fix docstrings

LCSB-BioCore · Jul 9, 2021 · 8972842 · 8972842
1 parent 7205fd1
commit 8972842
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Showing 4 changed files with 24 additions and 25 deletions.
diff --git a/src/base/docstrings/docstrings.jl b/src/base/docstrings/docstrings.jl
@@ -1,6 +1,6 @@
 macro _change_bound_s_bang(model_type, index_name, index_type, example, is_singular, is_inplace)
-    if eval(:($is_singular) != :singular)
-        if eval(:($is_inplace) == :inplace)
+    if eval(:($is_singular != :singular))
+        if eval(:($is_inplace == :inplace))
             add_bang = "!"
             descr_sentence = "Change the bounds of all reactions with `$(index_name)` in `model` in-place."
         else
@@ -14,13 +14,12 @@ macro _change_bound_s_bang(model_type, index_name, index_type, example, is_singu
         lbs = "fill(nothing, length($(index_name)))"
         ubs = "fill(nothing, length($(index_name)))"
     else
-        if eval(:($is_inplace) == :inplace)
+        if eval(:($is_inplace == :inplace))
             add_bang = "!"
             descr_sentence = "Change the bounds of a reaction `$(index_name)` in `model` in-place."
         else
             add_bang = ""
-            descr_sentence = "Return a shallow copy of the `model` where the bounds of reaction with
-            `$(index_name)` has been changed."
+            descr_sentence = "Return a shallow copy of the `model` where the bounds of reaction with `$(index_name)` has been changed."
         end
         add_s = ""
         bounds1 = "lower_bound=-10, upper_bound=10"
@@ -38,7 +37,7 @@ macro _change_bound_s_bang(model_type, index_name, index_type, example, is_singu
             upper_bound$($add_s) = $($ubs),
         )
     
-    $($descr_sentence) Note that if the bound argument is `nothing` then it is not changed. 
+    $($descr_sentence) Note, if the bound argument is `nothing` then it is not changed. 
     
     See also: [`change_bound`](@ref), [`change_bounds!`](@ref), [`change_bound!`](@ref), [`change_bounds!`](@ref)
     

diff --git a/src/reconstruction/CoreModel.jl b/src/reconstruction/CoreModel.jl
@@ -387,7 +387,7 @@ function change_bounds!(
     end
 end
 
-# @doc @_change_bound_s_bang("CoreModel", "rxn_idx", "Int", "2", not_plural, is_inplace)
+@doc @_change_bound_s_bang("CoreModel", "rxn_idx", "Int", "2", :singular, :inplace)
 function change_bound!(
     model::CoreModel,
     rxn::Int;
@@ -399,7 +399,7 @@ function change_bound!(
     return nothing # so that nothing gets printed
 end
 
-# @doc @_change_bound_s_bang("CoreModel", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", is_plural, is_inplace)
+@doc @_change_bound_s_bang("CoreModel", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", :plural, :inplace)
 function change_bounds!(
     model::CoreModel,
     rxn_ids::Vector{String};
@@ -409,7 +409,7 @@ function change_bounds!(
     change_bounds!(model, Int.(indexin(rxn_ids, reactions(model))); lower_bounds = lower_bounds, upper_bounds = upper_bounds)
 end
 
-# @doc @_change_bound_s_bang("CoreModel", "rxn_id", "String", "\"PFL\"", not_plural, is_inplace)
+@doc @_change_bound_s_bang("CoreModel", "rxn_id", "String", "\"PFL\"", :singular, :inplace)
 function change_bound!(
     model::CoreModel,
     rxn_id::String;
@@ -419,7 +419,7 @@ function change_bound!(
     change_bound!(model, first(indexin([rxn_id], reactions(model))); lower_bound = lower_bound, upper_bound = upper_bound)
 end
 
-# @doc @_change_bound_s_bang("CoreModel", "rxn_idxs", "Vector{Int}", "[2, 43]", is_plural, not_inplace)
+@doc @_change_bound_s_bang("CoreModel", "rxn_idxs", "Vector{Int}", "[2, 43]", :plural, :notinplace)
 function change_bounds(
     model::CoreModel,
     rxns::Vector{Int};
@@ -436,7 +436,7 @@ function change_bounds(
     return m
 end
 
-# @doc @_change_bound_s_bang("CoreModel", "rxn_idx", "Int", "2", not_plural, not_inplace)
+@doc @_change_bound_s_bang("CoreModel", "rxn_idx", "Int", "2", :singular, :notinplace)
 function change_bound(
     model::CoreModel,
     rxn::Int;
@@ -451,7 +451,7 @@ function change_bound(
     return m
 end
 
-# @doc @_change_bound_s_bang("CoreModel", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", is_plural, not_inplace)
+@doc @_change_bound_s_bang("CoreModel", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", :plural, :notinplace)
 function change_bounds(
     model::CoreModel,
     rxn_ids::Vector{String};
@@ -461,7 +461,7 @@ function change_bounds(
     change_bounds(model, Int.(indexin(rxn_ids, reactions(model))); lower_bounds = lower_bounds, upper_bounds = upper_bounds)
 end
 
-# @doc @_change_bound_s_bang("CoreModel", "rxn_id", "String", "\"PFL\"", not_plural, not_inplace)
+@doc @_change_bound_s_bang("CoreModel", "rxn_id", "String", "\"PFL\"", :singular, :notinplace)
 function change_bound(
     model::CoreModel,
     rxn_id::String;

diff --git a/src/reconstruction/CoreModelCoupled.jl b/src/reconstruction/CoreModelCoupled.jl
@@ -362,7 +362,7 @@ function change_coupling_bounds!(
     end
 end
 
