Merge pull request #32 from AlgebraicJulia/gatlab

Update for GATlab.jl and DataMigrations.jl

Project.toml

@@ -2,7 +2,7 @@ name = "AlgebraicRewriting"
 uuid = "725a01d3-f174-5bbd-84e1-b9417bad95d9"
 license = "MIT"
 authors = ["Kris Brown <[email protected]>"]
-version = "0.2.1"
+version = "0.3.0"
 
 [deps]
 ACSets = "227ef7b5-1206-438b-ac65-934d6da304b8"
@@ -15,13 +15,16 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [weakdeps]
 Luxor = "ae8d54c2-7ccd-5906-9d76-62fc9837b5bc"
+DataMigrations = "0c4ad18d-0c49-4bc2-90d5-5bca8f00d6ae"
 
 [extensions]
 AlgebraicRewritingLuxorExt = "Luxor"
+AlgebraicRewritingDataMigrationsExt = "DataMigrations"
 
 [compat]
 ACSets = "0.2.9"
-Catlab = "0.15.4, 0.16"
+Catlab = "0.16.1"
+DataMigrations = "0.0.2"
 DataStructures = "0.17, 0.18"
 Reexport = "^1"
 StructEquality = "2.1"

docs/Project.toml

@@ -1,16 +1,7 @@
 [deps]
-ACSets = "227ef7b5-1206-438b-ac65-934d6da304b8"
+AlgebraicPetri = "4f99eebe-17bf-4e98-b6a1-2c4f205a959b"
 AlgebraicRewriting = "725a01d3-f174-5bbd-84e1-b9417bad95d9"
-CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
+DataMigrations = "0c4ad18d-0c49-4bc2-90d5-5bca8f00d6ae"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
-LiveServer = "16fef848-5104-11e9-1b77-fb7a48bbb589"
-Luxor = "ae8d54c2-7ccd-5906-9d76-62fc9837b5bc"
-PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
-Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
-StructEquality = "6ec83bb0-ed9f-11e9-3b4c-2b04cb4e219c"
-
-[compat]
-ACSets = "0.2.6"
-Catlab = "0.15.5"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"

docs/src/full_demo.jl

@@ -1,6 +1,4 @@
-using AlgebraicRewriting
-using Catlab, Catlab.CategoricalAlgebra, Catlab.Graphics, Catlab.Graphs, Catlab.Programs
-import AlgebraicPetri
+using AlgebraicRewriting, Catlab, AlgebraicPetri, DataMigrations
 using Test
 
 
@@ -9,7 +7,7 @@ This is a self-contained walkthrough of the main features of AlgebraicRewriting.
 This is a regular julia file that can be run interactively.
 
 Importantly: 
- - use Julia 1.9 (not yet official released)
+ - use Julia 1.10
  - ]activate the environment in AlgebraicRewriting.jl/docs 
  - check that graphviz is installed locally (test via "which dot" in terminal)
 
@@ -54,8 +52,8 @@ We construct a rule by providing a span, L ← I → R
 L =  path_graph(Graph, 2)                         # • → •
 I = Graph(1)                                      # •
 R = @acset Graph begin V=1; E=1; src=1; tgt=1 end # •↺
-l = CSetTransformation(I, L; V=[1]) # graph homomorphism data
-r = CSetTransformation(I, R; V=[1])
+l = ACSetTransformation(I, L; V=[1]) # graph homomorphism data
+r = ACSetTransformation(I, R; V=[1])
 
 rule = Rule(l, r)
 G = path_graph(Graph, 5)  # • → • → • → • → •
@@ -139,7 +137,7 @@ rule_sqpo = Rule{:SqPO}(l, r) # same data as before)
 G = star_graph(Graph, 6) # a 5-pointed star
 to_graphviz(G; prog="neato") # changing "prog" can sometimes make it look better
 
-m = CSetTransformation(Graph(1), G; V=[6]) # point at the center
+m = ACSetTransformation(Graph(1), G; V=[6]) # point at the center
 res = rewrite_match(rule_sqpo, m) 
 to_graphviz(res; prog="neato")
 
@@ -163,7 +161,7 @@ r = id(K)
 L′ = @acset Graph begin V=3; E=6; 
     src=[1,1,1,2,3,3]; tgt=[1,2,3,3,3,1] 
 end 
-tl = CSetTransformation(L, L′; V=[2]) # 2 is the matched vertex
+tl = ACSetTransformation(L, L′; V=[2]) # 2 is the matched vertex
 to_graphviz(L′; node_labels=true)
 
 # The outneighbors of the matched vertex are duplicated (an edge connects the 
@@ -173,7 +171,7 @@ to_graphviz(L′; node_labels=true)
 K′ = @acset Graph begin V=5; E=9;
     src=[1,1,1,2,3,3,3,4,5]; tgt=[1,2,3,3,3,1,5,5,5] 
 end
-tk = CSetTransformation(K,K′; V=[2,4])
+tk = ACSetTransformation(K,K′; V=[2,4])
 to_graphviz(K′; node_labels=true)
 
 l′ = homomorphism(K′,L′; initial=(V=[1,2,3,2,3],))
@@ -205,14 +203,14 @@ category of (whole-grain) Petri nets, with States and Transitions.
 """
 
