initial_concentrations and _amounts return generators

...to make the work with custom datatypes easier.

src/utils.jl

@@ -56,71 +56,51 @@ end
 """
     initial_amounts(m::SBML.Model; convert_concentrations = false)
 
-Return a vector of initial amounts for each species, or `nothing` if the
-information is not available. If `convert_concentrations` is true and there is
-information about initial concentration available together with compartment
-size, the result is computed from the species' initial concentration.
+Return initial amounts for each species as a generator of pairs
+`species_name => initial_amount`; the amount is set to `nothing` if not
+available. If `convert_concentrations` is true and there is information about
+initial concentration available together with compartment size, the result is
+computed from the species' initial concentration.
 
 In the current version, units of the measurements are completely ignored.
-"""
-function initial_amounts(
-    m::SBML.Model;
-    convert_concentrations = false,
-)::Vector{Union{Float64,Nothing}}
-    function get_ia(x::Species)
-        if !isnothing(x.initial_amount)
-            x.initial_amount[1]
-        elseif !isnothing(x.initial_concentration) &&
-               haskey(m.compartments, x.compartment) &&
-               !isnothing(m.compartments[x.compartment].size)
-            x.initial_concentration[1] * m.compartments[x.compartment].size
-        else
-            nothing
-        end
-    end
 
-    if convert_concentrations
-        get_ia.(values(m.species))
+# Example
+```
+# get the initial amounts as dictionary
+Dict(initial_amounts(model, convert_concentrations = true))
+
+# remove the empty entries
+Dict(k => v for (k,v) in initial_amounts(model) if !isnothing(v))
+```
+"""
+const initial_amounts(m::SBML.Model; convert_concentrations = false) = (
+    k => if !isnothing(s.initial_amount)
+        s.initial_amount[1]
+    elseif convert_concentrations &&
+           !isnothing(s.initial_concentration) &&
+           haskey(m.compartments, s.compartment) &&
+           !isnothing(m.compartments[s.compartment].size)
+        s.initial_concentration[1] * m.compartments[s.compartment].size
     else
-        return broadcast(
-            x -> isnothing(x.initial_amount) ? nothing : x.initial_amount[1],
-            values(m.species),
-        )
-    end
-end
+        nothing
+    end for (k, s) in m.species
+)
 
 """
     initial_concentrations(m::SBML.Model; convert_amounts = false)
 
-Return a vector of initial concentrations for each species, or `nothing` if
-the information is not available. If `convert_amounts` is true and there is
-information about initial amount available together with compartment size, the
-result is computed from the species' initial amount.
-
-In the current version, units of the measurements are completely ignored.
+Return initial concentrations of the species in the model. Refer to work-alike
+[`initial_amounts`](@ref) for details.
 """
-function initial_concentrations(
-    m::SBML.Model;
-    convert_amounts = false,
-)::Vector{Union{Float64,Nothing}}
-    function get_ic(x::Species)
-        if !isnothing(x.initial_concentration)
-            x.initial_concentration[1]
-        elseif !isnothing(x.initial_amount) &&
-               haskey(m.compartments, x.compartment) &&
-               !isnothing(m.compartments[x.compartment].size)
-            x.initial_amount[1] / m.compartments[x.compartment].size
-        else
-            nothing
-        end
-    end
-
-    if convert_amounts
-        get_ic.(values(m.species))
+const initial_concentrations(m::SBML.Model; convert_amounts = false) = (
+    k => if !isnothing(s.initial_concentration)
+        s.initial_concentration[1]
+    elseif convert_amounts &&
+           !isnothing(s.initial_amount) &&
+           haskey(m.compartments, s.compartment) &&
+           !isnothing(m.compartments[s.compartment].size)
+        s.initial_amount[1] / m.compartments[s.compartment].size
     else
-        broadcast(
-            x -> isnothing(x.initial_concentration) ? nothing : x.initial_concentration[1],
-            values(m.species),
-        )
-    end
-end
+        nothing
+    end for (k, s) in m.species
+)

test/loadmodels.jl

@@ -72,8 +72,9 @@ end
 @testset "Initial amounts and concentrations" begin
     m = readSBML(joinpath(@__DIR__, "data", "sbml00852.xml"))
 
-    @test all(isnothing.(SBML.initial_concentrations(m)))
+    @test all(isnothing(ic) for (k, ic) in SBML.initial_concentrations(m))
     @test length(SBML.initial_amounts(m)) == 4
-    @test sum(SBML.initial_amounts(m)) == 0.001
-    @test sum(SBML.initial_concentrations(m, convert_amounts = true)) == 0.001
+    @test sum(ia for (sp, ia) in SBML.initial_amounts(m)) == 0.001
+    @test sum(ic for (sp, ic) in SBML.initial_concentrations(m, convert_amounts = true)) ==
+          0.001
 end