Updated Petri and Catlab APIs (#252)

* Updated Petri and Catlab APIs

* Added compat entries and version bump for final release

* Removed v1.0 test

.github/workflows/test.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        julia-version: ['1.0', '1.3', '1.4']
+        julia-version: ['1.3', '1.4']
         os: [ubuntu-latest]
 
     steps:

Project.toml

@@ -1,7 +1,7 @@
 name = "SemanticModels"
 uuid = "f5ac2a72-33c7-5caf-b863-f02fefdcf428"
 authors = ["James Fairbanks <james.fairbanks@gtri.gatech.edu>", "Micah Halter <micah.halter@gtri.gatech.edu>"]
-version = "0.3.0"
+version = "0.4.0"
 
 [deps]
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
@@ -10,6 +10,10 @@ MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 Petri = "4259d249-1051-49fa-8328-3f8ab9391c33"
 
 [compat]
+Catlab = "^0.7.0"
+LightGraphs = "^1.3.3"
+MacroTools = "^0.5.5"
+Petri = "^1.0.0"
 julia = "1.0"
 
 [extras]

src/CategoryTheory.jl

@@ -2,7 +2,7 @@
 module CategoryTheory
 
 using SemanticModels
-import Catlab.Doctrines: dom, codom
+import Catlab.Theories: dom, codom
 import Base: append!, push!, deleteat!, delete!
 
 export ⊔, AbstractMorph, FinSetMorph, dom, codom, verify, func, Decorated, decorations, undecorate, AbstractSpan, leftob, rightob, apexob, Span, left, right, DoublePushout, AbstractCospan, Cospan, pushout

src/OpenPetris.jl

@@ -5,8 +5,8 @@ import SemanticModels.PetriModels: PetriModel
 import SemanticModels.OpenModels: OpenModel
 using ModelingToolkit
 import ModelingToolkit: Constant
-using Catlab.Doctrines
-import Catlab.Doctrines: ⊗, compose, otimes
+using Catlab.Theories
+import Catlab.Theories: ⊗, compose, otimes
 
 export OpenPetri, eye, ⊕
 

src/PetriCospans.jl

@@ -1,7 +1,7 @@
 module PetriCospans
 
 using Catlab
-using Catlab.Doctrines
+using Catlab.Theories
 using Catlab.WiringDiagrams
 # using Catlab.Programs
 import Base: (==), length, show
@@ -10,7 +10,7 @@ using ..PetriModels
 using ..CategoryTheory
 import ..CategoryTheory: undecorate, ⊔
 
-import Catlab.Doctrines:
+import Catlab.Theories:
   Ob, Hom, dom, codom, compose, ⋅, ∘, id, oplus, otimes, ⊗, ⊕, munit, mzero, braid,
   dagger, dunit, dcounit, mcopy, Δ, delete, ◊, mmerge, ∇, create, □,
   plus, zero, coplus, cozero, meet, top, join, bottom
@@ -25,11 +25,11 @@ export Epidemiology, FreeEpidemiology, spontaneous, exposure, death,
     death(A)::Hom(A, munit()) ⊣ A::Ob
 end
 
-spontaneous(A::Ports, B::Ports) = singleton_diagram(Epidemiology.Hom, Box(:→, A, B))
-exposure(A::Ports, B::Ports, C::Ports) = singleton_diagram(Epidemiology.Hom, Box(:exposure, A⊗B, C⊗B))
-death(A::Ports) = singleton_diagram(Epidemiology.Hom, Box(:𝗫, A, Ports([])))
-mcopy(A::Ports{Epidemiology.Hom}, Symbol) = implicit_mcopy(A, 2)
-mmerge(A::Ports{Epidemiology.Hom}, Symbol) = implicit_mmerge(A, 2)
+spontaneous(A::Ports, B::Ports) = singleton_diagram(Box(:→, A, B))
+exposure(A::Ports, B::Ports, C::Ports) = singleton_diagram(Box(:exposure, A⊗B, C⊗B))
+death(A::Ports) = singleton_diagram(Box(:𝗫, A, Ports([])))
+mcopy(A::Ports{Epidemiology}, Symbol) = implicit_mcopy(A, 2)
+mmerge(A::Ports{Epidemiology}, Symbol) = implicit_mmerge(A, 2)
 