 
-function graph_slice(s::Slice) 
+function graph_slice(s::Slice)
     h = s.slice
     V, E = collect.([h[:V], h[:E]])
     g = dom(h)
     (S,T), (I,O) = [[findall(==(i),X) for i in 1:2] for X in [V,E]]
     nS,nT,nI,nO = length.([S,T,I,O])
     findS, findT = [x->findfirst(==(x), X) for X in [S,T]]
-    AlgebraicPetri.Graph(@acset AlgebraicPetri.PetriNet begin 
+    to_graphviz(@acset AlgebraicPetri.PetriNet begin 
         S=nS; T=nT; I=nI; O=nO
         is=findS.(g[I,:src]); it=findT.(g[I, :tgt])
         ot=findT.(g[O,:src]); os=findS.(g[O, :tgt]) end)

docs/src/lotka_volterra.jl

@@ -1,8 +1,6 @@
 module LotkaVolterra 
 
-using Catlab, Catlab.Theories, Catlab.CategoricalAlgebra, Catlab.Graphs, 
-      Catlab.Graphics, Catlab.WiringDiagrams, Catlab.Programs
-using AlgebraicRewriting
+using Catlab, DataMigrations, AlgebraicRewriting
 using Random, Test, StructEquality
 using Luxor
 
@@ -74,10 +72,9 @@ F2 = Migrate(
   Dict(x=>x for x in Symbol.(TheoryLV.generators[:Hom])), LV′; delta=false)
 
 """
-Create a nxn grid with periodic boundary conditions. Edges in each cardinal
+Create an n × n grid with periodic boundary conditions. Edges in each cardinal
 direction originate at every point
 
-
 (i,j+1) -> (i+1,j+1) -> ...
   ↑          ↑
 (i,j)   -> (i+1,j)   -> ...
@@ -410,6 +407,7 @@ cycle = ( agent(sheep; n=:sheep,  ret=I)
 # wrap in a while loop
 overall = while_schedule(cycle, curr -> nparts(curr,:Wolf) >= 0) |> F2
 # view_sched(overall; names=F2(N))
+
 X = initialize(3, .25, .25)
 res, = apply_schedule(overall, X; steps=50);
 

src/rewrite/Representable.jl → ext/AlgebraicRewritingDataMigrationsExt.jl

@@ -1,62 +1,12 @@
-module Representable 
-export yoneda_cache, SchRule, SchRulel, SchRuler, SchRule, SchPBPO
+module AlgebraicRewritingDataMigrationsExt 
 
-using Catlab, Catlab.CategoricalAlgebra
+using Catlab
 using ACSets.DenseACSets: constructor
-using Catlab.Programs.DiagrammaticPrograms: AST
+using DataMigrations
 
-import ..Utils: Rule
-import ..PBPO: PBPORule
+using AlgebraicRewriting
+import AlgebraicRewriting.Rewrite: Rule, PBPORule 
 
-# Rule schemas 
-##############
-
-@present SchRule_(FreeSchema) begin
-  L::Ob # inputs
-  R::Ob # outputs
-  K::Ob # keep
-end
-
-@present SchRulel <: SchRule_ begin 
-  l::Hom(L, K)
-end
-@present SchRuler <: SchRule_ begin 
-  r::Hom(R, K)
-end
-
-@present SchRule <: SchRulel begin 
-  r::Hom(R, K)
-end
-
-@present SchPBPO <: SchRule begin 
-  (L′, K′)::Ob 
-  tₗ::Hom(L′,L) 
-  tₖ::Hom(K′,K)
-  l′::Hom(L′,K′)
-end
-
-# Caching
-#########
-
-function yoneda_cache(T::Type,S=nothing; clear=false, cache="cache")
-  S = isnothing(S) ? Presentation(T) : S
-  tname = nameof(T) |> string
-  cache_dict = Dict{Symbol,Tuple{T,Int}}(map(generators(S, :Ob)) do ob
-    name = nameof(ob)
-    cache_dir = mkpath(joinpath(cache, "$tname"))
-    path, ipath = joinpath.(cache_dir, ["$name.json", "_id_$name.json"])
-    name => if !clear && isfile(path)
-      (read_json_acset(T, path), parse(Int,open(io->read(io, String), ipath)))
-    else 
-      @debug "Computing representable $name"
-      rep, i = representable(T, S, name; return_unit_id=true)
-      write_json_acset(rep, path)
-      write(ipath, string(i))
-      (rep, i)
-    end
-  end)
-  return yoneda(T; cache=cache_dict)
-end
 
 # Alternate constructors for rules 
 ##################################
@@ -129,4 +79,4 @@ function named_ob_generators(C::FinCat)
 end
 
