added constants to help make docstring generation clearer

LCSB-BioCore · Jul 9, 2021 · 0a94f77 · 0a94f77
1 parent 2f13056
commit 0a94f77
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Showing 4 changed files with 25 additions and 20 deletions.
diff --git a/src/base/docstrings/docstrings.jl b/src/base/docstrings/docstrings.jl
@@ -1,3 +1,8 @@
+const is_inplace = true
+const not_inplace = false
+const is_plural = true
+const not_plural = false
+
 macro _change_bound_s_bang(model_type, index_name, index_type, example, isplural, isinplace)
     if isplural
         if isinplace

diff --git a/src/reconstruction/CoreModel.jl b/src/reconstruction/CoreModel.jl
@@ -375,7 +375,7 @@ function remove_reactions(m::CoreModel, rxns::Vector{String})
     end
 end
 
-@doc @_change_bound_s_bang("CoreModel", "rxn_idxs", "Vector{Int}", "[2, 43]", true, true)
+@doc @_change_bound_s_bang("CoreModel", "rxn_idxs", "Vector{Int}", "[2, 43]", is_plural, is_inplace)
 function change_bounds!(
     model::CoreModel,
     reaction_idxs::Vector{Int};
@@ -387,7 +387,7 @@ function change_bounds!(
     end
 end
 
-@doc @_change_bound_s_bang("CoreModel", "rxn_idx", "Int", "2", false, true)
+@doc @_change_bound_s_bang("CoreModel", "rxn_idx", "Int", "2", not_plural, is_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\"]", true, true)
+@doc @_change_bound_s_bang("CoreModel", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", is_plural, is_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\"", false, true)
+@doc @_change_bound_s_bang("CoreModel", "rxn_id", "String", "\"PFL\"", not_plural, is_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]", true, false)
+@doc @_change_bound_s_bang("CoreModel", "rxn_idxs", "Vector{Int}", "[2, 43]", is_plural, not_inplace)
 function change_bounds(
     model::CoreModel,
     rxns::Vector{Int};
@@ -434,7 +434,7 @@ function change_bounds(
     return m
 end
 
-@doc @_change_bound_s_bang("CoreModel", "rxn_idx", "Int", "2", false, false)
+@doc @_change_bound_s_bang("CoreModel", "rxn_idx", "Int", "2", not_plural, not_inplace)
 function change_bound(
     model::CoreModel,
     rxn::Int;
@@ -449,7 +449,7 @@ function change_bound(
     return m
 end
 
-@doc @_change_bound_s_bang("CoreModel", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", true, false)
+@doc @_change_bound_s_bang("CoreModel", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", is_plural, not_inplace)
 function change_bounds(
     model::CoreModel,
     rxn_ids::Vector{String};
@@ -459,7 +459,7 @@ 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\"", false, false)
+@doc @_change_bound_s_bang("CoreModel", "rxn_id", "String", "\"PFL\"", not_plural, not_inplace)
 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]", true, true)
+@doc @_change_bound_s_bang("CoreModelCoupled", "rxn_idxs", "Vector{Int}", "[2, 43]", is_plural, is_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", false, true)
+@doc @_change_bound_s_bang("CoreModelCoupled", "rxn_idx", "Int", "2", not_plural, is_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\"]", true, true)
+@doc @_change_bound_s_bang("CoreModelCoupled", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", is_plural, is_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\"", false, true)
+@doc @_change_bound_s_bang("CoreModelCoupled", "rxn_id", "String", "\"PFL\"", not_plural, is_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]", true, false)
+@doc @_change_bound_s_bang("CoreModelCoupled", "rxn_idxs", "Vector{Int}", "[2, 43]", is_plural, not_inplace)
 function change_bounds(
     model::CoreModelCoupled,
     rxns::Vector{Int};
@@ -421,7 +421,7 @@ function change_bounds(
     return m
 end
 
-@doc @_change_bound_s_bang("CoreModelCoupled", "rxn_idx", "Int", "2", false, false)
+@doc @_change_bound_s_bang("CoreModelCoupled", "rxn_idx", "Int", "2", not_plural, not_inplace)
 function change_bound(
     model::CoreModelCoupled,
     reaction_idx::Int;
@@ -436,7 +436,7 @@ function change_bound(
     return m
 end
 
-@doc @_change_bound_s_bang("CoreModelCoupled", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", true, false)
+@doc @_change_bound_s_bang("CoreModelCoupled", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", is_plural, not_inplace)
 function change_bounds(
     model::CoreModelCoupled,
     rxn_ids::Vector{String};
@@ -446,7 +446,7 @@ 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\"", false, false)
+@doc @_change_bound_s_bang("CoreModelCoupled", "rxn_id", "String", "\"PFL\"", not_plural, not_inplace)
 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\"", false, true)
+@doc @_change_bound_s_bang("StandardModel", "rxn_id", "String", "\"PFL\"", not_plural, is_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\"]", true, true)
+@doc @_change_bound_s_bang("StandardModel", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", is_plural, is_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\"", false, false)
+@doc @_change_bound_s_bang("StandardModel", "rxn_id", "String", "\"PFL\"", not_plural, not_inplace)
 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\"]", true, false)
+@doc @_change_bound_s_bang("StandardModel", "rxn_ids", "Vector{String}", "[\"PFL\", \"FBA\"]", is_plural, not_inplace)
 function change_bounds(
     model::StandardModel,
     reaction_ids::Vector{String};