Merge pull request #1136 from isaacsas/update_test_extension_project

Update test extensions Project.toml

Author: isaacsas

ext/CatalystGraphMakieExtension/rn_graph_plot.jl

@@ -60,7 +60,7 @@ function gen_distances(g::SRGraphWrap; inc = 0.2)
 end
 
 """
-    plot_network(rn::ReactionSystem; interactive=false)
+    plot_network(rn::ReactionSystem)
 
 Converts a [`ReactionSystem`](@ref) into a GraphMakie plot of the species reaction graph
 (or Petri net representation). Reactions correspond to small green circles, and 
@@ -76,7 +76,6 @@ Notes:
   red arrow from `A` to the reaction node. In `k*A, A+B --> C`, there would be
   red and black arrows from `A` to the reaction node.
 """  
-# TODO: update docs for interacting with plots. The `interactive` flag sets the ability to interactively drag nodes and edges in the generated plot. Only allowed if `GLMakie` is the loaded Makie backend.
 function Catalyst.plot_network(rn::ReactionSystem)
     srg = SRGraphWrap(rn)
     ns = length(species(rn))
@@ -119,7 +118,7 @@ function Catalyst.plot_network(rn::ReactionSystem)
 end
 
 """
-    plot_complexes(rn::ReactionSystem; interactive=false)
+    plot_complexes(rn::ReactionSystem)
 
     Creates a GraphMakie plot of the [`ReactionComplex`](@ref)s in `rn`. Reactions
     correspond to arrows and reaction complexes to blue circles.

test/extensions/Project.toml

@@ -1,12 +1,13 @@
 [deps]
 BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
-Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
 GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
 JumpProcesses = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
-OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+OrdinaryDiffEqDefault = "50262376-6c5a-4cf5-baba-aaf4f84d72d7"
+OrdinaryDiffEqTsit5 = "b1df2697-797e-41e3-8120-5422d3b24e4a"
 SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
-# StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
+# StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"

test/extensions/graphmakie.jl

@@ -1,4 +1,4 @@
-using Catalyst, GraphMakie, GLMakie, Graphs
+using Catalyst, GraphMakie, CairoMakie, Graphs
 include("../test_networks.jl")
 
 # Test that speciesreactiongraph is generated correctly
@@ -103,4 +103,3 @@ let
     @test count(==(Graphs.Edge(1, s+2)), edges(srg)) == 2
     @test count(==(Graphs.Edge(2, s+3)), edges(srg)) == 2
 end
-

test/extensions/lattice_simulation_plotting.jl

@@ -1,7 +1,8 @@
 ### Preparations ###
 
 # Fetch packages.
-using Catalyst, CairoMakie, GraphMakie, Graphs, JumpProcesses, OrdinaryDiffEqDefault, OrdinaryDiffEq, Test
+using Catalyst, CairoMakie, GraphMakie, Graphs
+using JumpProcesses, OrdinaryDiffEqDefault, OrdinaryDiffEqTsit5, Test
 
 
 ### Checks Basic Plot Cases ###

test/runtests.jl

@@ -85,14 +85,15 @@ end
     if GROUP == "All" || GROUP == "Extensions"
         activate_extensions_env()
 
+        @time @safetestset "Graph visualization" begin include("extensions/graphmakie.jl") end
         @time @safetestset "BifurcationKit Extension" begin include("extensions/bifurcation_kit.jl") end
         @time @safetestset "HomotopyContinuation Extension" begin include("extensions/homotopy_continuation.jl") end
 
         # BROKEN
         # @time @safetestset "Structural Identifiability Extension" begin include("extensions/structural_identifiability.jl") end
 
         # Tests stability computation (but requires the HomotopyContinuation extension).
-        @time @safetestset "Steady State Stability Computations" begin include("extensions/stability_computation.jl") end
+        #@time @safetestset "Steady State Stability Computations" begin include("extensions/stability_computation.jl") end
 
         # Test spatial plotting, using CarioMakie and GraphMakie
         @time @safetestset "Lattice Simulation Plotting" begin include("extensions/lattice_simulation_plotting.jl") end