 
 @syntax FreeEpidemiology(ObExpr, HomExpr) Epidemiology begin
@@ -41,8 +41,8 @@ mmerge(A::Ports{Epidemiology.Hom}, Symbol) = implicit_mmerge(A, 2)
     copair(f::Hom, g::Hom) = (f ⊗ g) → ∇(codom(f))
     proj1(A::Ob, B::Ob) = id(A) ⊗ ◊(B)
     proj2(A::Ob, B::Ob) = ◊(A) ⊗ id(B)
-    incl1(A::Ob, B::Ob) = id(A) ⊗ □(B)
-    incl2(A::Ob, B::Ob) = □(A) ⊗ id(B)
+    coproj1(A::Ob, B::Ob) = id(A) ⊗ □(B)
+    coproj2(A::Ob, B::Ob) = □(A) ⊗ id(B)
     otimes(A::Ob, B::Ob) = associate_unit(new(A,B), munit)
     otimes(f::Hom, g::Hom) = associate(new(f,g))
 end
@@ -221,8 +221,8 @@ end
   proj1(A::FinSet,B::FinSet) = otimes(id(A), delete(B))
   proj2(A::FinSet,B::FinSet) = otimes(delete(A), id(B))
 
-  incl1(A::FinSet,B::FinSet) = otimes(id(A), create(B))
-  incl2(A::FinSet,B::FinSet) = otimes(create(A), id(B))
+  coproj1(A::FinSet,B::FinSet) = otimes(id(A), create(B))
+  coproj2(A::FinSet,B::FinSet) = otimes(create(A), id(B))
 
   spontaneous(A::FinSet, B::FinSet) = begin
       M, N = length(A), length(B)

src/RelOlogModels.jl

@@ -4,8 +4,8 @@ module RelOlogModels
 using Catlab
 using Catlab.Syntax
 using Catlab.WiringDiagrams
-using Catlab.Doctrines
-import Catlab.Doctrines.⊗
+using Catlab.Theories
+import Catlab.Theories.⊗
 
 using SemanticModels
 import SemanticModels: model

src/WiringDiagrams.jl

@@ -3,7 +3,7 @@
 module WiringDiagrams
 
 using Catlab.WiringDiagrams
-using Catlab.Doctrines
+using Catlab.Theories
 using Catlab.Graphics
 using Catlab.Graphics.Graphviz
 using MacroTools

test/epidemics.jl

@@ -1,6 +1,6 @@
 module TestEpidemics
 using Catlab
-using Catlab.Doctrines
+using Catlab.Theories
 using Catlab.Graphics
 using Catlab.WiringDiagrams
 using Catlab.Programs
@@ -18,7 +18,7 @@ import SemanticModels.PetriCospans: otimes_ipm, compose_pushout
 
 println("Done Importing SemanticModels")
 
-import Catlab.Doctrines:
+import Catlab.Theories:
   Ob, Hom, dom, codom, compose, ⋅, ∘, id, oplus, otimes, ⊗, ⊕, munit, mzero, braid,
   dagger, dunit, dcounit, mcopy, Δ, delete, ◊, mmerge, ∇, create, □,
   plus, zero, coplus, cozero, meet, top, join, bottom
@@ -199,7 +199,7 @@ Pseird = PetriModel(
             ([3],[2]),     # onset
             ([2],[4]),     # recovery
             ([2],[5]),     # death
-            ], missing, missing))
+          ]))
 inputs = FinSetMorph(1:5, [1,2,3])
 outputs = FinSetMorph(1:5, [1,2,3])
 Fcityd = PetriCospan(Cospan(Decorated(inputs, Pseird),

test/petricospans.jl

@@ -1,7 +1,7 @@
 module TestPetriCospans
 
 using Catlab
-using Catlab.Doctrines
+using Catlab.Theories
 using Catlab.WiringDiagrams
 using Catlab.Programs
 import Base.Multimedia: display
@@ -14,7 +14,7 @@ using SemanticModels.PetriModels
 using SemanticModels.PetriCospans
 import SemanticModels.PetriCospans: otimes_ipm, compose_pushout
 
-import Catlab.Doctrines:
+import Catlab.Theories:
   Ob, Hom, dom, codom, compose, ⋅, ∘, id, oplus, otimes, ⊗, ⊕, munit, mzero, braid,
   dagger, dunit, dcounit, mcopy, Δ, delete, ◊, mmerge, ∇, create, □,
   plus, zero, coplus, cozero, meet, top, join, bottom
@@ -28,7 +28,7 @@ Cospan(f,g), Cospan(f′, g′)
 pushout(Span(g,f′))
 
 
-spon = PetriModel(Petri.Model([1,2], [([1], [2])], missing, missing))
+spon = PetriModel(Petri.Model([1,2], [([1], [2])]))
 f = Decorated(FinSetMorph(1:2, [2]), [spon])
 g = Decorated(FinSetMorph(1:2, [1]), [spon])
 s = Span(g,f)