Merge pull request #831 from kris-brown/compat_markdeleted

Support for mark-as-deleted in acsets

src/categorical_algebra/ACSetsGATsInterop.jl

@@ -66,8 +66,9 @@ function Presentation(s::BasicSchema{Symbol})
 end
 
 function DenseACSets.struct_acset(name::Symbol, parent, p::Presentation;
-                                  index::Vector=[], unique_index::Vector=[])
-  DenseACSets.struct_acset(name, parent, Schema(p); index, unique_index)
+                                  index::Vector=[], unique_index::Vector=[], 
+                                  part_type::Type{<:PartsType}=IntParts)
+  DenseACSets.struct_acset(name, parent, Schema(p); index, unique_index, part_type)
 end
 
 function DenseACSets.DynamicACSet(

src/categorical_algebra/CSets.jl

@@ -6,7 +6,7 @@ export ACSetMorphism,
   StructTightACSetTransformation, TightACSetTransformation,
   LooseACSetTransformation, SubACSet, SubCSet,
   components, type_components, force,
-  naturality_failures, show_naturality_failures, is_natural,
+  naturality_failures, show_naturality_failures, is_natural, in_bounds,
   abstract_attributes
 
 using Base.Iterators: flatten
@@ -28,7 +28,7 @@ import ...Theories: ob, hom, dom, codom, compose, ⋅, id,
   meet, ∧, join, ∨, top, ⊤, bottom, ⊥, ⊕, ⊗
 
 using ..FreeDiagrams, ..Limits, ..Subobjects, ..Sets, ..FinSets, ..FinCats
-using ..FinSets: VarFunction, LooseVarFunction, IdentityFunction, VarSet
+using ..FinSets: VarFunction, LooseVarFunction, IdentityFunction, VarSet, AbsVarFunction
 import ..Limits: limit, colimit, universal
 import ..Subobjects: Subobject, implies, ⟹, subtract, \, negate, ¬, non, ~
 import ..Sets: SetOb, SetFunction, TypeSet
@@ -427,47 +427,51 @@ TightACSetTransformation(components, X::StructACSet{S}, Y::StructACSet{S}) where
 
 # Component coercion
 
-function coerce_components(S, components, X,Y)
+function coerce_components(S, components, X::ACSet{<:PT}, Y) where PT
   @assert keys(components) ⊆ objects(S) ∪ attrtypes(S)
-  ocomps = NamedTuple(
-    c => coerce_component(c, get(components,c,1:0), nparts(X,c), nparts(Y,c))
-    for c in objects(S))
+  kw = Dict(map(types(S)) do c  
+    c => PT <: MarkAsDeleted ? (dom_parts=parts(X,c), codom_parts=parts(Y,c)) : (;)
+  end)
+  ocomps = NamedTuple(map(objects(S)) do c
+    c => coerce_component(c, get(components, c, 1:0), 
+                          nparts(X,c), nparts(Y,c); kw[c]...)
+  end)
   acomps = NamedTuple(map(attrtypes(S)) do c
-    c => coerce_attrvar_component(c, get(components,c,1:0), 
-          TypeSet(X, c), TypeSet(Y, c), nparts(X,c), nparts(Y,c))
+    c => coerce_attrvar_component(c, get(components, c, 1:0), 
+          TypeSet(X, c), TypeSet(Y, c), nparts(X,c), nparts(Y,c); kw[c]...)
   end)
-    return merge(ocomps, acomps)
+  return merge(ocomps, acomps)
 end 
 
 function coerce_component(ob::Symbol, f::FinFunction{Int,Int},
-                          dom_size::Int, codom_size::Int)
+                          dom_size::Int, codom_size::Int; kw...)
   length(dom(f)) == dom_size || error("Domain error in component $ob")
-  length(codom(f)) == codom_size || error("Codomain error in component $ob")
-  return f
+  # length(codom(f)) == codom_size || error("Codomain error in component $ob") # codom size is now Maxpart not nparts
+  return f 
 end
 
-coerce_component(::Symbol, f, dom_size::Int, codom_size::Int) =
-  FinFunction(f, dom_size, codom_size)
+coerce_component(::Symbol, f, dom_size::Int, codom_size::Int; kw...) =
+  FinFunction(f, dom_size, codom_size; kw...)
 
 function coerce_attrvar_component(
     ob::Symbol, f::AbstractVector,::TypeSet{T}, ::TypeSet{T},
-    dom_size::Int, codom_size::Int) where {T}
+    dom_size::Int, codom_size::Int; kw...) where {T}
   e = "Domain error in component $ob variable assignment $(length(f)) != $dom_size"
   length(f) == dom_size || error(e)
   return VarFunction{T}(f, FinSet(codom_size))
 end
 
 function coerce_attrvar_component(
     ob::Symbol, f::VarFunction,::TypeSet{T},::TypeSet{T},
-    dom_size::Int, codom_size::Int) where {T}
+    dom_size::Int, codom_size::Int; kw...) where {T}
   # length(dom(f.fun)) == dom_size || error("Domain error in component $ob: $(dom(f.fun))!=$dom_size")
   length(f.codom) == codom_size || error("Codomain error in component $ob: $(f.fun.codom)!=$codom_size")
   return f
 end
 
 function coerce_attrvar_component(
     ob::Symbol, f::LooseVarFunction,d::TypeSet{T},cd::TypeSet{T′},
-    dom_size::Int, codom_size::Int) where {T,T′}
+    dom_size::Int, codom_size::Int; kw...) where {T,T′}
   length(dom(f.fun)) == dom_size || error("Domain error in component $ob")
   length(f.codom) == codom_size || error("Codomain error in component $ob: $(f.fun.codom)!=$codom_size")
   # We do not check types (equality is too strict)
@@ -478,7 +482,7 @@ end
 
