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SciML · Jun 2, 2024 · 8e369d7 · 8e369d7
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Showing 10 changed files with 35 additions and 28 deletions.
diff --git a/docs/make.jl b/docs/make.jl
@@ -19,7 +19,7 @@ makedocs(;
         assets = ["assets/favicon.ico"]),
     pages = [
         "Home" => "index.md",
-        "API documentation" => "api.md",
+        "API documentation" => "api.md"
     ])
 
 deploydocs(;

diff --git a/src/SBMLToolkit.jl b/src/SBMLToolkit.jl
@@ -15,7 +15,7 @@ include("utils.jl")
 
 export ReactionSystem, ODESystem
 export readSBML, readSBMLFromString, set_level_and_version, convert_simplify_math,
-    convert_promotelocals_expandfuns
+       convert_promotelocals_expandfuns
 export DefaultImporter, ReactionSystemImporter, ODESystemImporter
 
 end
diff --git a/src/reactions.jl b/src/reactions.jl
@@ -53,11 +53,11 @@ function get_unidirectional_components(bidirectional_math)
 end
 
 function add_reaction!(rxs::Vector{Reaction},
-    kl::Num,
-    reactant_references::Vector{SBML.SpeciesReference},
-    product_references::Vector{SBML.SpeciesReference},
-    model::SBML.Model;
-    enforce_rate = false)
+        kl::Num,
+        reactant_references::Vector{SBML.SpeciesReference},
+        product_references::Vector{SBML.SpeciesReference},
+        model::SBML.Model;
+        enforce_rate = false)
     reactants, products, rstoichvals, pstoichvals = get_reagents(reactant_references,
         product_references, model)
     isnothing(reactants) && isnothing(products) && return
@@ -78,8 +78,8 @@ end
 Get reagents
 """
 function get_reagents(reactant_references::Vector{SBML.SpeciesReference},
-    product_references::Vector{SBML.SpeciesReference},
-    model::SBML.Model)
+        product_references::Vector{SBML.SpeciesReference},
+        model::SBML.Model)
     reactants = String[]
     products = String[]
     rstoich = Float64[]
@@ -146,7 +146,7 @@ end
 Get kineticLaw for use in MTK.Reaction
 """
 function use_rate(kl::Num, react::Union{Vector{Num}, Nothing},
-    stoich::Union{Vector{<:Real}, Nothing})
+        stoich::Union{Vector{<:Real}, Nothing})
     rate_const = get_massaction(kl, react, stoich)
     if !isnan(rate_const)
         kl = rate_const
@@ -161,7 +161,7 @@ end
 Get rate constant of mass action kineticLaws
 """
 function get_massaction(kl::Num, reactants::Union{Vector{Num}, Nothing},
-    stoich::Union{Vector{<:Real}, Nothing})
+        stoich::Union{Vector{<:Real}, Nothing})
     function check_args(x::SymbolicUtils.BasicSymbolic{Real})
         check_args(Val(SymbolicUtils.istree(x)), x)
     end

diff --git a/src/systems.jl b/src/systems.jl
@@ -38,7 +38,7 @@ Create a `ModelingToolkit.ODESystem` from an SBML file, using the default import
 See also [`Model`](@ref) and [`ODESystemImporter`](@ref).
 """
 function SBML.readSBML(sbmlfile::String, ::ODESystemImporter;
-    include_zero_odes::Bool = true, kwargs...)  # Returns an MTK.ODESystem
+        include_zero_odes::Bool = true, kwargs...)  # Returns an MTK.ODESystem
     convert(ODESystem, readSBML(sbmlfile, ReactionSystemImporter(), kwargs...),
         include_zero_odes = include_zero_odes)
 end
@@ -105,7 +105,7 @@ Create an `ODESystem` from an `SBML.Model`.
 See also [`ReactionSystem`](@ref).
 """
 function ModelingToolkit.ODESystem(model::SBML.Model; include_zero_odes::Bool = true,
-    kwargs...)
+        kwargs...)
     rs = ReactionSystem(model; kwargs...)
     convert(ODESystem, rs; include_zero_odes = include_zero_odes)
 end

diff --git a/src/utils.jl b/src/utils.jl
@@ -83,7 +83,7 @@ function create_var(x, iv; isbcspecies = false, irreducible = false)
     sym = Symbol(x)
     Symbolics.unwrap(first(@species $sym(iv) [
         isbcspecies = isbcspecies,
-        irreducible = irreducible,
+        irreducible = irreducible
     ]))
 end
 function create_param(x; isconstantspecies = false)

