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 ...@@ -12,3 +12,9 @@ Pages = map(file -> joinpath("base", "types", "abstract", file), readdir("../src
Modules = [COBREXA] Modules = [COBREXA]
Pages = map(file -> joinpath("base", "types", file), readdir("../src/base/types")) 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"))
```
...@@ -31,7 +31,7 @@ end ...@@ -31,7 +31,7 @@ end
Return a vector of metabolite identifiers in a model. The vector precisely Return a vector of metabolite identifiers in a model. The vector precisely
corresponds to the rows in [`stoichiometry`](@ref) matrix. 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. representing purely technical equality constraints.
""" """
function metabolites(a::MetabolicModel)::Vector{String} function metabolites(a::MetabolicModel)::Vector{String}
......
...@@ -34,9 +34,10 @@ gene_product_mass_group_dict(model::GeckoModel, opt_model) = ...@@ -34,9 +34,10 @@ gene_product_mass_group_dict(model::GeckoModel, opt_model) =
""" """
gene_product_mass_group_dict(model::GeckoModel) 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) gene_product_mass(model::SMomentModel)
......
...@@ -21,7 +21,7 @@ refining genome annotation." *Proceedings of the National Academy of Sciences* ...@@ -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 The function returns a solved JuMP optimization model, with the boolean
reaction inclusion indicators in variable vector `y`. Use 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. information in Julia datatypes.
To reduce the uncertainty in the MILP solver (and likely reduce the To reduce the uncertainty in the MILP solver (and likely reduce the
......
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