First pass at GATlab integration.

Project.toml

@@ -7,6 +7,7 @@ version = "0.2.1"
 [deps]
 ACSets = "227ef7b5-1206-438b-ac65-934d6da304b8"
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
+DataMigrations = "0c4ad18d-0c49-4bc2-90d5-5bca8f00d6ae"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"

docs/src/lotka_volterra.jl

@@ -1,11 +1,12 @@
 module LotkaVolterra 
 
-using Catlab, Catlab.Theories, Catlab.CategoricalAlgebra, Catlab.Graphs, 
-      Catlab.Graphics, Catlab.WiringDiagrams, Catlab.Programs
-using AlgebraicRewriting
 using Random, Test, StructEquality
 using Luxor
 
+using Catlab
+using DataMigrations: @acset_colim
+using AlgebraicRewriting
+
 Random.seed!(123);
 
 using Catlab.Graphics.Graphviz: Attributes, Statement, Node

src/rewrite/PBPO.jl

@@ -3,7 +3,7 @@ export PBPORule
 
 using Catlab, Catlab.CategoricalAlgebra
 import Catlab.CategoricalAlgebra: left, right
-using Catlab.CategoricalAlgebra.CSets: backtracking_search, abstract_attributes
+using Catlab.CategoricalAlgebra.HomSearch: backtracking_search, abstract_attributes
 
 using StructEquality
 using DataStructures: DefaultDict

src/rewrite/Representable.jl

@@ -2,8 +2,8 @@ module Representable
 export yoneda_cache, SchRule, SchRulel, SchRuler, SchRule, SchPBPO
 
 using Catlab, Catlab.CategoricalAlgebra
+using Catlab.CategoricalAlgebra.FunctorialDataMigrations: AbstractDataMigration
 using ACSets.DenseACSets: constructor
-using Catlab.Programs.DiagrammaticPrograms: AST
 
 import ..Utils: Rule
 import ..PBPO: PBPORule
@@ -73,7 +73,7 @@ genuine application conditions because we want to be able to apply the rule
 even when the conditions don't hold. (We track them to be able to report user 
 errors.)
 """
-function Rule(rule_schema::DataMigration, y; semantics=:DPO, kw...)
+function Rule(rule_schema::AbstractDataMigration, y; semantics=:DPO, kw...)
   rule = colimit_representables(rule_schema, y)
   L, R, K = [rule_ob_map(rule, Symbol(x)) for x in "LRK"]
   l = rule_hom_map(rule, :l, K, L)

src/rewrite/Utils.jl

@@ -5,7 +5,7 @@ export Rule, ruletype,rewrite, rewrite_match, rewrite_full_output,
 
 using Catlab, Catlab.Theories
 using Catlab.CategoricalAlgebra
-using Catlab.CategoricalAlgebra.CSets: backtracking_search
+using Catlab.CategoricalAlgebra.HomSearch: backtracking_search
 import Catlab.CategoricalAlgebra: left, right
 
 using Random

src/schedules/Theories.jl

@@ -1,30 +1,31 @@
 module Theories
 
-using Catlab, Catlab.Theories, Catlab.WiringDiagrams
+using Catlab.Theories, Catlab.WiringDiagrams
 import Catlab.Theories: Ob,Hom,id, create, compose, otimes, ⋅, ⊗, ∇,□, trace, munit, braid, dom, codom, mmerge
 using Catlab.WiringDiagrams.MonoidalDirectedWiringDiagrams: implicit_mmerge
 
 
-@signature ThTracedMonoidalWithBidiagonals{Ob,Hom} <: ThTracedMonoidalCategory{Ob,Hom} begin
+@signature ThTracedMonoidalWithBidiagonals <: ThTracedMonoidalCategory begin
   mmerge(A::Ob)::((A ⊗ A) → A)
   @op (∇) := mmerge
   create(A::Ob)::(munit() → A)
   @op (□) := create
 end
 
-@syntax TM{ObExpr,HomExpr} ThTracedMonoidalWithBidiagonals begin
+@symbolic_model TM{ObExpr,HomExpr} ThTracedMonoidalWithBidiagonals begin
   otimes(A::Ob, B::Ob) = associate_unit(new(A,B), mzero)
   otimes(f::Hom, g::Hom) = associate(new(f,g))
-  function compose(f, g)
+  function compose(f::Hom, g::Hom)
     cf = codom(f); dg = dom(g) 
     if cf != dg println("$cf\n$dg") end 
     associate_unit(new(f,g; strict=true), id)
   end
 end
-# compose(f::TM.Hom{S}, g::TM.Hom{T}) where {S,T} = compose(TM.Hom(f),TM.Hom(g))
 
-mmerge(A::Ports{ThTracedMonoidalWithBidiagonals}, n::Int) = implicit_mmerge(A, n)
-trace(X::Ports{ThTracedMonoidalWithBidiagonals}, A::Ports{ThTracedMonoidalWithBidiagonals},
-  B::Ports{ThTracedMonoidalWithBidiagonals}, f::WiringDiagram{ThTracedMonoidalWithBidiagonals}) = trace(X, f)
+const ThT = ThTracedMonoidalWithBidiagonals.Meta.T
+
+mmerge(A::Ports{ThT}, n::Int) = implicit_mmerge(A, n)
+trace(X::Ports{ThT}, A::Ports{ThT}, B::Ports{ThT},
+      f::WiringDiagram{ThT}) = trace(X, f)
 
 end # module 

src/schedules/Wiring.jl

@@ -137,13 +137,13 @@ function singleton(b::AgentBox)::Schedule
 end
 
 
-const WD = WiringDiagram{ThTracedMonoidalWithBidiagonals, StructACSet,
+const WD = WiringDiagram{ThTracedMonoidalWithBidiagonals.Meta.T, StructACSet,
                          StructACSet, AgentBox}
 
 # It would be nice if ⊗ and ⋅ preserved the type of WDs, then we could more
 # strongly type our code.
 struct Schedule 
-  d::WiringDiagram{<:ThTracedMonoidalWithBidiagonals}
+  d::WiringDiagram{<:ThTracedMonoidalWithBidiagonals.Meta.T}
   x::GATExpr
   function Schedule(d,x) 
     wd = WiringDiagram{ThTracedMonoidalWithBidiagonals,Any,Any,Any}([],[])

test/Project.toml

@@ -2,6 +2,7 @@
 ACSets = "227ef7b5-1206-438b-ac65-934d6da304b8"
 AlgebraicRewriting = "725a01d3-f174-5bbd-84e1-b9417bad95d9"
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
+DataMigrations = "0c4ad18d-0c49-4bc2-90d5-5bca8f00d6ae"
 Luxor = "ae8d54c2-7ccd-5906-9d76-62fc9837b5bc"
 PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"