 
-end # module 
+end # module 

src/analysis/Processes.jl

@@ -1,7 +1,8 @@
 module Processes 
 export find_deps 
 
-using Catlab.CategoricalAlgebra, Catlab.Graphs
+using Catlab
+using Catlab.Theories: ⋅
 
 using ..Rewrite.Utils
 

src/categorical_algebra/CSets.jl

@@ -408,6 +408,7 @@ end
 (F::Migrate)(d::Dict{V,<:ACSet}) where V = Dict([k=>F(v) for (k,v) in collect(d)])
 (F::Migrate)(d::Dict{<:ACSet,V}) where V = Dict([F(k)=>v for (k,v) in collect(d)])
 (m::Migrate)(::Nothing) = nothing
+(m::Migrate)(s::Union{String,Symbol}) = s
 function (m::Migrate)(Y::ACSet)
   if m.delta
      typeof(Y) <: m.T1 || error("Cannot Δ migrate a $(typeof(Y))")

src/categorical_algebra/PartialMap.jl

@@ -110,8 +110,8 @@ the same data for a morphism lifted from X⟶Y to T(X)⟶T(Y).
 However, we still need to map the extra stuff in T(X) to the proper extra stuff
 in T(Y).
 """
-function partial_map_functor_hom(f::CSetTransformation;
-    pres::Union{Nothing, Presentation}=nothing)::CSetTransformation
+function partial_map_functor_hom(f::ACSetTransformation;
+    pres::Union{Nothing, Presentation}=nothing)::ACSetTransformation
   X, Y = dom(f), codom(f)
   S = acset_schema(X)
   (d, _), (cd, cddict) = [partial_map_functor_ob(x; pres=pres) for x in [X,Y]]
@@ -132,19 +132,19 @@ function partial_map_functor_hom(f::CSetTransformation;
       end
     end
   end
-  return CSetTransformation(d,cd;comps...)
+  ACSetTransformation(d, cd; comps...)
 end
 
 """
 The natural injection from X ⟶ T(X)
 When evaluated on the terminal object, this gives the subobject classfier.
 """
 function partial_map_classifier_eta(x::StructCSet;
-    pres::Union{Nothing, Presentation}=nothing)::CSetTransformation
+    pres::Union{Nothing, Presentation}=nothing)::ACSetTransformation
   S = acset_schema(x)
   codom = partial_map_functor_ob(x; pres=pres)[1]
   d = Dict([k=>collect(v) for (k,v) in pairs(id(x).components)])
-  return CSetTransformation(x, codom; d...)
+  ACSetTransformation(x, codom; d...)
 end
 
 
@@ -165,9 +165,9 @@ the subobject picked out by X. When A is 'deleted', it picks out the right
 element of the additional data added by T(B).
 """
 function partial_map_classifier_universal_property(
-    m::CSetTransformation, f::CSetTransformation;
+    m::ACSetTransformation, f::ACSetTransformation;
     pres::Union{Nothing, Presentation}=nothing, check=false
-    )::CSetTransformation
+    )::ACSetTransformation
   S = acset_schema(dom(m))
   hdata   = collect(homs(S))
   A, B    = codom(m), codom(f)
@@ -196,7 +196,7 @@ function partial_map_classifier_universal_property(
       end
     end
   end
-  ϕ = CSetTransformation(A, TB; res...)
+  ϕ = ACSetTransformation(A, TB; res...)
   if check
     is_natural(ηB) || error("ηB not natural $ηB")
     is_natural(ϕ) || error("ϕ not natural $ϕ")

src/rewrite/Migration.jl

@@ -0,0 +1,57 @@
+module Migration 
+export yoneda_cache, SchRule, SchRulel, SchRuler, SchRule, SchPBPO
+
+using Catlab
+using ..Utils 
+
+# Rule schemas 
+##############
+
+@present SchRule_(FreeSchema) begin
+  L::Ob # inputs
+  R::Ob # outputs
+  K::Ob # keep
+end
+
+@present SchRulel <: SchRule_ begin 
+  l::Hom(L, K)
+end
+@present SchRuler <: SchRule_ begin 
+  r::Hom(R, K)
+end
+
+@present SchRule <: SchRulel begin 
+  r::Hom(R, K)
+end
+
+@present SchPBPO <: SchRule begin 
+  (L′, K′)::Ob 
+  tₗ::Hom(L′,L) 
+  tₖ::Hom(K′,K)
+  l′::Hom(L′,K′)
+end
+
+# Caching
+#########
+
+function yoneda_cache(T::Type,S=nothing; clear=false, cache="cache")
+  S = isnothing(S) ? Presentation(T) : S
+  tname = nameof(T) |> string
+  cache_dict = Dict{Symbol,Tuple{T,Int}}(map(generators(S, :Ob)) do ob
+    name = nameof(ob)
+    cache_dir = mkpath(joinpath(cache, "$tname"))
+    path, ipath = joinpath.(cache_dir, ["$name.json", "_id_$name.json"])
+    name => if !clear && isfile(path)
+      (read_json_acset(T, path), parse(Int,open(io->read(io, String), ipath)))
+    else 
+      @debug "Computing representable $name"
+      rep, i = representable(T, S, name; return_unit_id=true)
+      write_json_acset(rep, path)
+      write(ipath, string(i))
+      (rep, i)
+    end
+  end)
+  return yoneda(T; cache=cache_dict)
+end
+
+end # module