Merge branch 'main' into cm/buildkite

Project.toml

@@ -2,7 +2,7 @@ name = "Catlab"
 uuid = "134e5e36-593f-5add-ad60-77f754baafbe"
 license = "MIT"
 authors = ["Evan Patterson <[email protected]>"]
-version = "0.16.16"
+version = "0.16.18"
 
 [deps]
 ACSets = "227ef7b5-1206-438b-ac65-934d6da304b8"
@@ -48,7 +48,7 @@ CatlabTikzPicturesExt = "TikzPictures"
 [compat]
 ACSets = "0.2.20"
 AlgebraicInterfaces = "0.1.3"
-Colors = "0.12"
+Colors = "0.12, 0.13"
 CompTime = "0.1"
 Compose = "0.7, 0.8, 0.9"
 Convex = "0.16"

src/categorical_algebra/CSets.jl

@@ -462,7 +462,11 @@ function coerce_component(ob::Symbol, f::FinFunction{Int,Int},
   return f 
 end
 
-coerce_component(::Symbol, f, dom_size::Int, codom_size::Int; kw...) =
+coerce_component(ob::Symbol, f::T, dom_size::Int, codom_size::Int; kw...) where {T<:Integer} =
+  error("Scalar component for $ob not allowed; " *
+  "this is probably from a scalar component in an ACSetTransformation, please use a vector")
+
+coerce_component(::Symbol, f::T, dom_size::Int, codom_size::Int; kw...) where {T<:AbstractVector{<:Integer}}=
   FinFunction(f, dom_size, codom_size; kw...)
 
 function coerce_attrvar_component(
@@ -831,12 +835,12 @@ the combinatorial part of the limit legs. The type components of the j'th leg of
 the limit is just the j'th cartesian projection.
 """
 function limit(::Type{Tuple{ACS,Hom}}, diagram; product_attrs::Bool=false) where
-    {S, Ts, ACS <: StructACSet{S,Ts}, Hom <: LooseACSetTransformation}
+    {S, ACS <: StructACSet{S}, Hom <: LooseACSetTransformation}
   limits = map(limit, unpack_diagram(diagram, S=S, all=!product_attrs))
   Xs = cone_objects(diagram)
 
   attr_lims = (product_attrs ?
-    map(limit, unpack_diagram(DiscreteDiagram(Xs, Hom), S=S,Ts=Ts,all=true)) : limits )
+    map(limit, unpack_diagram(DiscreteDiagram(Xs, Hom), S=S, all=true)) : limits )
 
   LimitACS = if isempty(attrtypes(S)); ACS
   else

src/categorical_algebra/HomSearch.jl

@@ -264,7 +264,7 @@ function backtracking_search(f, X::ACSet, Y::ACSet;
   for a_type in attrtypes(S) 
     a_type ∈ (monic ∪ iso ∪ no_bind) && continue # attrvars ↦ attrvars
     attrs′ = attrs(S, just_names=true, to=a_type)
-    avars = union(collect.([filter(x->x isa AttrVar, X[f]) for f in attrs′])...)
+    avars = union(AttrVar[],collect.([filter(x->x isa AttrVar, X[f]) for f in attrs′])...)
     assigned = partial_assignments(get(initial, a_type, []); is_attr=true)
     assigned′ = first.(collect(assigned))
     unassigned = setdiff(parts(X, a_type), [v.val for v in avars] ∪ assigned′)

src/graphics/Graphviz.jl

@@ -7,7 +7,7 @@ References:
 """
 module Graphviz
 export Expression, Statement, Attributes, Graph, Digraph, Subgraph,
-  Node, NodeID, Edge, Label, pprint, run_graphviz
+  Node, NodeID, Edge, Label, pprint, run_graphviz, view_graphviz
 
 using DataStructures: OrderedDict
 using StructEquality
@@ -172,6 +172,20 @@ function Base.show(io::IO, ::MIME"image/svg+xml", graph::Graph)
   run_graphviz(io, graph, format="svg")
 end
 
+function view_graphviz(g::Graph; path::String="")
+    filepath = isempty(path) ? "$(tempname()).png" : path
+    open(filepath, "w") do io
+        run_graphviz(io, g, format="png")
+    end
+    if Sys.islinux()
+        run(`xdg-open $filepath`, wait=false)
+    elseif Sys.isapple()
+        run(`open $filepath`, wait=false)
+    elseif Sys.iswindows()
+        run(`start $filepath`, wait=false)
+    end
+end
+
 # Pretty-print
 ##############
 

src/programs/RelationalPrograms.jl

@@ -145,10 +145,10 @@ function parse_relation_diagram(head::Expr, body::Expr)
     Expr(:where, expr, context) => (expr, parse_relation_context(context)...)
     _ => (head, nothing, nothing)
   end
-  var_types = if isnothing(all_types) # Untyped case.
+  var_types = if isnothing(all_types)    # Untyped case
     vars -> length(vars)
-  else # Typed case.
-    var_type_map = Dict{Symbol,Symbol}(zip(all_vars, all_types))
+  else
+    var_type_map = Dict(zip(all_vars, all_types)) 
     vars -> getindex.(Ref(var_type_map), vars)
   end
 
@@ -194,19 +194,24 @@ function parse_relation_context(context)
   vars = map(terms) do term
     @match term begin
       Expr(:(::), var::Symbol, type::Symbol) => (var => type)
+      Expr(:(::), var::Symbol, type::Expr) => (var => type)
+      Expr(:(::), var::Symbol, type::Integer) => (var => type)
       var::Symbol => var
-      _ => error("Invalid syntax in term $expr of context")
+      _ => error("Invalid syntax in term $term of context")
     end
   end
+
   if vars isa AbstractVector{Symbol}
     (vars, nothing)
-  elseif vars isa AbstractVector{Pair{Symbol,Symbol}}
+  elseif eltype(vars) <: Pair
     (first.(vars), last.(vars))
   else
     error("Context $context mixes typed and untyped variables")
   end
+
 end
 