diff --git a/test/reactions.jl b/test/reactions.jl
@@ -21,8 +21,9 @@ SPECIES3 = SBML.Species(name = "s1s2", compartment = "c1", initial_amount = 1.0,
     boundary_condition = false, constant = false)
 KINETICMATH1 = SBML.MathIdent("k1")
 KINETICMATH2 = SBML.MathApply("*", SBML.Math[SBML.MathIdent("k1"), SBML.MathIdent("s2")])
-REACTION1 = SBML.Reaction(products = [
-        SBML.SpeciesReference(species = "s1", stoichiometry = 1),
+REACTION1 = SBML.Reaction(
+    products = [
+        SBML.SpeciesReference(species = "s1", stoichiometry = 1)
     ],
     kinetic_math = KINETICMATH1,
     reversible = false)
@@ -40,8 +41,9 @@ truereaction = Catalyst.Reaction(k1, nothing, [s1], nothing, [1])  # Todo: imple
 @test isequal(reaction, truereaction)
 
 km = SBML.MathTime("x")
-reac = SBML.Reaction(reactants = [
-        SBML.SpeciesReference(species = "s1", stoichiometry = 1.0),
+reac = SBML.Reaction(
+    reactants = [
+        SBML.SpeciesReference(species = "s1", stoichiometry = 1.0)
     ],
     kinetic_math = km,
     reversible = false)
@@ -114,7 +116,8 @@ m = SBML.Model(species = Dict("s" => s), reactions = Dict("r1" => r))
 @test isequal((nothing, nothing, nothing, nothing),
     SBMLToolkit.get_reagents(r.products, r.reactants, m))
 
-r = SBML.Reaction(reactants = [SBML.SpeciesReference(species = "s", stoichiometry = 1.0),
+r = SBML.Reaction(
+    reactants = [SBML.SpeciesReference(species = "s", stoichiometry = 1.0),
         SBML.SpeciesReference(species = "s", stoichiometry = 1.0)],
     reversible = false)
 m = SBML.Model(species = Dict("s" => s), reactions = Dict("r1" => r))

diff --git a/test/rules.jl b/test/rules.jl
@@ -43,7 +43,8 @@ assignment_true = 7 * compartment
 @test isequal(assignment, assignment_true)
 
 r = SBML.AssignmentRule("S2", SBML.MathVal(1))
-@test_throws ErrorException("Cannot find target for rule with ID `S2`") SBMLToolkit.get_var_and_assignment(m,
+@test_throws ErrorException("Cannot find target for rule with ID `S2`") SBMLToolkit.get_var_and_assignment(
+    m,
     r)
 
 # Test get_volume_correction

diff --git a/test/simresults.jl b/test/simresults.jl
@@ -8,8 +8,7 @@ const case_ids = [7,  # boundary_condition
     140,  # compartment size overridden with assignmentRule
     170,  # Model using parameters and rules only
     325,  # One reactions and two rate rules with four species in a 2D compartment
-    679,  # Initial value calculated by assignmentRule in compartment of non-unit size
-    # 1208, # Non-hOSU species with rateRule in variable compartment -> require MTK fix.
+    679  # Initial value calculated by assignmentRule in compartment of non-unit size    # 1208, # Non-hOSU species with rateRule in variable compartment -> require MTK fix.
 ]
 
 const logdir = joinpath(@__DIR__, "logs")

diff --git a/test/systems.jl b/test/systems.jl
@@ -22,13 +22,15 @@ KINETICMATH3 = SBML.MathApply("-",
             SBML.Math[SBML.MathIdent("k1"),
                 SBML.MathIdent("s1")]),
         KINETICMATH1])
-REACTION1 = SBML.Reaction(products = [
-        SBML.SpeciesReference(species = "s1", stoichiometry = 1.0),
+REACTION1 = SBML.Reaction(
+    products = [
+        SBML.SpeciesReference(species = "s1", stoichiometry = 1.0)
     ],
     kinetic_math = KINETICMATH1,
     reversible = false)
-REACTION2 = SBML.Reaction(reactants = [
-        SBML.SpeciesReference(species = "s1", stoichiometry = 1.0),
+REACTION2 = SBML.Reaction(
+    reactants = [
+        SBML.SpeciesReference(species = "s1", stoichiometry = 1.0)
     ],
     kinetic_math = KINETICMATH3,
     reversible = true)

diff --git a/test/utils.jl b/test/utils.jl
@@ -42,8 +42,10 @@ sym = SBMLToolkit.map_symbolics_ident(SBML.MathIdent("B"), MODEL1)
 @parameters C D Bc
 
 test = SBML.MathApply("*",
-    SBML.Math[SBML.MathApply("+",
-            SBML.Math[SBML.MathApply("*",
+    SBML.Math[
+        SBML.MathApply("+",
+            SBML.Math[
+                SBML.MathApply("*",
                     SBML.Math[SBML.MathAvogadro("A"),
                         SBML.MathIdent("B")]),
                 SBML.MathApply("-",