Commit 6b49d8f7 authored by anand jain's avatar anand jain
Browse files

docstringextensions

parent 4ef5b4b3
...@@ -4,6 +4,7 @@ authors = ["Mirek Kratochvil <miroslav.kratochvil@uni.lu>", "LCSB R3 team <lcsb- ...@@ -4,6 +4,7 @@ authors = ["Mirek Kratochvil <miroslav.kratochvil@uni.lu>", "LCSB R3 team <lcsb-
version = "0.6.0" version = "0.6.0"
[deps] [deps]
DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
IfElse = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" IfElse = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173"
Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb" Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
SBML_jll = "bb12108a-f4ef-5f88-8ef3-0b33ff7017f1" SBML_jll = "bb12108a-f4ef-5f88-8ef3-0b33ff7017f1"
......
"""
$(DocStringExtensions.README)
"""
module SBML module SBML
using DocStringExtensions
using SBML_jll, Libdl using SBML_jll, Libdl
using SparseArrays using SparseArrays
using Symbolics using Symbolics
......
...@@ -77,7 +77,12 @@ struct MathLambda <: Math ...@@ -77,7 +77,12 @@ struct MathLambda <: Math
end end
""" """
$(TYPEDEF)
SBML Compartment with sizing information. SBML Compartment with sizing information.
# Fields
$(FIELDS)
""" """
struct Compartment struct Compartment
name::Maybe{String} name::Maybe{String}
...@@ -91,10 +96,15 @@ struct Compartment ...@@ -91,10 +96,15 @@ struct Compartment
end end
""" """
$(TYPEDEF)
Reaction with stoichiometry that assigns reactants and products their relative Reaction with stoichiometry that assigns reactants and products their relative
consumption/production rates (accessible in field `stoichiometry`), lower/upper consumption/production rates (accessible in field `stoichiometry`), lower/upper
bounds (in tuples `lb` and `ub`, with unit names), and objective coefficient bounds (in tuples `lb` and `ub`, with unit names), and objective coefficient
(`oc`). Also may contains `notes` and `annotation`. (`oc`). Also may contains `notes` and `annotation`.
# Fields
$(FIELDS)
""" """
struct Reaction struct Reaction
stoichiometry::Dict{String,Float64} stoichiometry::Dict{String,Float64}
...@@ -111,8 +121,13 @@ struct Reaction ...@@ -111,8 +121,13 @@ struct Reaction
end end
""" """
$(TYPEDEF)
Species metadata -- contains a human-readable `name`, a `compartment` Species metadata -- contains a human-readable `name`, a `compartment`
identifier, `formula`, `charge`, and additional `notes` and `annotation`. identifier, `formula`, `charge`, and additional `notes` and `annotation`.
# Fields
$(FIELDS)
""" """
struct Species struct Species
name::Maybe{String} name::Maybe{String}
...@@ -130,7 +145,12 @@ struct Species ...@@ -130,7 +145,12 @@ struct Species
end end
""" """
$(TYPEDEF)
Gene product metadata. Gene product metadata.
# Fields
$(FIELDS)
""" """
struct GeneProduct struct GeneProduct
name::Maybe{String} name::Maybe{String}
...@@ -152,11 +172,16 @@ struct FunctionDefinition ...@@ -152,11 +172,16 @@ struct FunctionDefinition
end end
""" """
$(TYPEDEF)
Structure that collects the model-related data. Contains `parameters`, `units`, Structure that collects the model-related data. Contains `parameters`, `units`,
`compartments`, `species` and `reactions` and `gene_products`, and additional `compartments`, `species` and `reactions` and `gene_products`, and additional
`notes` and `annotation` (also present internally in some of the data fields). `notes` and `annotation` (also present internally in some of the data fields).
The contained dictionaries are indexed by identifiers of the corresponding The contained dictionaries are indexed by identifiers of the corresponding
objects. objects.
# Fields
$(FIELDS)
""" """
struct Model struct Model
parameters::Dict{String,Float64} parameters::Dict{String,Float64}
......
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