remove SymbolicUtils and related stuff

Author: TorkelE

Project.toml

@@ -21,7 +21,6 @@ Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 RuntimeGeneratedFunctions = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47"
 Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
-SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 TermInterface = "8ea1fca8-c5ef-4a55-8b96-4e9afe9c9a3c"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
@@ -57,7 +56,6 @@ RuntimeGeneratedFunctions = "0.5.12"
 Setfield = "1"
 StructuralIdentifiability = "0.5.1"
 Symbolics = "5.27"
-SymbolicUtils = "2.0.2"
 TermInterface = "0.4.1"
 Unitful = "1.12.4"
 julia = "1.10"

src/Catalyst.jl

@@ -23,7 +23,6 @@ using RuntimeGeneratedFunctions
 RuntimeGeneratedFunctions.init(@__MODULE__)
 
 import Symbolics: BasicSymbolic
-import SymbolicUtils
 using TermInterface: iscall
 using ModelingToolkit: Symbolic, value, get_unknowns, get_ps, get_iv, get_systems,
                        get_eqs, get_defaults, toparam, get_var_to_name, get_observed,

src/chemistry_functionality.jl

@@ -182,7 +182,7 @@ function make_compounds(expr)
     end
     push!(compound_declarations.args, :($(Expr(:escape, :($(compound_syms))))))
 
-    # The output needs to be converted to Vector{Num} (from  Vector{SymbolicUtils.BasicSymbolic{Real}}) to be consistent with e.g. @variables.
+    # The output needs to be converted to Vector{Num} (from  Vector{BasicSymbolic{Real}}) to be consistent with e.g. @variables.
     compound_declarations.args[end] = :([ModelingToolkit.wrap(cmp) for cmp in $(compound_declarations.args[end])])
 
     # Returns output that.

src/reactionsystem_serialisation/serialisation_support.jl

@@ -103,9 +103,9 @@ function sym_2_declaration_string(sym; multiline_format = false)
     dec_string = "$(sym)"
 
     # If the symbol have a non-default type, appends the declaration of this.
-    # Assumes that the type is on the form `SymbolicUtils.BasicSymbolic{X}`. Contain error checks
+    # Assumes that the type is on the form `BasicSymbolic{X}`. Contain error checks
     # to ensure that this is the case.
-    if !(sym isa SymbolicUtils.BasicSymbolic{Real})
+    if !(sym isa 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) != '}')
             error("Encountered symbolic of unexpected type: $sym_type.")
@@ -139,7 +139,7 @@ end
 # and metadata values (which hopefully almost exclusively) has simple, supported, types. Ideally,
 # more supported types can be added here.
 x_2_string(x::Num) = expression_2_string(x)
-x_2_string(x::SymbolicUtils.BasicSymbolic{<:Real}) = expression_2_string(x)
+x_2_string(x::BasicSymbolic{<:Real}) = expression_2_string(x)
 x_2_string(x::Bool) = string(x)
 x_2_string(x::String) = "\"$x\""
 x_2_string(x::Char) = "\'$x\'"
@@ -293,6 +293,6 @@ end
 function complicated_declaration(sym)
     isempty(get_metadata_to_declare(sym)) || (return true)
     ModelingToolkit.hasdefault(sym) && (return true)
-    (sym isa SymbolicUtils.BasicSymbolic{Real}) || (return true)
+    (sym isa BasicSymbolic{Real}) || (return true)
     return false
 end

src/reactionsystem_serialisation/serialise_fields.jl

@@ -445,7 +445,7 @@ function discrete_event_string(discrete_event, strip_call_dict)
     # Creates the string corresponding to the conditions. The special check is if the condition is
     # an expression like `X > 5.0`. Here, "(...)" is added for purely aesthetic reasons.
     condition_string = x_2_string(discrete_event.condition)
-    if discrete_event.condition isa SymbolicUtils.BasicSymbolic
+    if discrete_event.condition isa BasicSymbolic
         @string_prepend! "(" condition_string
         @string_append! condition_string ")"
     end

src/spatial_reaction_systems/utility.jl

@@ -203,7 +203,7 @@ end
 # If all parameters the rate depend on are uniform all edges, this becomes a length 1 vector.
 # Else a vector with each value corresponding to the rate at one specific edge.
 function compute_transport_rates(rate_law::Num,
-                                p_val_dict::Dict{SymbolicUtils.BasicSymbolic{Real}, Vector{Float64}}, num_edges::Int64)
+                                p_val_dict::Dict{BasicSymbolic{Real}, Vector{Float64}}, num_edges::Int64)
     # Finds parameters involved in rate and create a function evaluating the rate law.
     relevant_ps = Symbolics.get_variables(rate_law)
     rate_law_func = drop_expr(@RuntimeGeneratedFunction(build_function(rate_law, relevant_ps...)))

