Merge pull request #383 from LCSB-BioCore/mk-final-doc-fixes

final doc fixes for 1.0.3

docs/src/advanced/2_custom_model.md

@@ -21,12 +21,13 @@ and overload the required accessors. The accessors are functions that extract
 some relevant information, such as [`stoichiometry`](@ref) and
 [`bounds`](@ref), returning a fixed simple data type that can be further used
 by COBREXA.  You may see a complete list of accessors
-[here](../functions#Base-Types).
+[here](../functions.md#Base-Types).
 
 A good solution to the second concern is a slightly more involved, as writing
 generic data modifiers is notoriously hard. Still, there is support for easily
 making small changes to the model using the modifications system, with
-functions such as [`with_added_reactions`](@ref) and [`with_set_bound`](@ref).
+functions such as [`with_added_reactions`](@ref) and
+[`with_changed_bound`](@ref).
 
 !!! tip "Notebook available"
     A better example of using a custom model structure is available

docs/src/functions.md

@@ -77,6 +77,11 @@ Modules = [COBREXA]
 Pages = map(file -> joinpath("base", "utils", file), readdir("../src/base/utils"))
 ```
 
+```@autodocs
+Modules = [COBREXA]
+Pages = map(file -> joinpath("base", "macros", file), readdir("../src/base/macros"))
+```
+
 ### Logging and debugging helpers
 
 ```@autodocs

src/base/macros/change_bounds.jl

@@ -27,7 +27,7 @@ macro _change_bounds_fn(model_type, idx_type, args...)
     docstring = """
         $fname(
             model::$model_type,
-            $idx_var::$idx_type,
+            $idx_var::$idx_type;
             lower = $missing_default,
             upper = $missing_default,
         )

src/base/types/Reaction.jl

 """
-Reaction struct.
+    mutable struct Reaction
+        id::String
+        name::Maybe{String}
+        metabolites::Dict{String,Float64}
+        lb::Float64
+        ub::Float64
+        grr::Maybe{GeneAssociation}
+        subsystem::Maybe{String}
+        notes::Notes
+        annotations::Annotations
+        objective_coefficient::Float64
+    end
 
-# Fields
-````
-id :: String
-name :: String
-metabolites :: Dict{Metabolite, Float64}
-lb :: Float64
-ub :: Float64
-grr :: Vector{Vector{Gene}}
-subsystem :: String
-notes :: Dict{String, Vector{String}}
-annotation :: Dict{String, Union{Vector{String}, String}}
-objective_coefficient :: Float64
-````
+A structure for representing a single reaction in a [`StandardModel`](@ref).
 """
 mutable struct Reaction
     id::String
@@ -29,7 +28,7 @@ mutable struct Reaction
 end
 
 """
-Reaction(
+    Reaction(
         id = "";
         name = nothing,
         metabolites = Dict{String,Float64}(),
@@ -40,7 +39,7 @@ Reaction(
         notes = Notes(),
         annotations = Annotations(),
         objective_coefficient = 0.0,
-)
+    )
 
 A constructor for Reaction that only takes a reaction `id` and
 assigns default/uninformative values to all the fields that are not
@@ -74,12 +73,12 @@ function Reaction(
 end
 
 """
-Reaction(
+    Reaction(
         id::String,
         metabolites::Dict{String,Union{Int, Float64}},
         dir = :bidirectional;
         default_bound = _constants.default_reaction_bound,
-)
+    )
 
 Convenience constructor for `Reaction`. The reaction equation is specified using
 `metabolites`, which is a dictionary mapping metabolite ids to stoichiometric