Commit 02e0c7fa authored by Miroslav Kratochvil's avatar Miroslav Kratochvil
Browse files

fix documentation issues and warnings

parent 78eb5bd4
Pipeline #56598 passed with stages
in 12 minutes and 55 seconds
......@@ -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
Modules = [COBREXA]
Pages = map(file -> joinpath("base", "types", "wrappers", file), readdir("../src/base/types/wrappers"))
......@@ -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}
......@@ -34,9 +34,10 @@ gene_product_mass_group_dict(model::GeckoModel, opt_model) =
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)
......@@ -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
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