+
 function parse_relation_call(call)
   @match call begin
     Expr(:call, name::Symbol, Expr(:parameters, args)) =>
@@ -242,6 +247,7 @@ function parse_relation_inferred_args(args)
       Expr(:kw, name::Symbol, var::Symbol) => (name => var)
       Expr(:(=), name::Symbol, var::Symbol) => (name => var)
       var::Symbol => var
+      Expr(:(::), _, _) => error("All variable types must be included in the where clause and not in the argument list")
       _ => error("Expected name as positional or keyword argument")
     end
   end

test/categorical_algebra/CSets.jl

@@ -64,6 +64,7 @@ f = ACSetTransformation(X,X; V=[1,2], E=[1,2,3])
 @test components(f) == (V=FinFunction([1,2]), E=FinFunction([1,2,3]), 
                         Weight=VarFunction{Float64}([], FinSet(0)))
 
+@test_throws ErrorException ACSetTransformation(Y,X; V=[1,2], E=1)
 g = ACSetTransformation(Y,X; V=[1,2], E=[1])
 @test is_natural(g)
 @test compose(g,f) |> force == g
@@ -300,6 +301,7 @@ diagram = FreeDiagram([g, ob(terminal(Graph)), Graph(1)], [(α,3,1), (β,3,2)])
 # Constructors and accessors. Test type conversion as well Int -> Float64
 g = path_graph(WeightedGraph{Float64}, 2, E=(weight=2,))
 h = path_graph(WeightedGraph{Float64}, 4, E=(weight=[1,2,3],))
+@test_throws ErrorException ACSetTransformation((V=[2,3], E=2), g, h)
 α = ACSetTransformation((V=[2,3], E=[2]), g, h)
 @test length(components(α)) == 3
 

test/categorical_algebra/HomSearch.jl

@@ -7,7 +7,7 @@ using Random: seed!
 # Setup
 #######
 
-seed!(100)
+seed!(10)
 
 @present SchSetAttr(FreeSchema) begin
   X::Ob

test/programs/RelationalPrograms.jl

@@ -1,4 +1,5 @@
 module TestRelationalPrograms
+
 using Test
 
 using Catlab.CategoricalAlgebra.CSets
@@ -49,14 +50,16 @@ d = RelationDiagram(0)
 add_box!(d, 0, name=:A)
 @test parsed == d
 
-# Typed
+
+# Typed by Symbols
 #------
 
 parsed = @relation (x,y,z) where (x::X, y::Y, z::Z, w::W) begin
   R(x,w)
   S(y,w)
   T(z,w)
 end
+
 d = RelationDiagram([:X,:Y,:Z])
 add_box!(d, [:X,:W], name=:R)
 add_box!(d, [:Y,:W], name=:S)
@@ -66,6 +69,67 @@ set_junction!(d, [1,4,2,4,3,4])
 set_junction!(d, [1,2,3], outer=true)
 @test parsed == d
 
+
+# Typed by Integers
+#------
+
+parsed = @relation (x,y,z) where (x::1, y::2, z::3, w::4) begin
+  R(x,w)
+  S(y,w)
+  T(z,w)
+end
+
+d = RelationDiagram([:1,:2,:3])
+add_box!(d, [:1,:4], name=:R)
+add_box!(d, [:2,:4], name=:S)
+add_box!(d, [:3,:4], name=:T)
+add_junctions!(d, [:1,:2,:3,:4], variable=[:x,:y,:z,:w])
+set_junction!(d, [1,4,2,4,3,4])
+set_junction!(d, [1,2,3], outer=true)
+@test parsed == d
+
+
+
+# Typed by Expressions
+#------
+
+parsed = @relation (x,y,z) where (x::n(1), y::n(2), z::n(3), w::n(4)) begin
+  R(x,w)
+  S(y,w)
+  T(z,w)
+end
+
+d = RelationDiagram([:(n(1)), :(n(2)), :(n(3))])
+add_box!(d, [:(n(1)),:(n(4))], name=:R)
+add_box!(d, [:(n(2)),:(n(4))], name=:S)
+add_box!(d, [:(n(3)),:(n(4))], name=:T)
+add_junctions!(d, [:(n(1)),:(n(2)),:(n(3)),:(n(4))], variable=[:x,:y,:z,:w])
+set_junction!(d, [1,4,2,4,3,4])
+set_junction!(d, [1,2,3], outer=true)
+@test parsed == d
+
+# Mixed types
+#------
+
+parsed = @relation (x,y,z) where (x::n(1), y::2, z::C, w::nothing) begin
+  R(x,w)
+  S(y,w)
+  T(z,w)
+end
+
+d = RelationDiagram([:(n(1)), :2, :C])
+add_box!(d, [:(n(1)),:nothing], name=:R)
+add_box!(d, [:2,:nothing], name=:S)
+add_box!(d, [:C,:nothing], name=:T)
+add_junctions!(d, [:(n(1)),:2,:C,:nothing], variable=[:x,:y,:z,:w])
+set_junction!(d, [1,4,2,4,3,4])
+set_junction!(d, [1,2,3], outer=true)
+@test parsed == d
+
+
+
+
+
 # Special case: closed diagram.
 sird_uwd = @relation () where (S::Pop, I::Pop, R::Pop, D::Pop) begin
   infect(S,I,I,I) # inf