fix: Update to new Catlab exports and bump version

AlgebraicJulia · Jun 15, 2023 · 534381f · 534381f
1 parent a22fd3a
commit 534381f
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Showing 11 changed files with 3 additions and 19 deletions.
diff --git a/Project.toml b/Project.toml
@@ -21,7 +21,7 @@ AlgebraicPetriOrdinaryDiffEqExt = "OrdinaryDiffEq"
 
 [compat]
 Catalyst = "13"
-Catlab = "0.14.16"
+Catlab = "0.15"
 GeneralizedGenerated = "0.3"
 LabelledArrays = "1"
 ModelingToolkit = "8"

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -9,6 +9,5 @@ LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-Petri = "4259d249-1051-49fa-8328-3f8ab9391c33"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
diff --git a/docs/literate/covid/coexist/coexist.jl → docs/literate/covid/coexist/_coexist.jl b/docs/literate/covid/coexist/coexist.jl → docs/literate/covid/coexist/_coexist.jl
diff --git a/docs/make.jl b/docs/make.jl
@@ -46,7 +46,6 @@ makedocs(
     "Examples" => Any[
       "generated/predation/lotka-volterra.md",
       "generated/covid/epidemiology.md",
-      "generated/covid/coexist/coexist.md",
       "generated/enzymes/enzyme_reactions.md",
       "generated/covid/bilayerconversion.md",
       "generated/covid/stratification.md",

diff --git a/src/AlgebraicPetri.jl b/src/AlgebraicPetri.jl
@@ -19,10 +19,6 @@ export SchPetriNet, PetriNet, OpenPetriNetOb, AbstractPetriNet,
   OpenPropertyPetriNetOb, OpenPropertyLabelledPetriNetOb, OpenPropertyReactionNetOb, OpenPropertyLabelledReactionNetOb
 
 using Catlab
-using Catlab.CategoricalAlgebra
-using Catlab.CategoricalAlgebra.FinSets
-using Catlab.Present
-using Catlab.Theories
 using LabelledArrays
 using GeneralizedGenerated: mk_function
 

diff --git a/src/BilayerNetworks.jl b/src/BilayerNetworks.jl
@@ -2,8 +2,6 @@ module BilayerNetworks
 
 using AlgebraicPetri
 using Catlab
-using Catlab.CategoricalAlgebra
-using Catlab.Graphics
 import Catlab.CategoricalAlgebra: migrate!
 
 export ThBilayerNetwork, AbstractBilayerNetwork, BilayerNetwork,

diff --git a/src/Epidemiology.jl b/src/Epidemiology.jl
@@ -5,9 +5,6 @@ module Epidemiology
 
 using AlgebraicPetri
 using Catlab
-using Catlab.Theories
-using Catlab.WiringDiagrams
-using Catlab.CategoricalAlgebra.FinSets
 
 export oapply_epi, infection, exposure, illness, recovery, death
 

diff --git a/src/ModelComparison.jl b/src/ModelComparison.jl
@@ -5,7 +5,6 @@ module ModelComparison
 
 using AlgebraicPetri
 using Catlab
-using Catlab.CategoricalAlgebra
 import Catlab.CategoricalAlgebra: Subobject
 
 export petri_homomorphisms, compare, PetriSubobject

diff --git a/src/OpenTransitions.jl b/src/OpenTransitions.jl
@@ -7,7 +7,6 @@ using AlgebraicPetri:
     LabelledPetriNetUntyped, LabelledPetriNet, PetriNet, AbstractPetriNet, 
     ns, nt, tname
 using Catlab
-using Catlab.CategoricalAlgebra
 
 export OpenLabelledPetriNetObT, OpenLabelledPetriNetT, OpenT,
     OpenPetriNetObT, OpenPetriNetT

diff --git a/src/TypedPetri.jl b/src/TypedPetri.jl
@@ -3,9 +3,6 @@ export prim_petri, strip_names, prim_cospan, oapply_typed, typed_product,
   add_params, add_reflexives, pairwise_id_petri, pairwise_id_typed_petri
 
 using Catlab
-using Catlab.CategoricalAlgebra
-using Catlab.Theories
-using Catlab.WiringDiagrams
 using AlgebraicPetri
 using AlgebraicPetri: LabelledPetriNetUntyped, OpenLabelledPetriNetUntyped, LabelledReactionNetUntyped
 

diff --git a/src/visualization.jl b/src/visualization.jl
@@ -1,5 +1,5 @@
-using Catlab.CategoricalAlgebra, Catlab.Graphics.Graphviz
-using Catlab.Graphs: PropertyGraph
+using Catlab, Catlab.Graphics.Graphviz
+using Catlab.Graphics.Graphviz: Graph
 
 import Catlab.Graphics.Graphviz: Subgraph
 import Catlab.Graphics: to_graphviz, to_graphviz_property_graph