Fix awkward line splits from JuliaFormatter

- Keep tuple assignments (fig, ax, plt) on single lines
- Fix split function calls and constant definitions
- Improve readability by keeping related elements together
- Binary operations with long warnings kept more readable

These changes address formatting issues introduced by JuliaFormatter
that made the code less readable by splitting logical units across lines.

Author: ChrisRackauckas

ext/CatalystCairoMakieExtension/cairo_makie_extension_spatial_modelling.jl

@@ -24,8 +24,7 @@ function lattice_animation(
     vals, plot_min, plot_max = Catalyst.extract_vals(sol, sp, lrs, plot_min, plot_max, t)
 
     # Creates the base figure (which is modified in the animation).
-    fig, ax,
-    plt = scatterlines(vals[1];
+    fig, ax, plt = scatterlines(vals[1];
         axis = (xlabel = "Compartment", ylabel = "$(sp)",
             limits = (nothing, nothing, plot_min, plot_max)),
         markersize = markersize, kwargs...)
@@ -101,8 +100,7 @@ function lattice_animation(
     x_vals, y_vals = Catalyst.extract_grid_axes(lrs)
 
     # Creates the base figure (which is modified in the animation).
-    fig, ax,
-    hm = heatmap(x_vals, y_vals, vals[1];
+    fig, ax, hm = heatmap(x_vals, y_vals, vals[1];
         axis = (xgridvisible = false, ygridvisible = false,
             xlabel = "Compartment", ylabel = "Compartment"),
         colormap, colorrange = (plot_min, plot_max),

ext/CatalystGraphMakieExtension/graph_makie_extension_spatial_modelling.jl

@@ -27,10 +27,8 @@ function lattice_animation(
     vals, plot_min, plot_max = Catalyst.extract_vals(sol, sp, lrs, plot_min, plot_max, t)
 
     # Creates the base figure (which is modified in the animation).
-    fig, ax,
-    plt = graphplot(plot_graph; node_color = vals[1],
-        node_attr = (colorrange = (plot_min, plot_max), colormap), node_size, kwargs...
-    )
+    fig, ax, plt = graphplot(plot_graph; node_color = vals[1],
+        node_attr = (colorrange = (plot_min, plot_max), colormap), node_size, kwargs...)
     ttitle && (ax.title = "Time: $(round(t[1]; sigdigits = 3))")
 
     # Creates the animation.

src/chemistry_functionality.jl

@@ -275,8 +275,7 @@ function balance_reaction(reaction::Reaction)
     end
 
     isempty(balancedrxs) && (@warn "Unable to balance reaction.")
-    (length(balancedrxs) > 1) &&
-        (@warn "The space of possible balanced versions of the reaction ($reaction) is greater than one-dimension. This prevents the selection of a single appropriate balanced reaction. Instead, a basis for balanced reactions is returned. Note that we do not check if they preserve the set of substrates and products from the original reaction.")
+    (length(balancedrxs) > 1) && (@warn "The space of possible balanced versions of the reaction ($reaction) is greater than one-dimension. This prevents the selection of a single appropriate balanced reaction. Instead, a basis for balanced reactions is returned. Note that we do not check if they preserve the set of substrates and products from the original reaction.")
     return balancedrxs
 end
 

src/dsl.jl

@@ -3,15 +3,14 @@
 # Declare various arrow types symbols used for the empty set (also 0).
 const empty_set = Set{Symbol}([:∅, :Ø])
 const fwd_arrows = Set{Symbol}([:>, :(=>), :→, :↣, :↦, :⇾, :⟶, :⟼, :⥟, :⥟, :⇀, :⇁, :⇒, :⟾])
-const bwd_arrows = Set{Symbol}([:<, :(<=), :←, :↢, :↤, :⇽, :⟵, :⟻, :⥚, :⥞, :↼, :↽, :⇐, :⟽,
-    Symbol("<--")])
+const bwd_arrows = Set{Symbol}([:<, :(<=), :←, :↢, :↤, :⇽, :⟵, :⟻, :⥚, :⥞, :↼, :↽, :⇐, :⟽, Symbol("<--")])
 const double_arrows = Set{Symbol}([:↔, :⟷, :⇄, :⇆, :⇌, :⇋, :⇔, :⟺, Symbol("<-->")])
 const pure_rate_arrows = Set{Symbol}([:(=>), :(<=), :⇐, :⟽, :⇒, :⟾, :⇔, :⟺])
 
