update docs

Author: isaacsas

docs/src/api/catalyst_api.md

@@ -11,8 +11,9 @@ be converted to other `ModelingToolkit.AbstractSystem`s, including a
 `ModelingToolkit.ODESystem`, `ModelingToolkit.SDESystem`, or
 `ModelingToolkit.JumpSystem`.
 
-An empty network can be generated using [`@reaction_network`](@ref) with no arguments or
-the [`make_empty_network`](@ref) function. These can then be extended
+An empty network can be generated using [`@reaction_network`](@ref) with no
+arguments (or one argument to name the system), or the
+[`make_empty_network`](@ref) function. These can then be extended
 programmatically using [`addspecies!`](@ref), [`addparam!`](@ref), and
 [`addreaction!`](@ref).
 

docs/src/tutorials/generated_systems.md

@@ -33,7 +33,7 @@ Each `Reaction` within `reactions(rn)` has a number of subfields. For `rx` a
   non-filled arrows and should ignore mass action kinetics. `false` by default.
 
 Empty `ReactionSystem`s can be generated via [`make_empty_network`](@ref) or
-[`@reaction_network`](@ref) with no arguments. `ReactionSystem`s can be
-programmatically extended using [`addspecies!`](@ref), [`addparam!`](@ref),
-[`addreaction!`](@ref), [`@add_reactions`](@ref), or composed using `merge` and
-`merge!`.
+[`@reaction_network`](@ref) with no arguments (giving one argument to the latter
+will specify a system name). `ReactionSystem`s can be programmatically extended
+using [`addspecies!`](@ref), [`addparam!`](@ref), [`addreaction!`](@ref),
+[`@add_reactions`](@ref), or composed using `merge` and `merge!`.

src/networkapi.jl

@@ -219,10 +219,11 @@ end
 ######################## functions to extend a network ####################
 
 """
-    make_empty_network(; iv=Sym{ModelingToolkit.Parameter{Real}}(:t), name=gensym(:ReactionSystem))
+    make_empty_network(; iv=Sym{ModelingToolkit.Parameter{Real}}(:t), 
+                         name=gensym(:ReactionSystem))
 
 Construct an empty [`ReactionSystem`](@ref). `iv` is the independent variable,
-usually time.
+usually time, and `name` is the name to give the `ReactionSystem`.
 """
 function make_empty_network(; iv=Sym{ModelingToolkit.Parameter{Real}}(:t), name=gensym(:ReactionSystem))
     ReactionSystem(Reaction[], iv, [], [], Equation[], name, ReactionSystem[])

src/reaction_network.jl

@@ -65,6 +65,14 @@ bwd_arrows = Set{Symbol}([:<, :←, :↢, :↤, :⇽, :⟵, :⟻, :⥚, :⥞, :
 double_arrows = Set{Symbol}([:↔, :⟷, :⇄, :⇆, :⇌, :⇋, :⇔, :⟺])
 pure_rate_arrows = Set{Symbol}([:⇐, :⟽, :⇒, :⟾, :⇔, :⟺])
 
+# unfortunately the following doesn't seem to work on 1.5, so supporting these 
+# operators seems to require us to only support 1.6 and up...
+# @static if VERSION >= v"1.6.0"
+#     push!(bwd_arrows, :<--)
+#     push!(double_arrows, :<-->)
+# end
+
+
 # Declares symbols which may neither be used as parameters not varriables.
 forbidden_symbols = [:t, :π, :pi, :ℯ, :im, :nothing, :∅]
 
@@ -78,6 +86,27 @@ network.
 
 See the [Catalyst.jl for Reaction Models](@ref) documentation for details on
 parameters to the macro.
+
+Examples:
+```julia
+# a basic SIR model, with name SIR
+sir_model = @reaction_network SIR begin
+    c1, s + i --> 2i
+    c2, i --> r
+end c1 c2
+
+# a basic SIR model, with random generated name
+sir_model = @reaction_network begin
+    c1, s + i --> 2i
+    c2, i --> r
+end c1 c2
+
+# an empty network with name empty
+emptyrn = @reaction_network empty
+
+# an empty network with random generated name
+emptyrn = @reaction_network 
+```
 """
 macro reaction_network(name::Symbol, ex::Expr, parameters...)
     make_reaction_system(MacroTools.striplines(ex), parameters; name=name)
@@ -87,10 +116,7 @@ macro reaction_network(ex::Expr, parameters...)
     make_reaction_system(MacroTools.striplines(ex), parameters)
 end
 
-
-### Macros used for manipulating, and successively builing up, reaction systems. ###
-
-#Returns a empty network (with, or without, parameters declared)
+#Returns a empty network (with, or without, a declared name)
 macro reaction_network(name::Symbol=gensym(:ReactionSystem))
     return Expr(:block,:(@parameters t),
                 :(ReactionSystem(Reaction[],
@@ -102,6 +128,8 @@ macro reaction_network(name::Symbol=gensym(:ReactionSystem))
                                  ReactionSystem[])))
 end
 
+### Macros used for manipulating, and successively builing up, reaction systems. ###
+
 """
     @add_reactions