merge fixes

Author: TorkelE

docs/make.jl

@@ -41,8 +41,7 @@ makedocs(sitename = "Catalyst.jl",
     clean = true,
     pages = pages,
     pagesonly = true,
-    warnonly = true)
-         warnonly = [:missing_docs])
+    warnonly = [:missing_docs])
 
 deploydocs(repo = "github.com/SciML/Catalyst.jl.git";
     push_preview = true)

docs/pages.jl

@@ -26,7 +26,7 @@ pages = Any[
         "model_simulation/simulation_plotting.md",
         "model_simulation/simulation_structure_interfacing.md",
         "model_simulation/ensemble_simulations.md",
-        "model_simulation/ode_simulation_performance.md",
+        "model_simulation/ode_simulation_performance.md"
     ],
     "Steady state analysis" => Any[
         "steady_state_functionality/homotopy_continuation.md",

src/reactionsystem_serialisation/serialise_fields.jl

@@ -43,7 +43,8 @@ SIVS_FS = (seri_has_sivs, get_sivs_string, get_sivs_annotation)
 
 # Function which handles the addition of species, variable, and parameter declarations to the file
 # text. These must be handled as a unity in case there are default value dependencies between these.
-function handle_us_n_ps(file_text::String, rn::ReactionSystem, annotate::Bool, top_level::Bool)
+function handle_us_n_ps(file_text::String, rn::ReactionSystem, annotate::Bool,
+        top_level::Bool)
     # Fetches the system's parameters, species, and variables. Computes the `has_` `Bool`s.
     ps_all = get_ps(rn)
     sps_all = get_species(rn)
@@ -408,7 +409,8 @@ 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 ###
 
@@ -464,17 +466,19 @@ 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 ###
 
 # Specific `push_field` function, which is used for the system field (where the annotation option
 # must be passed to the `get_component_string` function). Since non-ReactionSystem systems cannot be 
 # written to file, this function throws an error if any such systems are encountered.
-function push_systems_field(file_text::String, rn::ReactionSystem, annotate::Bool, top_level::Bool)
+function push_systems_field(file_text::String, rn::ReactionSystem, annotate::Bool, 
+        top_level::Bool)
     # Checks whether there are any subsystems, and if these are ReactionSystems.
     seri_has_systems(rn) || (return (file_text, false))
-    if any(!(system isa ReactionSystem) for system in MT.get_systems(rn)) 
+    if any(!(system isa ReactionSystem) for system in MT.get_systems(rn))
         error("Tries to write a ReactionSystem to file which have non-ReactionSystem subs-systems. This is currently not possible.")
     end
 
@@ -538,4 +542,5 @@ 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)

src/reactionsystem_serialisation/serialise_reactionsystem.jl

@@ -75,23 +75,25 @@ function get_full_system_string(rn::ReactionSystem, annotate::Bool, top_level::B
 
     # Finalise the system. Creates the final `ReactionSystem` call.
     # Enclose everything in a `let ... end` block.
-    rs_creation_code = make_reaction_system_call(rn, annotate, top_level, has_sivs, has_species, 
-                                                 has_variables, has_parameters, has_reactions, 
-                                                 has_equations, has_observed, has_continuous_events, 
-                                                 has_discrete_events, has_systems, has_connection_type)
-    annotate || (@string_prepend! "\n" file_text) 
-    @string_prepend! "let" file_text 
+    rs_creation_code = make_reaction_system_call(
+        rn, annotate, top_level, has_sivs, has_species,
+        has_variables, has_parameters, has_reactions,
+        has_equations, has_observed, has_continuous_events,
+        has_discrete_events, has_systems, has_connection_type)
+    annotate || (@string_prepend! "\n" file_text)
+    @string_prepend! "let" file_text
     @string_append! file_text "\n\n" rs_creation_code "\n\nend"
 
     return file_text
 end
 
 # Creates a ReactionSystem call for creating the model. Adds all the correct inputs to it. The input
 # `has_` `Bool`s described which inputs are used. If the model is `complete`, this is handled here.
-function make_reaction_system_call(rs::ReactionSystem, annotate, top_level, has_sivs, has_species, 
-                                   has_variables, has_parameters, has_reactions, has_equations, 
-                                   has_observed, has_continuous_events, has_discrete_events,
-                                   has_systems, has_connection_type)
+function make_reaction_system_call(
+        rs::ReactionSystem, annotate, top_level, has_sivs, has_species,
+        has_variables, has_parameters, has_reactions, has_equations,
+        has_observed, has_continuous_events, has_discrete_events,
+        has_systems, has_connection_type)
 
     # Gets the independent variable input.
     iv = x_2_string(get_iv(rs))