-# @doc @_change_bound_s_bang("CoreModelCoupled", "rxn_idxs", "Vector{Int}", "[2, 43]", is_plural, is_inplace)
+@doc @_change_bound_s_bang("CoreModelCoupled", "rxn_idxs", "Vector{Int}", "[2, 43]", :plural, :inplace)
 function change_bounds!(
     model::CoreModelCoupled,
     reaction_idxs::Vector{Int};
@@ -374,7 +374,7 @@ function change_bounds!(
     end
 end
 
-# @doc @_change_bound_s_bang("CoreModelCoupled", "rxn_idx", "Int", "2", not_plural, is_inplace)
+@doc @_change_bound_s_bang("CoreModelCoupled", "rxn_idx", "Int", "2", :singular, :inplace)
 function change_bound!(
     model::CoreModelCoupled,
     rxn::Int;
@@ -386,7 +386,7 @@ function change_bound!(
     return nothing # so that nothing gets printed
 end
 
-# @doc @_change_bound_s_bang("CoreModelCoupled", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", is_plural, is_inplace)
+@doc @_change_bound_s_bang("CoreModelCoupled", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", :plural, :inplace)
 function change_bounds!(
     model::CoreModelCoupled,
     rxn_ids::Vector{String};
@@ -396,7 +396,7 @@ function change_bounds!(
     change_bounds!(model, Int.(indexin(rxn_ids, reactions(model))); lower_bounds = lower_bounds, upper_bounds = upper_bounds)
 end
 
-# @doc @_change_bound_s_bang("CoreModelCoupled", "rxn_id", "String", "\"PFL\"", not_plural, is_inplace)
+@doc @_change_bound_s_bang("CoreModelCoupled", "rxn_id", "String", "\"PFL\"", :singular, :inplace)
 function change_bound!(
     model::CoreModelCoupled,
     rxn_id::String;
@@ -406,7 +406,7 @@ function change_bound!(
     change_bound!(model, first(indexin([rxn_id], reactions(model))); lower_bound = lower_bound, upper_bound = upper_bound)
 end
 
-# @doc @_change_bound_s_bang("CoreModelCoupled", "rxn_idxs", "Vector{Int}", "[2, 43]", is_plural, not_inplace)
+@doc @_change_bound_s_bang("CoreModelCoupled", "rxn_idxs", "Vector{Int}", "[2, 43]", :plural, :notinplace)
 function change_bounds(
     model::CoreModelCoupled,
     rxns::Vector{Int};
@@ -423,7 +423,7 @@ function change_bounds(
     return m
 end
 
-# @doc @_change_bound_s_bang("CoreModelCoupled", "rxn_idx", "Int", "2", not_plural, not_inplace)
+@doc @_change_bound_s_bang("CoreModelCoupled", "rxn_idx", "Int", "2", :singular, :notinplace)
 function change_bound(
     model::CoreModelCoupled,
     reaction_idx::Int;
@@ -438,7 +438,7 @@ function change_bound(
     return m
 end
 
-# @doc @_change_bound_s_bang("CoreModelCoupled", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", is_plural, not_inplace)
+@doc @_change_bound_s_bang("CoreModelCoupled", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", :plural, :notinplace)
 function change_bounds(
     model::CoreModelCoupled,
     rxn_ids::Vector{String};
@@ -448,7 +448,7 @@ function change_bounds(
     change_bounds(model, Int.(indexin(rxn_ids, reactions(model))); lower_bounds = lower_bounds, upper_bounds = upper_bounds)
 end
 
-# @doc @_change_bound_s_bang("CoreModelCoupled", "rxn_id", "String", "\"PFL\"", not_plural, not_inplace)
+@doc @_change_bound_s_bang("CoreModelCoupled", "rxn_id", "String", "\"PFL\"", :singular, :notinplace)
 function change_bound(
     model::CoreModelCoupled,
     rxn_id::String;

diff --git a/src/reconstruction/StandardModel.jl b/src/reconstruction/StandardModel.jl
@@ -213,7 +213,7 @@ remove_gene!(model, "g1")
 remove_gene!(model::StandardModel, gid::String; knockout_reactions::Bool = false) =
     remove_genes!(model, [gid]; knockout_reactions = knockout_reactions)
 
-# @doc @_change_bound_s_bang("StandardModel", "rxn_id", "String", "\"PFL\"", not_plural, is_inplace)
+@doc @_change_bound_s_bang("StandardModel", "rxn_id", "String", "\"PFL\"", :singular, :inplace)
 function change_bound!(
     model::StandardModel,
     reaction_id::String;
@@ -226,7 +226,7 @@ function change_bound!(
     return nothing # so that nothing gets printed
 end
 
-# @doc @_change_bound_s_bang("StandardModel", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", is_plural, is_inplace)
+@doc @_change_bound_s_bang("StandardModel", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", :plural, :inplace)
 function change_bounds!(
     model::StandardModel,
     reaction_ids::Vector{String};
@@ -238,7 +238,7 @@ function change_bounds!(
     end
 end
 
-# @doc @_change_bound_s_bang("StandardModel", "rxn_id", "String", "\"PFL\"", not_plural, not_inplace)
+@doc @_change_bound_s_bang("StandardModel", "rxn_id", "String", "\"PFL\"", :singular, :notinplace)
 function change_bound(
     model::StandardModel,
     reaction_id::String;
@@ -253,7 +253,7 @@ function change_bound(
     return m
 end
 
-# @doc @_change_bound_s_bang("StandardModel", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", is_plural, not_inplace)
+@doc @_change_bound_s_bang("StandardModel", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", :plural, :notinplace)
 function change_bounds(
     model::StandardModel,
     reaction_ids::Vector{String};