    p_vals = ModelingToolkit.varmap_to_vars(pre_varmap, parameters(ns);
         defaults = ModelingToolkit.defaults(ns))
     p_dict = Dict(parameters(ns) .=> p_vals)
     eqs_pars_funcs = vcat(equations(ns), conservedequations(rs))

ext/CatalystStructuralIdentifiabilityExtension/structural_identifiability_extension.jl

@@ -31,8 +31,8 @@ function Catalyst.make_si_ode(rs::ReactionSystem; measured_quantities = [], know
     # Creates a MTK ODESystem, and a list of measured quantities (there are equations).
     # Gives these to SI to create an SI ode model of its preferred form.
     osys, conseqs, _ = make_osys(rs; remove_conserved)
-    measured_quantities = make_measured_quantities( rs, measured_quantities, known_p, conseqs;
-        ignore_no_measured_warn)
+    measured_quantities = make_measured_quantities(rs, measured_quantities, known_p,
+        conseqs; ignore_no_measured_warn)
     return SI.mtk_to_si(osys, measured_quantities)[1]
 end
 
@@ -64,16 +64,16 @@ Notes:
 - `measured_quantities` and `known_p` input may also be symbolic (e.g. measured_quantities = [rs.X])
 """
 function SI.assess_local_identifiability(rs::ReactionSystem, args...;
-        measured_quantities = [], known_p = [], funcs_to_check = Vector(), 
+        measured_quantities = [], known_p = [], funcs_to_check = Vector(),
         remove_conserved = true, ignore_no_measured_warn = false, kwargs...)
     # Creates a ODESystem, list of measured quantities, and functions to check, of SI's preferred form.
     osys, conseqs, vars = make_osys(rs; remove_conserved)
-    measured_quantities = make_measured_quantities( rs, measured_quantities, known_p, conseqs;
-        ignore_no_measured_warn)
+    measured_quantities = make_measured_quantities(rs, measured_quantities, known_p,
+        conseqs; ignore_no_measured_warn)
     funcs_to_check = make_ftc(funcs_to_check, conseqs, vars)
 
     # Computes identifiability and converts it to a easy to read form.
-    out = SI.assess_local_identifiability( sys, args...; measured_quantities, 
+    out = SI.assess_local_identifiability(sys, args...; measured_quantities,
         funcs_to_check, kwargs...)
     return make_output(out, funcs_to_check, reverse.(conseqs))
 end
@@ -103,13 +103,13 @@ Notes:
 - This function is part of the StructuralIdentifiability.jl extension. StructuralIdentifiability.jl must be imported to access it.
 - `measured_quantities` and `known_p` input may also be symbolic (e.g. measured_quantities = [rs.X])
 """
-function SI.assess_identifiability( rs::ReactionSystem, args...; 
-        measured_quantities = [], known_p = [], funcs_to_check = Vector(), 
+function SI.assess_identifiability(rs::ReactionSystem, args...;
+        measured_quantities = [], known_p = [], funcs_to_check = Vector(),
         remove_conserved = true, ignore_no_measured_warn = false, kwargs...)
     # Creates a ODESystem, list of measured quantities, and functions to check, of SI's preferred form.
     osys, conseqs, vars = make_osys(rs; remove_conserved)
-    measured_quantities = make_measured_quantities(rs, measured_quantities, known_p, conseqs; 
-        ignore_no_measured_warn)
+    measured_quantities = make_measured_quantities(rs, measured_quantities, known_p,
+        conseqs; ignore_no_measured_warn)
     funcs_to_check = make_ftc(funcs_to_check, conseqs, vars)
 
     # Computes identifiability and converts it to a easy to read form.
@@ -143,13 +143,13 @@ Notes:
 - This function is part of the StructuralIdentifiability.jl extension. StructuralIdentifiability.jl must be imported to access it.
 - `measured_quantities` and `known_p` input may also be symbolic (e.g. measured_quantities = [rs.X])
 """
-function SI.find_identifiable_functions(rs::ReactionSystem, args...; 
-        measured_quantities = [], known_p = [], remove_conserved = true, 
+function SI.find_identifiable_functions(rs::ReactionSystem, args...;
+        measured_quantities = [], known_p = [], remove_conserved = true,
         ignore_no_measured_warn = false, kwargs...)
     # Creates a ODESystem, and list of measured quantities, of SI's preferred form.
     osys, conseqs = make_osys(rs; remove_conserved)
-    measured_quantities = make_measured_quantities(
-        rs, measured_quantities, known_p, conseqs; ignore_no_measured_warn)
+    measured_quantities = make_measured_quantities(rs, measured_quantities, known_p,
+        conseqs; ignore_no_measured_warn)
 