test/miscellaneous_tests/reactionsystem_serialisation.jl

@@ -4,10 +4,11 @@
 using Catalyst, Test
 using Catalyst: get_rxs
 using ModelingToolkit: getdefault, getdescription, get_metadata
+using Symbolics: getmetadata
 
 # Creates missing getters for MTK metadata (can be removed once added to MTK).
-getmisc(x) = SymbolicUtils.getmetadata(Symbolics.unwrap(x), ModelingToolkit.VariableMisc, nothing)
-getinput(x) = SymbolicUtils.getmetadata(Symbolics.unwrap(x), ModelingToolkit.VariableInput, nothing)
+getmisc(x) = getmetadata(Symbolics.unwrap(x), ModelingToolkit.VariableMisc, nothing)
+getinput(x) = getmetadata(Symbolics.unwrap(x), ModelingToolkit.VariableInput, nothing)
 
 # Sets the default `t` and `D` to use.
 t = default_t()

test/reactionsystem_core/parameter_type_designation.jl

@@ -2,7 +2,7 @@
 
 # Fetch packages.
 using Catalyst, JumpProcesses, NonlinearSolve, OrdinaryDiffEq, StochasticDiffEq, Test
-using Symbolics: unwrap
+using Symbolics: BasicSymbolic, unwrap
 
 # Sets stable rng number.
 using StableRNGs
@@ -47,16 +47,16 @@ end
 
 # Tests that parameters stored in the system have the correct type.
 let
-    @test Symbolics.unwrap(rs.p1) isa SymbolicUtils.BasicSymbolic{Real}
-    @test Symbolics.unwrap(rs.d1) isa SymbolicUtils.BasicSymbolic{Real}
-    @test Symbolics.unwrap(rs.p2) isa SymbolicUtils.BasicSymbolic{Float64}
-    @test Symbolics.unwrap(rs.d2) isa SymbolicUtils.BasicSymbolic{Float64}
-    @test Symbolics.unwrap(rs.p3) isa SymbolicUtils.BasicSymbolic{Int64}
-    @test Symbolics.unwrap(rs.d3) isa SymbolicUtils.BasicSymbolic{Int64}
-    @test Symbolics.unwrap(rs.p4) isa SymbolicUtils.BasicSymbolic{Float32}
-    @test Symbolics.unwrap(rs.d4) isa SymbolicUtils.BasicSymbolic{Rational{Int64}}
-    @test Symbolics.unwrap(rs.p5) isa SymbolicUtils.BasicSymbolic{Rational{Int64}}
-    @test Symbolics.unwrap(rs.d5) isa SymbolicUtils.BasicSymbolic{Float32}
+    @test Symbolics.unwrap(rs.p1) isa BasicSymbolic{Real}
+    @test Symbolics.unwrap(rs.d1) isa BasicSymbolic{Real}
+    @test Symbolics.unwrap(rs.p2) isa BasicSymbolic{Float64}
+    @test Symbolics.unwrap(rs.d2) isa BasicSymbolic{Float64}
+    @test Symbolics.unwrap(rs.p3) isa BasicSymbolic{Int64}
+    @test Symbolics.unwrap(rs.d3) isa BasicSymbolic{Int64}
+    @test Symbolics.unwrap(rs.p4) isa BasicSymbolic{Float32}
+    @test Symbolics.unwrap(rs.d4) isa BasicSymbolic{Rational{Int64}}
+    @test Symbolics.unwrap(rs.p5) isa BasicSymbolic{Rational{Int64}}
+    @test Symbolics.unwrap(rs.d5) isa BasicSymbolic{Float32}
 end
 
 # Tests that simulations with differentially typed variables yields correct results.

test/reactionsystem_core/symbolic_stoichiometry.jl

@@ -2,7 +2,7 @@
 
 # Fetch packages.
 using Catalyst, JumpProcesses, OrdinaryDiffEq, StochasticDiffEq, Statistics, Test
-using Symbolics: unwrap
+using Symbolics: BasicSymbolic, unwrap
 
