add tests

Author: vyudu

ext/CatalystGraphMakieExtension.jl

@@ -4,7 +4,6 @@ module CatalystGraphMakieExtension
 using Catalyst, GraphMakie, Graphs, Symbolics, SparseArrays
 using Symbolics: get_variables!
 import Catalyst: species_reaction_graph, incidencematgraph, lattice_plot, lattice_animation
-import SparseArrays: rowvals, nonzeros, nzrange
 
 # Creates and exports graph plotting functions.
 include("CatalystGraphMakieExtension/graph_makie_extension_spatial_modelling.jl")

ext/CatalystGraphMakieExtension/rn_graph_plot.jl

@@ -62,20 +62,38 @@ function Graphs.edges(g::MultiGraphWrap)
     edgelist = vcat(collect(Graphs.edges(g.g)), g.multiedges)[g.edgeorder]
 end
 
-function gen_distances(g::MultiGraphWrap; inc = 0.25) 
+function gen_distances(g::MultiGraphWrap; inc = 0.4) 
     edgelist = edges(g)
     distances = zeros(length(edgelist))
-    for (i,e) in enumerate(edgelist)
-        fwd = findall(==(e), edgelist); rev = findall(==(reverse(e)), edgelist)
-        distances[i] != 0 && continue
-        distances[fwd] = collect(0:inc:inc*(length(fwd)-1))
-        distances[rev] = collect(inc:inc:inc*(length(rev)))
+    edgedict = Dict(edgelist[1] => [1])
+    for (i, e) in enumerate(edgelist[2:end])
+        if edgelist[i] != edgelist[i+1]
+            edgedict[e] = [i+1]
+        else
+            push!(edgedict[e], i+1)
+        end
+    end
+
+    for (edge, inds) in edgedict
+        if haskey(edgedict, Edge(dst(edge), src(edge)))
+            distances[inds[1]] != 0. && continue
+            inds_ = edgedict[Edge(dst(edge), src(edge))]
+
+            len = length(inds) + length(inds_)
+            sp = -inc/2*(len-1)
+            ep = sp + inc*(len-1)
+            dists = collect(sp:inc:ep)
+            distances[inds] = dists[1:length(inds)]
+            distances[inds_] = -dists[length(inds)+1:end]
+        else
+            sp = -inc/2*(length(inds)-1)
+            ep = sp + inc*(length(inds)-1)
+            distances[inds] = collect(sp:inc:ep)
+        end
     end
     distances
 end
 
-Base.copy(g::MultiGraphWrap) = MultiGraphWrap(g.g, g.multiedges, g.edgeorder)
-
 """
     plot_network(rn::ReactionSystem)
 
@@ -154,12 +172,14 @@ function Catalyst.plot_complexes(rn::ReactionSystem)
 
     deps = Set()
     edgelist = Vector{Graphs.SimpleEdge{Int}}()
-    rows = SparseArrays.rowvals(D); vals = SparseArrays.nonzeros(D)
+    rows = rowvals(D)
+    vals = nonzeros(D)
 
     # Construct the edge order for reactions.
     for (i, rx) in enumerate(rxs)
-        inds = SparseArrays.nzrange(D, i)
-        val = vals[inds]; row = rows[inds]
+        inds = nzrange(D, i)
+        val = vals[inds]
+        row = rows[inds]
         (sub, prod) = val[1] == -1 ? (row[1], row[2]) : (row[2], row[1])
         push!(edgelist, Graphs.SimpleEdge(sub, prod))
 

test/extensions/graphmakie.jl

@@ -1,4 +1,4 @@
-using Catalyst, GraphMakie, CairoMakie, Graphs
+using Catalyst, GraphMakie, CairoMakie, Graphs, SparseArrays
 include("../test_networks.jl")
 