 # Declares the keys used for various options.
 const option_keys = (:species, :parameters, :variables, :ivs, :compounds, :observables,
-    :default_noise_scaling, :differentials, :equations,
-    :continuous_events, :discrete_events, :combinatoric_ratelaws, :require_declaration)
+    :default_noise_scaling, :differentials, :equations, :continuous_events, :discrete_events,
+    :combinatoric_ratelaws, :require_declaration)
 
 ### `@species` Macro ###
 
@@ -298,14 +297,12 @@ function make_reaction_system(ex::Expr, name)
     requiredec = haskey(options, :require_declaration)
     reactions = get_reactions(reaction_lines)
     sps_inferred, ps_pre_inferred = extract_sps_and_ps(reactions, syms_declared; requiredec)
-    vs_inferred, diffs_inferred,
-    equations = read_equations_option!(diffsexpr, options,
+    vs_inferred, diffs_inferred, equations = read_equations_option!(diffsexpr, options,
         union(syms_declared, sps_inferred), tiv; requiredec)
     ps_inferred = setdiff(ps_pre_inferred, vs_inferred, diffs_inferred)
     syms_inferred = union(sps_inferred, ps_inferred, vs_inferred, diffs_inferred)
     all_syms = union(syms_declared, syms_inferred)
-    obsexpr, obs_eqs,
-    obs_syms = read_observables_option(options, ivs,
+    obsexpr, obs_eqs, obs_syms = read_observables_option(options, ivs,
         union(sps_declared, vs_declared), all_syms; requiredec)
 
     # Read options not related to the declaration or inference of symbols.

src/reaction.jl

@@ -702,8 +702,7 @@ Notes: The following values are possible:
 end
 
 const JUMP_SCALES = (PhysicalScale.Jump, PhysicalScale.VariableRateJump)
-const NON_CONSTANT_JUMP_SCALES = (
-    PhysicalScale.ODE, PhysicalScale.SDE, PhysicalScale.VariableRateJump)
+const NON_CONSTANT_JUMP_SCALES = (PhysicalScale.ODE, PhysicalScale.SDE, PhysicalScale.VariableRateJump)
 
 """
     has_physical_scale(rx::Reaction)

src/reactionsystem_serialisation/serialise_fields.jl

@@ -102,12 +102,9 @@ function handle_us_n_ps(file_text::String, rn::ReactionSystem, annotate::Bool,
         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,
-                [remaining_ps; remaining_sps; remaining_vars])
-            writable_sps = dependency_split!(remaining_sps,
-                [remaining_ps; remaining_sps; remaining_vars])
-            writable_vars = dependency_split!(remaining_vars,
-                [remaining_ps; remaining_sps; remaining_vars])
+            writable_ps = dependency_split!(remaining_ps, [remaining_ps; remaining_sps; remaining_vars])
+            writable_sps = dependency_split!(remaining_sps, [remaining_ps; remaining_sps; remaining_vars])
+            writable_vars = dependency_split!(remaining_vars, [remaining_ps; remaining_sps; remaining_vars])
 
             # Writes those that can be written.
             isempty(writable_ps) ||
@@ -430,8 +427,7 @@ function get_continuous_events_annotation(rn::ReactionSystem)
 end
 
 # Combines the 3 -related functions in a constant tuple.
-CONTINUOUS_EVENTS_FS = (seri_has_continuous_events, get_continuous_events_string,
-    get_continuous_events_annotation)
+CONTINUOUS_EVENTS_FS = (seri_has_continuous_events, get_continuous_events_string, get_continuous_events_annotation)
 
 ### Handles Discrete Events ###
 
@@ -487,8 +483,7 @@ function get_discrete_events_annotation(rn::ReactionSystem)
 end
 
 # Combines the 3 -related functions in a constant tuple.
-DISCRETE_EVENTS_FS = (seri_has_discrete_events, get_discrete_events_string,
-    get_discrete_events_annotation)
+DISCRETE_EVENTS_FS = (seri_has_discrete_events, get_discrete_events_string, get_discrete_events_annotation)
 
 ### Handles Systems ###
 
@@ -563,5 +558,4 @@ function get_connection_type_annotation(rn::ReactionSystem)
 end
 
 # Combines the 3 connection types-related functions in a constant tuple.
-CONNECTION_TYPE_FS = (
-    seri_has_connection_type, get_connection_type_string, get_connection_type_annotation)
+CONNECTION_TYPE_FS = (seri_has_connection_type, get_connection_type_string, get_connection_type_annotation)