 # Sets stable rng number.
 using StableRNGs
@@ -46,8 +46,8 @@ let
     @test rs1 == rs2 == rs3
     @test issetequal(unknowns(rs1), [X, Y])
     @test issetequal(parameters(rs1), [p, k, d, n1, n2, n3])
-    @test unwrap(d) isa SymbolicUtils.BasicSymbolic{Float64}
-    @test unwrap(n1) isa SymbolicUtils.BasicSymbolic{Int64}
+    @test unwrap(d) isa BasicSymbolic{Float64}
+    @test unwrap(n1) isa BasicSymbolic{Int64}
 end
 
 # Declares a network, parameter values, and initial conditions, to be used for the next couple of tests.

test/spatial_modelling/lattice_reaction_systems.jl

@@ -2,7 +2,7 @@
 
 # Fetch packages.
 using Catalyst, Graphs, Test
-using Symbolics: unwrap
+using Symbolics: BasicSymbolic, unwrap
 t = default_t()
 
 # Pre declares a grid.
@@ -311,19 +311,19 @@ end
 
     # Loops through all parameters, ensuring that they have the correct type
     p_types = Dict([ModelingToolkit.nameof(p) => typeof(unwrap(p)) for p in parameters(lrs)])
-    @test p_types[:k1] == SymbolicUtils.BasicSymbolic{Real}
-    @test p_types[:l1] == SymbolicUtils.BasicSymbolic{Real}
-    @test p_types[:k2] == SymbolicUtils.BasicSymbolic{Float64}
-    @test p_types[:l2] == SymbolicUtils.BasicSymbolic{Float64}
-    @test p_types[:k3] == SymbolicUtils.BasicSymbolic{Int64}
-    @test p_types[:l3] == SymbolicUtils.BasicSymbolic{Int64}
-    @test p_types[:k4] == SymbolicUtils.BasicSymbolic{Float32}
-    @test p_types[:l4] == SymbolicUtils.BasicSymbolic{Float32}
-    @test p_types[:k5] == SymbolicUtils.BasicSymbolic{Rational{Int64}}
-    @test p_types[:l5] == SymbolicUtils.BasicSymbolic{Rational{Int64}}
-    @test p_types[:D1] == SymbolicUtils.BasicSymbolic{Float32}
-    @test p_types[:D2] == SymbolicUtils.BasicSymbolic{Real}
-    @test p_types[:D3] == SymbolicUtils.BasicSymbolic{Rational{Int64}}
+    @test p_types[:k1] == BasicSymbolic{Real}
+    @test p_types[:l1] == BasicSymbolic{Real}
+    @test p_types[:k2] == BasicSymbolic{Float64}
+    @test p_types[:l2] == BasicSymbolic{Float64}
+    @test p_types[:k3] == BasicSymbolic{Int64}
+    @test p_types[:l3] == BasicSymbolic{Int64}
+    @test p_types[:k4] == BasicSymbolic{Float32}
+    @test p_types[:l4] == BasicSymbolic{Float32}
+    @test p_types[:k5] == BasicSymbolic{Rational{Int64}}
+    @test p_types[:l5] == BasicSymbolic{Rational{Int64}}
+    @test p_types[:D1] == BasicSymbolic{Float32}
+    @test p_types[:D2] == BasicSymbolic{Real}
+    @test p_types[:D3] == BasicSymbolic{Rational{Int64}}
 end
 
 # Checks that programmatically declared parameters (with types) can be used in `TransportReaction`s.
@@ -338,9 +338,9 @@ end
     lrs = LatticeReactionSystem(rs, [tr], grid)
 
     p_types = Dict([ModelingToolkit.nameof(p) => typeof(unwrap(p)) for p in parameters(lrs)])
-    @test p_types[:p] == SymbolicUtils.BasicSymbolic{Float32}
-    @test p_types[:d] == SymbolicUtils.BasicSymbolic{Real}
-    @test p_types[:D] == SymbolicUtils.BasicSymbolic{Rational{Int64}}
+    @test p_types[:p] == BasicSymbolic{Float32}
+    @test p_types[:d] == BasicSymbolic{Real}
+    @test p_types[:D] == BasicSymbolic{Rational{Int64}}
 
     u0 = [:X => [0.25, 0.5, 2.0, 4.0]]
     ps = [rs.p => 2.0, rs.d => 1.0, D => 1//2]