Merge pull request #17 from COBREXA/sew-pretty-print-canonical

Add simple pretty printing and tests for CanonicalModel

docs/src/canonical.jl

@@ -90,6 +90,15 @@ m.reactions["exchange2"] = Reaction(
 )
 nothing #hide
 
+show_contains(x, y) = contains(sprint(show, MIME"text/plain"(), x), y) #src
+@test show_contains(m, "reactions = ") #src
+@test show_contains(m, "metabolites = ") #src
+@test show_contains(m, "genes = ") #src
+@test show_contains(m.reactions["and_back"], "\"export\"") #src
+@test show_contains(m.reactions["forward"], "\"g1\"") #src
+@test show_contains(m.metabolites["m1"], "\"inside\"") #src
+@test show_contains(m.genes["g1"], "name = nothing") #src
+
 # We should immediately find the basic accessors working:
 A.stoichiometry(m)
 

src/canonical.jl

@@ -26,6 +26,8 @@ Base.@kwdef mutable struct Reaction
     notes::A.Notes = A.Notes()
 end
 
+Base.show(io::Base.IO, ::MIME"text/plain", x::Reaction) = A.pretty_print_kwdef(io, x)
+
 """
 $(TYPEDEF)
 
@@ -44,6 +46,8 @@ Base.@kwdef mutable struct Metabolite
     notes::A.Notes = A.Notes()
 end
 
+Base.show(io::Base.IO, ::MIME"text/plain", x::Metabolite) = A.pretty_print_kwdef(io, x)
+
 """
 $(TYPEDEF)
 
@@ -58,6 +62,8 @@ Base.@kwdef mutable struct Gene
     notes::A.Notes = A.Notes()
 end
 
+Base.show(io::Base.IO, ::MIME"text/plain", x::Gene) = A.pretty_print_kwdef(io, x)
+
 """
 $(TYPEDEF)
 
@@ -81,6 +87,8 @@ Base.@kwdef struct Model <: A.AbstractFBCModel
     genes::Dict{String,Gene} = Dict()
 end
 
+Base.show(io::Base.IO, ::MIME"text/plain", x::Model) = A.pretty_print_kwdef(io, x)
+
 A.reactions(m::Model) = sort(collect(keys(m.reactions)))
 A.metabolites(m::Model) = sort(collect(keys(m.metabolites)))
 A.genes(m::Model) = sort(collect(keys(m.genes)))
@@ -97,16 +105,20 @@ A.reaction_notes(m::Model, id::String) = m.reactions[id].notes
 A.metabolite_notes(m::Model, id::String) = m.metabolites[id].notes
 A.gene_notes(m::Model, id::String) = m.genes[id].notes
 
-A.stoichiometry(m::Model) =
-    let rids = A.reactions(m)
-        #TODO this is dense
-        sparse(
-            Float64[
-                get(m.reactions[rid].stoichiometry, mid, 0.0) for mid in A.metabolites(m),
-                rid in rids
-            ],
-        )
+function A.stoichiometry(m::Model)
+    midxs = Dict(mid => idx for (idx, (mid, _)) in enumerate(m.metabolites))
+    I = Int[]
+    J = Int[]
+    V = Float64[]
+    for (ridx, (_, r)) in enumerate(m.reactions)
+        for (smid, v) in r.stoichiometry
+            push!(I, midxs[smid])
+            push!(J, ridx)
+            push!(V, v)
+        end
     end
+    sparse(I, J, V, length(m.metabolites), length(m.reactions))
+end
 
 A.bounds(m::Model) = (
     [m.reactions[rid].lower_bound for rid in A.reactions(m)],

src/io.jl

@@ -64,6 +64,28 @@ time.
 """
 load(path::String) = load(guess_model_type_from_filename(path), path)
 
+"""
+$(TYPEDSIGNATURES)
+
+Helper for nicely showing the contents of possibly complicated model
+structures.
+"""
+function pretty_print_kwdef(io::Base.IO, x::T) where {T}
+    println(io, "$T(")
+    (_, cols) = displaysize(io)
+    for fn in fieldnames(T)
+        shw = repr(getfield(x, fn))
+        tgt_cols = max(16, cols - (2 + length(String(fn)) + 3 + 1))
+        if get(io, :limit, true)::Bool && length(shw) >= tgt_cols
+            shw = join(collect(shw)[begin:tgt_cols]) * "…"
+        else
+            shw *= ","
+        end
+        println(io, "  $fn = $shw")
+    end
+    println(io, ")")
+end
+
 Base.show(io::Base.IO, ::MIME"text/plain", m::AbstractFBCModel) = print(
     io,
     "$(typeof(m))(#= $(n_reactions(m)) reactions, $(n_metabolites(m)) metabolites =#)",