     # Computes identifiable functions and converts it to a easy to read form.
     out = SI.find_identifiable_functions(osys, args...; measured_quantities, kwargs...)

src/chemistry_functionality.jl

@@ -85,7 +85,7 @@ function make_compound(expr)
     # Loops through all components, add the component and the coefficients to the corresponding vectors
     # Cannot extract directly using e.g. "getfield.(composition, :reactant)" because then 
     # we get something like :([:C, :O]), rather than :([C, O]).
-    composition = Catalyst.recursive_find_reactants!( xpr.args[3], 1, 
+    composition = Catalyst.recursive_find_reactants!(xpr.args[3], 1,
         Vector{ReactantStruct}(undef, 0))
     components = :([])                                      # Becomes something like :([C, O]).                                         
     coefficients = :([])                                    # Becomes something like :([1, 2]). 
@@ -122,12 +122,12 @@ function make_compound(expr)
     species_declaration_expr = Expr(:escape, :(@species $species_expr))
     multiple_ivs_error_check_expr = Expr(:escape,
         :($(isempty(ivs)) && (length($ivs_get_expr) > 1) &&
-            error($COMPOUND_CREATION_ERROR_DEPENDENT_VAR_REQUIRED)))
+          error($COMPOUND_CREATION_ERROR_DEPENDENT_VAR_REQUIRED)))
     iv_designation_expr = Expr(:escape,
         :($(isempty(ivs)) && ($species_name = $(species_name)($(ivs_get_expr)...))))
     iv_check_expr = Expr(:escape,
         :(issetequal(arguments(ModelingToolkit.unwrap($species_name)), $ivs_get_expr) ||
-            error("The independent variable(S) provided to the compound ($(arguments(ModelingToolkit.unwrap($species_name)))), and those of its components ($($ivs_get_expr)))), are not identical.")))
+          error("The independent variable(S) provided to the compound ($(arguments(ModelingToolkit.unwrap($species_name)))), and those of its components ($($ivs_get_expr)))), are not identical.")))
     compound_designation_expr = Expr(:escape,
         :($species_name = ModelingToolkit.setmetadata(
             $species_name, Catalyst.CompoundSpecies, true)))
@@ -197,7 +197,7 @@ function make_compounds(expr)
 
     # The output needs to be converted to Vector{Num} (from  Vector{SymbolicUtils.BasicSymbolic{Real}}) to be consistent with e.g. @variables.
     compound_declarations.args[end] = :([ModelingToolkit.wrap(cmp)
-        for cmp in $(compound_declarations.args[end])])
+                                         for cmp in $(compound_declarations.args[end])])
 
     # Returns output that.
     return compound_declarations
@@ -264,7 +264,7 @@ function balance_reaction(reaction::Reaction)
         prodstoich = stoich[(length(reaction.substrates) + 1):end]
 
         # Create a new reaction with the balanced stoichiometries
-        balancedrx = Reaction(reaction.rate, reaction.substrates, reaction.products, 
+        balancedrx = Reaction(reaction.rate, reaction.substrates, reaction.products,
             substoich, prodstoich)
 
         # Add the reaction to the vector of all reactions

src/dsl.jl

@@ -417,7 +417,7 @@ function get_reactions(exprs::Vector{Expr}, reactions = Vector{ReactionStruct}(u
             push_reactions!(reactions, reaction.args[3], reaction.args[2],
                 rate.args[2], metadata.args[2], arrow)
         elseif in(arrow, fwd_arrows)
-            push_reactions!( reactions, reaction.args[2], reaction.args[3], 
+            push_reactions!(reactions, reaction.args[2], reaction.args[3],
                 rate, metadata, arrow)
         elseif in(arrow, bwd_arrows)
             push_reactions!(reactions, reaction.args[3], reaction.args[2],
@@ -476,7 +476,7 @@ function push_reactions!(reactions::Vector{ReactionStruct}, sub_line::ExprValues
             error("Some reaction metadata fields where repeated: $(metadata_entries)")
         end
 
-        push!(reactions, ReactionStruct(get_tup_arg(sub_line, i), 
+        push!(reactions,ReactionStruct(get_tup_arg(sub_line, i),
             get_tup_arg(prod_line, i), get_tup_arg(rate, i), metadata_i))
     end
 end
@@ -640,11 +640,11 @@ function read_events_option(options, event_type::Symbol)
         # Formatting error checks.
         # NOTE: Maybe we should move these deeper into the system (rather than the DSL), throwing errors more generally?
         if (arg isa Expr) && (arg.head != :call) || (arg.args[1] != :(=>)) ||
-                (length(arg.args) != 3)
+           (length(arg.args) != 3)
             error("Events should be on form `condition => affect`, separated by a `=>`. This appears not to be the case for: $(arg).")
         end
         if (arg isa Expr) && (arg.args[2] isa Expr) && (arg.args[2].head != :vect) &&
-                (event_type == :continuous_events)
+           (event_type == :continuous_events)
             error("The condition part of continious events (the left-hand side) must be a vector. This is not the case for: $(arg).")
         end
         if (arg isa Expr) && (arg.args[3] isa Expr) && (arg.args[3].head != :vect)
@@ -668,7 +668,7 @@ function read_equations_options(options, variables_declared)
     eqs_input = haskey(options, :equations) ? options[:equations].args[3] : :(begin end)
     eqs_input = option_block_form(eqs_input)
     equations = Expr[]
-    ModelingToolkit.parse_equations!(Expr(:block), equations, 
+    ModelingToolkit.parse_equations!(Expr(:block), equations,
         Dict{Symbol, Any}(), eqs_input)
 
