Model -> SBML.Model

docs/src/index.md

@@ -5,12 +5,12 @@ This package provides a straightforward way to load model- and
 simulation-relevant information from SBML files.
 
 The library provides a single function [`readSBML`](@ref) to load a
-[`Model`](@ref):
+[`SBML.Model`](@ref):
 
 ```julia
 julia> using SBML
 julia> mdl = readSBML("Ec_core_flux1.xml")
-Model(…)
+SBML.Model(…)
 
 julia> mdl.compartments
 2-element Array{String,1}:

src/readsbml.jl

@@ -75,11 +75,11 @@ function get_optional_double(x::VPtr, is_sym, get_sym)::Maybe{Float64}
 end
 
 """
-    function readSBML(fn::String)::Model
+    function readSBML(fn::String)::SBML.Model
 
-Read the SBML from a XML file in `fn` and return the contained `Model`.
+Read the SBML from a XML file in `fn` and return the contained `SBML.Model`.
 """
-function readSBML(fn::String)::Model
+function readSBML(fn::String)::SBML.Model
     doc = ccall(sbml(:readSBML), VPtr, (Cstring,), fn)
     try
         n_errs = ccall(sbml(:SBMLDocument_getNumErrors), Cuint, (VPtr,), doc)
@@ -138,12 +138,12 @@ end
 
 
 """"
-    function extractModel(mdl::VPtr)::Model
+    function extractModel(mdl::VPtr)::SBML.Model
 
 Take the `SBMLModel_t` pointer and extract all information required to make a
-valid [`Model`](@ref) structure.
+valid [`SBML.Model`](@ref) structure.
 """
-function extractModel(mdl::VPtr)::Model
+function extractModel(mdl::VPtr)::SBML.Model
     # get the FBC plugin pointer (FbcModelPlugin_t)
     mdl_fbc = ccall(sbml(:SBase_getPlugin), VPtr, (VPtr, Cstring), mdl, "fbc")
 

src/structs.jl

@@ -18,7 +18,7 @@ of `Unit`. For example, the unit "per square megahour", Mh^(-2), is written as:
 
 Compound units (such as "volt-amperes" and "dozens of yards per ounce") are
 built from multiple `UnitPart`s; see the definition of field `units` in
-[`Model`](@ref).
+[`SBML.Model`](@ref).
 """
 struct UnitPart
     kind::String

src/utils.jl

 """
-    function getS(m::Model; zeros=spzeros)::Tuple{Vector{String},Vector{String},AbstractMatrix{Float64}}
+    function getS(m::SBML.Model; zeros=spzeros)::Tuple{Vector{String},Vector{String},AbstractMatrix{Float64}}
 
 Extract the vector of species (aka metabolite) identifiers, vector of reaction
-identifiers, and the (dense) stoichiometry matrix from an existing `Model`.
+identifiers, and the (dense) stoichiometry matrix from an existing `SBML.Model`.
 Returns a tuple with these values.
 
 The matrix is sparse by default (initially constructed by
@@ -10,7 +10,7 @@ The matrix is sparse by default (initially constructed by
 argument `zeros`; e.g. running with `zeros=zeros` will produce a dense matrix.
 """
 function getS(
-    m::Model;
+    m::SBML.Model;
     zeros = spzeros,
 )::Tuple{Vector{String},Vector{String},AbstractMatrix{Float64}}
     rows = [k for k in keys(m.species)]
@@ -25,30 +25,30 @@ function getS(
 end
 
 """
-    function getLBs(m::Model)::Vector{Tuple{Float64,String}}
+    function getLBs(m::SBML.Model)::Vector{Tuple{Float64,String}}
 
 Extract a vector of lower bounds of reaction rates from the model. All bounds
 are accompanied with the unit of the corresponding value (this behavior is
 based on SBML specification).
 """
-function getLBs(m::Model)::Vector{Tuple{Float64,String}}
+function getLBs(m::SBML.Model)::Vector{Tuple{Float64,String}}
     return broadcast(x -> x.lb, values(m.reactions))
 end
 
 """
-    function getUBs(m::Model)::Vector{Tuple{Float64,String}}
+    function getUBs(m::SBML.Model)::Vector{Tuple{Float64,String}}
 
 Likewise to `getLBs`, extract the upper bounds.
 """
-function getUBs(m::Model)::Vector{Tuple{Float64,String}}
+function getUBs(m::SBML.Model)::Vector{Tuple{Float64,String}}
     return broadcast(x -> x.ub, values(m.reactions))
 end
 
 """
-    function getOCs(m::Model)::Vector{Float64}
+    function getOCs(m::SBML.Model)::Vector{Float64}
 
 Extract the vector of objective coefficients of each reaction.
 """
-function getOCs(m::Model)::Vector{Float64}
+function getOCs(m::SBML.Model)::Vector{Float64}
     return broadcast(x -> x.oc, values(m.reactions))
 end

test/runtests.jl

 
 using Test, SHA, SparseArrays
 using SBML
+using SBML: Model, Reaction, Species
 import Pkg
 
 @testset "SBML test suite" begin