format

Author: isaacsas

src/systems/abstractsystem.jl

@@ -930,7 +930,7 @@ function complete(sys::AbstractSystem; split = true, flatten = true)
     # don't update unknowns to not disturb `structural_simplify` order
     # `GlobalScope`d unknowns will be picked up and added there
     @set! sys.ps = unique!(vcat(get_ps(sys), collect(newparams)))
-    
+
     if flatten
         eqs = equations(sys)
         if eqs isa AbstractArray && eltype(eqs) <: Equation

src/systems/jumps/jumpsystem.jl

@@ -174,14 +174,15 @@ function JumpSystem(eqs, iv, unknowns, ps;
             "`default_u0` and `default_p` are deprecated. Use `defaults` instead.",
             :JumpSystem, force = true)
     end
-    defaults = Dict{Any,Any}(todict(defaults))
+    defaults = Dict{Any, Any}(todict(defaults))
     var_to_name = Dict()
     process_variables!(var_to_name, defaults, us′)
     process_variables!(var_to_name, defaults, ps′)
     process_variables!(var_to_name, defaults, [eq.lhs for eq in parameter_dependencies])
     process_variables!(var_to_name, defaults, [eq.rhs for eq in parameter_dependencies])
-    defaults = Dict{Any, Any}(value(k) => value(v) for (k, v) in pairs(defaults) 
-        if value(v) !== nothing)
+    #! format: off
+    defaults = Dict{Any, Any}(value(k) => value(v) for (k, v) in pairs(defaults) if value(v) !== nothing)
+    #! format: on
     isempty(observed) || collect_var_to_name!(var_to_name, (eq.lhs for eq in observed))
 
     sysnames = nameof.(systems)
@@ -218,8 +219,8 @@ end
 
 ##### MTK dispatches for JumpSystems #####
 eqtype_supports_collect_vars(j::MassActionJump) = true
-function collect_vars!(unknowns, parameters, j::MassActionJump, iv; depth = 0, 
-        op = Differential)    
+function collect_vars!(unknowns, parameters, j::MassActionJump, iv; depth = 0,
+        op = Differential)
     collect_vars!(unknowns, parameters, j.scaled_rates, iv; depth, op)
     for field in (j.reactant_stoch, j.net_stoch)
         for el in field
@@ -229,8 +230,8 @@ function collect_vars!(unknowns, parameters, j::MassActionJump, iv; depth = 0,
     return nothing
 end
 
-eqtype_supports_collect_vars(j::Union{ConstantRateJump,VariableRateJump}) = true
-function collect_vars!(unknowns, parameters, j::Union{ConstantRateJump,VariableRateJump}, 
+eqtype_supports_collect_vars(j::Union{ConstantRateJump, VariableRateJump}) = true
+function collect_vars!(unknowns, parameters, j::Union{ConstantRateJump, VariableRateJump},
         iv; depth = 0, op = Differential)
     collect_vars!(unknowns, parameters, j.rate, iv; depth, op)
     for eq in j.affect!
@@ -278,7 +279,7 @@ function assemble_vrj(
 
     outputvars = (value(affect.lhs) for affect in vrj.affect!)
     outputidxs = [unknowntoid[var] for var in outputvars]
-    affect = eval_or_rgf(generate_affect_function(js, vrj.affect!, outputidxs); 
+    affect = eval_or_rgf(generate_affect_function(js, vrj.affect!, outputidxs);
         eval_expression, eval_module)
     VariableRateJump(rate, affect)
 end
@@ -306,7 +307,7 @@ function assemble_crj(
 
     outputvars = (value(affect.lhs) for affect in crj.affect!)
     outputidxs = [unknowntoid[var] for var in outputvars]
-    affect = eval_or_rgf(generate_affect_function(js, crj.affect!, outputidxs); 
+    affect = eval_or_rgf(generate_affect_function(js, crj.affect!, outputidxs);
         eval_expression, eval_module)
     ConstantRateJump(rate, affect)
 end

test/jumpsystem.jl

@@ -341,15 +341,14 @@ let
     @test all(abs.(cmean .- cmean2) .<= 0.05 .* cmean)
 end
 
-
 # collect_vars! tests for jumps
-let 
+let
     @variables x1(t) x2(t) x3(t) x4(t) x5(t)
     @parameters p1 p2 p3 p4 p5
     j1 = ConstantRateJump(p1, [x1 ~ x1 + 1])
     j2 = MassActionJump(p2, [x2 => 1], [x3 => -1])
     j3 = VariableRateJump(p3, [x3 ~ x3 + 1, x4 ~ x4 + 1])
-    j4 = MassActionJump(p4*p5, [x1 => 1, x5 => 1], [x1 => -1, x5 => -1, x2 => 1])
+    j4 = MassActionJump(p4 * p5, [x1 => 1, x5 => 1], [x1 => -1, x5 => -1, x2 => 1])
     us = Set()
     ps = Set()
     iv = t
@@ -389,35 +388,36 @@ let
     p3 = ParentScope(ParentScope(p3))
     p4 = DelayParentScope(p4, 2)
     p5 = GlobalScope(p5)
-    
+
     j1 = ConstantRateJump(p1, [x1 ~ x1 + 1])
     j2 = MassActionJump(p2, [x2 => 1], [x3 => -1])
     j3 = VariableRateJump(p3, [x3 ~ x3 + 1, x4 ~ x4 + 1])
-    j4 = MassActionJump(p4*p5, [x1 => 1, x5 => 1], [x1 => -1, x5 => -1, x2 => 1])
+    j4 = MassActionJump(p4 * p5, [x1 => 1, x5 => 1], [x1 => -1, x5 => -1, x2 => 1])
     @named js = JumpSystem([j1, j2, j3, j4], t, [x1, x2, x3, x4, x5], [p1, p2, p3, p4, p5])
 
-    us = Set(); ps = Set()
+    us = Set()
+    ps = Set()
     iv = t
     MT.collect_scoped_vars!(us, ps, js, iv)
     @test issetequal(us, [x2])
     @test issetequal(ps, [p2])
 
-    empty!.((us,ps))
+    empty!.((us, ps))
     MT.collect_scoped_vars!(us, ps, js, iv; depth = 0)
     @test issetequal(us, [x1])
     @test issetequal(ps, [p1])
 
-    empty!.((us,ps))
+    empty!.((us, ps))
     MT.collect_scoped_vars!(us, ps, js, iv; depth = 1)
     @test issetequal(us, [x2])
     @test issetequal(ps, [p2])
 
-    empty!.((us,ps))
+    empty!.((us, ps))
     MT.collect_scoped_vars!(us, ps, js, iv; depth = 2)
     @test issetequal(us, [x3, x4])
     @test issetequal(ps, [p3, p4])
 
-    empty!.((us,ps))
+    empty!.((us, ps))
     MT.collect_scoped_vars!(us, ps, js, iv; depth = -1)
     @test issetequal(us, [x5])
     @test issetequal(ps, [p5])