     # Loops through all equations, checks for lhs of the form `D(X) ~ ...`.
@@ -687,7 +687,7 @@ function read_equations_options(options, variables_declared)
         lhs = eq.args[2]
         # if lhs: is an expression. Is a function call. The function's name is D. Calls a single symbol.
         if (lhs isa Expr) && (lhs.head == :call) && (lhs.args[1] == :D) &&
-                (lhs.args[2] isa Symbol)
+           (lhs.args[2] isa Symbol)
             diff_var = lhs.args[2]
             if in(diff_var, forbidden_symbols_error)
                 error("A forbidden symbol ($(diff_var)) was used as an variable in this differential equation: $eq")
@@ -755,7 +755,7 @@ function read_observed_options(options, species_n_vars_declared, ivs_sorted)
                 error("An interpoalted observable have been used, which has also been explicitly delcared within the system using eitehr @species or @variables. This is not permited.")
             end
             if ((obs_name in species_n_vars_declared) || is_escaped_expr(obs_eq.args[2])) &&
-                    !isnothing(metadata)
+               !isnothing(metadata)
                 error("Metadata was provided to observable $obs_name in the `@observables` macro. However, the obervable was also declared separately (using either @species or @variables). When this is done, metadata should instead be provided within the original @species or @variable declaration.")
             end
 
@@ -771,7 +771,7 @@ function read_observed_options(options, species_n_vars_declared, ivs_sorted)
                 # Adds a line to the `observed_vars` expression, setting the ivs for this observable.
                 # Cannot extract directly using e.g. "getfield.(dependants_structs, :reactant)" because
                 # then we get something like :([:X1, :X2]), rather than :([X1, X2]).
-                dep_var_expr = :(filter(!MT.isparameter, 
+                dep_var_expr = :(filter(!MT.isparameter,
                     Symbolics.get_variables($(obs_eq.args[3]))))
                 ivs_get_expr = :(unique(reduce(vcat, [arguments(MT.unwrap(dep))
                     for dep in $dep_var_expr])))

src/expression_utils.jl

@@ -82,7 +82,7 @@ function find_varinfo_in_declaration(expr)
         # Case: X(t) = 1.0        
         (expr.args[1].head == :call) &&
             (return expr.args[1].args[1], expr.args[1].args[2:end], expr.args[2].args[1],
-                nothing)
+            nothing)
     end
     if expr.head == :tuple
         # Case: X, [metadata=true]

src/reactionsystem.jl

@@ -463,7 +463,7 @@ end
 # While species are ordered before variables in the unknowns vector, this ordering is not imposed here,
 # but carried out at a later stage.
 function make_ReactionSystem_internal(rxs_and_eqs::Vector, iv, us_in, ps_in;
-        spatial_ivs = nothing, continuous_events = [], discrete_events = [], 
+        spatial_ivs = nothing, continuous_events = [], discrete_events = [],
         observed = [], kwargs...)
 
     # Filters away any potential obervables from `states` and `spcs`.

src/reactionsystem_conversions.jl

@@ -607,7 +607,7 @@ function Base.convert(::Type{<:SDESystem}, rs::ReactionSystem;
     ists, ispcs = get_indep_sts(flatrs, remove_conserved)
     eqs = assemble_drift(flatrs, ispcs; combinatoric_ratelaws, include_zero_odes,
         remove_conserved)
-    noiseeqs = assemble_diffusion(flatrs, ists, ispcs; 
+    noiseeqs = assemble_diffusion(flatrs, ists, ispcs;
         combinatoric_ratelaws, remove_conserved)
     eqs, us, ps, obs, defs = addconstraints!(eqs, flatrs, ists, ispcs; remove_conserved)
 

