Merge pull request #621 from LCSB-BioCore/mk-fix-doc

fix documentation issues and warnings

docs/src/functions/types.md

@@ -12,3 +12,9 @@ Pages = map(file -> joinpath("base", "types", "abstract", file), readdir("../src
 Modules = [COBREXA]
 Pages = map(file -> joinpath("base", "types", file), readdir("../src/base/types"))
 ```
+
+## Model type wrappers
+```@autodocs
+Modules = [COBREXA]
+Pages = map(file -> joinpath("base", "types", "wrappers", file), readdir("../src/base/types/wrappers"))
+```

src/base/types/MetabolicModel.jl

@@ -31,7 +31,7 @@ end
 Return a vector of metabolite identifiers in a model. The vector precisely
 corresponds to the rows in [`stoichiometry`](@ref) matrix.
 
-As with [`reaction`](@ref)s, some metabolites in models may be virtual,
+As with [`reactions`](@ref)s, some metabolites in models may be virtual,
 representing purely technical equality constraints.
 """
 function metabolites(a::MetabolicModel)::Vector{String}

src/base/utils/enzymes.jl

@@ -34,9 +34,10 @@ gene_product_mass_group_dict(model::GeckoModel, opt_model) =
 """
     gene_product_mass_group_dict(model::GeckoModel)
 
-A pipe-able variant of [`mass_group_dict`](@ref).
+A pipe-able variant of [`gene_product_mass_group_dict`](@ref).
 """
-gene_product_mass_group_dict(model::GeckoModel) = x -> mass_group_dict(model, x)
+gene_product_mass_group_dict(model::GeckoModel) =
+    x -> gene_product_mass_group_dict(model, x)
 
 """
     gene_product_mass(model::SMomentModel)

src/reconstruction/gapfill_minimum_reactions.jl

@@ -21,7 +21,7 @@ refining genome annotation." *Proceedings of the National Academy of Sciences*
 
 The function returns a solved JuMP optimization model, with the boolean
 reaction inclusion indicators in variable vector `y`. Use
-[`mask`](@ref) or [`gapfilled_rids`](@ref) to collect the reaction
+[`gapfilled_mask`](@ref) or [`gapfilled_rids`](@ref) to collect the reaction
 information in Julia datatypes.
 
 To reduce the uncertainty in the MILP solver (and likely reduce the