 # Test that speciesreactiongraph is generated correctly
@@ -77,8 +77,8 @@ let
     srg = CGME.MultiGraphWrap(rn)
     s = length(species(rn))
     @test ne(srg) == 8
-    @test Graphs.Edge(3, s+2) ∈ srg.rateedges 
-    @test Graphs.Edge(2, s+3) ∈ srg.rateedges 
+    @test Graphs.Edge(3, s+2) ∈ srg.multiedges
+    @test Graphs.Edge(2, s+3) ∈ srg.multiedges
     # Since B is both a dep and a reactant
     @test count(==(Graphs.Edge(2, s+3)), edges(srg)) == 2
 
@@ -103,3 +103,81 @@ let
     @test count(==(Graphs.Edge(1, s+2)), edges(srg)) == 2
     @test count(==(Graphs.Edge(2, s+3)), edges(srg)) == 2
 end
+
+function test_edgeorder(rn) 
+    # The initial edgelabels in `plot_complexes` is given by the order of reactions in reactions(rn).
+    D = incidencemat(rn; sparse=true); img = incidencematgraph(rn)
+    rxs = reactions(rn)
+    edgelist = Vector{Graphs.SimpleEdge{Int}}()
+    rows = rowvals(D)
+    vals = nonzeros(D)
+
+    for (i, rx) in enumerate(rxs)
+        inds = nzrange(D, i)
+        val = vals[inds]
+        row = rows[inds]
+        (sub, prod) = val[1] == -1 ? (row[1], row[2]) : (row[2], row[1])
+        push!(edgelist, Graphs.SimpleEdge(sub, prod))
+    end
+
+    rxorder = sortperm(edgelist); sortededgelist = edgelist[rxorder] 
+    multiedges = Vector{Graphs.SimpleEdge{Int}}()
+    for i in 2:length(sortededgelist)
+        isequal(sortededgelist[i], sortededgelist[i-1]) && push!(multiedges, sortededgelist[i])
+    end
+    img_ = CGME.MultiGraphWrap(img, multiedges)
+
+    # Label iteration order is given by edgelist[rxorder. Actual edge drawing iteration order is given by edges(g)
+    @test edgelist[rxorder] == Graphs.edges(img_)
+    return rxorder
+end
+
+# Test edge order for complexes.
+let
+    # Multiple edges
+    rn = @reaction_network begin
+        k1, A --> B
+        (k2, k3), C <--> D
+        k4, A --> B
+    end
+    rxorder = test_edgeorder(rn)
+    edgelabels = [repr(rx.rate) for rx in reactions(rn)]
+    # Test internal order of labels is preserved
+    @test edgelabels[rxorder][1] == "k1"
+    @test edgelabels[rxorder][2] == "k4"
+
+    # Multiple edges with species dependencies
+    rn = @reaction_network begin
+        k1, A --> B
+        (k2, k3), C <--> D
+        k4, A --> B
+        hillr(D, α, K, n), C --> D
+        k5*B, A --> B
+    end
+    rxorder = test_edgeorder(rn)
+    edgelabels = [repr(rx.rate) for rx in reactions(rn)]
+    labels = ["k1", "k4", "k5*B(t)", "k2", "Catalyst.hillr(D(t), α, K, n)", "k3"]
+    @test edgelabels[rxorder] == labels
+
+    rs = @reaction_network begin
+        ka, Depot --> Central
+        (k12, k21), Central <--> Peripheral
+        ke, Central --> 0
+    end
+    test_edgeorder(rs)
+
+    rn = @reaction_network begin
+        (k1, k2), A <--> B
+        k3, C --> B
+        (α, β), (A, B) --> C
+        k4, B --> A
+        (k5, k6), B <--> A
+        k7, B --> C
+        (k8, k9), C <--> A
+        (k10, k11), (A, C) --> B
+        (k12, k13), (C, B) --> A
+    end
+    rxorder = test_edgeorder(rn)
+    edgelabels = [repr(rx.rate) for rx in reactions(rn)]
+    @test edgelabels[rxorder][1:3] == ["k1", "k6", "k10"]
+end