src/reactionsystem_serialisation/serialisation_support.jl

@@ -69,7 +69,7 @@ end
 
 # Converts a numeric expression (e.g. p*X + 2Y) to a string (e.g. "p*X + 2Y"). Also ensures that for
 # any variables (e.g. X(t)) the call part is stripped, and only variable name (e.g. X) is written.
-function expression_2_string(expr; 
+function expression_2_string(expr;
         strip_call_dict = make_strip_call_dict(Symbolics.get_variables(expr)))
     strip_called_expr = substitute(expr, strip_call_dict)
     return repr(strip_called_expr)
@@ -89,7 +89,7 @@ function syms_2_declaration_string(syms; multiline_format = false)
     decs_string = (multiline_format ? " begin" : "")
     for sym in syms
         delimiter = (multiline_format ? "\n\t" : " ")
-        @string_append! decs_string delimiter sym_2_declaration_string(sym; 
+        @string_append! decs_string delimiter sym_2_declaration_string(sym;
             multiline_format)
     end
     multiline_format && (@string_append! decs_string "\nend")
@@ -109,7 +109,7 @@ function sym_2_declaration_string(sym; multiline_format = false)
     if !(sym isa SymbolicUtils.BasicSymbolic{Real})
         sym_type = String(Symbol(typeof(Symbolics.unwrap(sym))))
         if (get_substring(sym_type, 1, 28) != "SymbolicUtils.BasicSymbolic{") ||
-                (get_char_end(sym_type, 0) != '}')
+           (get_char_end(sym_type, 0) != '}')
             error("Encountered symbolic of unexpected type: $sym_type.")
         end
         @string_append! dec_string "::" get_substring_end(sym_type, 29, -1)

src/reactionsystem_serialisation/serialise_fields.jl

@@ -43,7 +43,7 @@ SIVS_FS = (has_sivs, get_sivs_string, get_sivs_annotation)
 
 # Function which handles the addition of species, variable, and parameter declarations to the file
 # text. These must be handled as a unity in case there are default value dependencies between these.
-function handle_us_n_ps(file_text::String, rn::ReactionSystem, 
+function handle_us_n_ps(file_text::String, rn::ReactionSystem,
         annotate::Bool, top_level::Bool)
     # Fetches the systems parameters, species, and variables. Computes the `has_` `Bool`s.
     ps_all = get_ps(rn)
@@ -102,11 +102,11 @@ function handle_us_n_ps(file_text::String, rn::ReactionSystem,
         while !(isempty(remaining_ps) && isempty(remaining_sps) && isempty(remaining_vars))
             # Checks which parameters/species/variables can be written. The `dependency_split`
             # function updates the `remaining_` input.
-            writable_ps = dependency_split!(remaining_ps, 
+            writable_ps = dependency_split!(remaining_ps,
                 [remaining_ps; remaining_sps; remaining_vars])
-            writable_sps = dependency_split!(remaining_sps, 
+            writable_sps = dependency_split!(remaining_sps,
                 [remaining_ps; remaining_sps; remaining_vars])
-            writable_vars = dependency_split!(remaining_vars, 
+            writable_vars = dependency_split!(remaining_vars,
                 [remaining_ps; remaining_sps; remaining_vars])
 
             # Writes those that can be written.
@@ -409,7 +409,7 @@ function get_continuous_events_annotation(rn::ReactionSystem)
 end
 
 # Combines the 3 -related functions in a constant tuple.
-CONTINUOUS_EVENTS_FS = (has_continuous_events, get_continuous_events_string, 
+CONTINUOUS_EVENTS_FS = (has_continuous_events, get_continuous_events_string,
     get_continuous_events_annotation)
 
 ### Handles Discrete Events ###
@@ -466,15 +466,15 @@ function get_discrete_events_annotation(rn::ReactionSystem)
 end
 
 # Combines the 3 -related functions in a constant tuple.
-DISCRETE_EVENTS_FS = (has_discrete_events, get_discrete_events_string, 
+DISCRETE_EVENTS_FS = (has_discrete_events, get_discrete_events_string,
     get_discrete_events_annotation)
 
 ### Handles Systems ###
 
 # Specific `push_field` function, which is used for the system field (where the annotation option
 # must be passed to the `get_component_string` function). Since non-ReactionSystem systems cannot be 
 # written to file, this functions throws an error if any such systems are encountered.
-function push_systems_field(file_text::String, rn::ReactionSystem, 
+function push_systems_field(file_text::String, rn::ReactionSystem,
         annotate::Bool, top_level::Bool)
     # Checks whther there are any subsystems, and if these are ReactionSystems.
     has_systems(rn) || (return (file_text, false))
@@ -542,5 +542,5 @@ function get_connection_type_annotation(rn::ReactionSystem)
 end
 
 # Combines the 3 connection types-related functions in a constant tuple.
-CONNECTION_TYPE_FS = (has_connection_type, get_connection_type_string, 
+CONNECTION_TYPE_FS = (has_connection_type, get_connection_type_string,
     get_connection_type_annotation)