Merge branch 'formatting' of github.com:SciML/Catalyst.jl into formatting

Author: TorkelE

src/network_analysis.jl

@@ -398,7 +398,7 @@ end
 # Used in the subsequent function.
 function subnetworkmapping(linkageclass, allrxs, complextorxsmap, p)
     rxinds = sort!(collect(Set(rxidx for rcidx in linkageclass
-    for rxidx in complextorxsmap[rcidx])))
+        for rxidx in complextorxsmap[rcidx])))
     rxs = allrxs[rxinds]
     specset = Set(s for rx in rxs for s in rx.substrates if !isconstant(s))
     for rx in rxs

src/reaction.jl

@@ -334,8 +334,8 @@ function MT.namespace_equation(rx::Reaction, name; kw...)
         ns = similar(rx.netstoich)
         map!(n -> f(n[1]) => f(n[2]), ns, rx.netstoich)
     end
-    Reaction(
-        rate, subs, prods, substoich, prodstoich, netstoich, rx.only_use_rate, rx.metadata)
+    Reaction(rate, subs, prods, substoich, prodstoich, netstoich, 
+        rx.only_use_rate, rx.metadata)
 end
 
 # Overwrites equation-type functions to give the correct input for `Reaction`s.
@@ -497,7 +497,7 @@ function getmetadata(reaction::Reaction, md_key::Symbol)
     end
     metadata = getmetadata_dict(reaction)
     return metadata[findfirst(isequal(md_key, entry[1])
-    for entry in getmetadata_dict(reaction))][2]
+        for entry in getmetadata_dict(reaction))][2]
 end
 
 ### Implemented Reaction Metadata ###

src/reactionsystem.jl

@@ -1251,9 +1251,8 @@ function set_default_metadata(rs::ReactionSystem; default_reaction_metadata = []
         ns_syms = [Symbolics.unwrap(sym) for sym in get_variables(ns_expr)]
         ns_ps = Iterators.filter(ModelingToolkit.isparameter, ns_syms)
         ns_sps = Iterators.filter(Catalyst.isspecies, ns_syms)
-        ns_vs = Iterators.filter(
-            sym -> !Catalyst.isspecies(sym) &&
-                !ModelingToolkit.isparameter(sym), ns_syms)
+        ns_vs = Iterators.filter(sym -> !Catalyst.isspecies(sym) &&
+            !ModelingToolkit.isparameter(sym), ns_syms)
         # Adds parameters, species, and variables to the `ReactionSystem`.
         @set! rs.ps = union(get_ps(rs), ns_ps)
         sps_new = union(get_species(rs), ns_sps)

src/reactionsystem_conversions.jl

@@ -472,8 +472,8 @@ Keyword args and default values:
 function Base.convert(::Type{<:ODESystem}, rs::ReactionSystem; name = nameof(rs),
         combinatoric_ratelaws = get_combinatoric_ratelaws(rs),
         include_zero_odes = true, remove_conserved = false, checks = false,
-        default_u0 = Dict(), default_p = Dict(), defaults = _merge(
-            Dict(default_u0), Dict(default_p)),
+        default_u0 = Dict(), default_p = Dict(), 
+        defaults = _merge(Dict(default_u0), Dict(default_p)),
         kwargs...)
     iscomplete(rs) || error(COMPLETENESS_ERROR)
     spatial_convert_err(rs::ReactionSystem, ODESystem)
@@ -514,8 +514,8 @@ Keyword args and default values:
 function Base.convert(::Type{<:NonlinearSystem}, rs::ReactionSystem; name = nameof(rs),
         combinatoric_ratelaws = get_combinatoric_ratelaws(rs),
         include_zero_odes = true, remove_conserved = false, checks = false,
-        default_u0 = Dict(), default_p = Dict(), defaults = _merge(
-            Dict(default_u0), Dict(default_p)),
+        default_u0 = Dict(), default_p = Dict(), 
+        defaults = _merge(Dict(default_u0), Dict(default_p)),
         all_differentials_permitted = false, kwargs...)
     # Error checks.
     iscomplete(rs) || error(COMPLETENESS_ERROR)
@@ -596,8 +596,8 @@ Notes:
 function Base.convert(::Type{<:SDESystem}, rs::ReactionSystem;
         name = nameof(rs), combinatoric_ratelaws = get_combinatoric_ratelaws(rs),
         include_zero_odes = true, checks = false, remove_conserved = false,
-        default_u0 = Dict(), default_p = Dict(), defaults = _merge(
-            Dict(default_u0), Dict(default_p)),
+        default_u0 = Dict(), default_p = Dict(), 
+        defaults = _merge(Dict(default_u0), Dict(default_p)),
         kwargs...)
     iscomplete(rs) || error(COMPLETENESS_ERROR)
     spatial_convert_err(rs::ReactionSystem, SDESystem)
@@ -647,8 +647,8 @@ Notes:
 function Base.convert(::Type{<:JumpSystem}, rs::ReactionSystem; name = nameof(rs),
         combinatoric_ratelaws = get_combinatoric_ratelaws(rs),
         remove_conserved = nothing, checks = false,
-        default_u0 = Dict(), default_p = Dict(), defaults = _merge(
-            Dict(default_u0), Dict(default_p)),
+        default_u0 = Dict(), default_p = Dict(), 
+        defaults = _merge(Dict(default_u0), Dict(default_p)),
         kwargs...)
     iscomplete(rs) || error(COMPLETENESS_ERROR)
     spatial_convert_err(rs::ReactionSystem, JumpSystem)