 """Coerce an arbitrary julia function to a LooseVarFunction assuming no variables"""
 function coerce_attrvar_component(ob::Symbol, f::Function, d::TypeSet{T},cd::TypeSet{T′},
-  dom_size::Int, codom_size::Int) where {T,T′}
+  dom_size::Int, codom_size::Int; kw...) where {T,T′}
   dom_size == 0 || error("Cannot specify $ob component with $f with $dom_size domain variables")
   coerce_attrvar_component(ob, LooseVarFunction{T,T′}([], f, FinSet(codom_size)), 
                            d, cd, dom_size,codom_size)
@@ -606,21 +610,16 @@ Xₕ ↓  ✓  ↓ Yₕ
 
 You're allowed to run this on a named tuple partly specifying an ACSetTransformation,
 though at this time the domain and codomain must be fully specified ACSets.
-
-`only_combinatorial=true` means to only test naturality in combinatorial data
 """
-function is_natural(α::LooseACSetTransformation; only_combinatorial=false) 
-  is_natural(dom(α),codom(α),α.components,type_components(α); only_combinatorial)
+function is_natural(α::LooseACSetTransformation) 
+  is_natural(dom(α), codom(α), α.components, type_components(α))
 end
-function is_natural(α::ACSetTransformation; only_combinatorial=false)
-  is_natural(dom(α),codom(α),α.components; only_combinatorial)
-end
-function is_natural(α::CSetTransformation; only_combinatorial=true)
-  is_natural(dom(α),codom(α),α.components; only_combinatorial)
+function is_natural(α::ACSetMorphism)
+  is_natural(dom(α), codom(α), α.components)
 end
 
-is_natural(dom,codom,comps...; only_combinatorial=false) =
-  all(isempty, last.(collect(naturality_failures(dom, codom, comps...; only_combinatorial))))
+is_natural(dom, codom, comps...) =
+  all(isempty, last.(collect(naturality_failures(dom, codom, comps...))))
 
 """
 Returns a dictionary whose keys are contained in the names in `arrows(S)`
@@ -629,32 +628,29 @@ over the elements of X(c) on which α's naturality square
 for f does not commute. Components should be a NamedTuple or Dictionary
 with keys contained in the names of S's morphisms and values vectors or dicts
 defining partial functions from X(c) to Y(c).
-
-`only_combinatorial=true` means to only look for naturality failures in combinatorial 
-data.
 """
-function naturality_failures(X,Y,comps; only_combinatorial=false)
+function naturality_failures(X, Y, comps)
   type_comps = Dict(attr => SetFunction(identity, SetOb(X,attr), SetOb(X,attr)) 
                     for attr in attrtype(acset_schema(X)))
-  naturality_failures(X, Y, comps, type_comps; only_combinatorial)
+  naturality_failures(X, Y, comps, type_comps)
 end
-function naturality_failures(X, Y, comps, type_comps; only_combinatorial=false)
+function naturality_failures(X, Y, comps, type_comps)
   S = acset_schema(X)
-  Fun = Union{SetFunction,VarFunction,LooseVarFunction}
+  Fun = Union{SetFunction, VarFunction, LooseVarFunction}
   comps = Dict(a => isa(comps[a],Fun) ? comps[a] : FinDomFunction(comps[a])  
                for a in keys(comps))
-
   type_comps = Dict(a => isa(type_comps[a], Fun) ? type_comps[a] : 
                         SetFunction(type_comps[a],TypeSet(X,a),TypeSet(Y,a)) 
                     for a in keys(type_comps))
-  α = merge(comps, only_combinatorial ? Dict() : type_comps)
-  arrs = [(f,c,d) for (f,c,d) in arrows(S) if haskey(α,c) && haskey(α,d)]
+  α(o::Symbol, i::AttrVar) = comps[o](i)
+  α(o::Symbol, i::Any) = o ∈ ob(S) ? comps[o](i) : type_comps[o](i)
+  ks = union(keys(comps), keys(type_comps))
+  arrs = filter(((f,c,d),) -> c ∈ ks && d ∈ ks, arrows(S))
   ps = Iterators.map(arrs) do (f,c,d)
-    Xf,Yf,α_c,α_d = subpart(X,f),subpart(Y,f), α[c], α[d]
     Pair(f,
-    Iterators.map(i->(i,Yf[α_c(i)],α_d(Xf[i])),
-      Iterators.filter(dom(α_c)) do i
-        Xf[i] in dom(α_d) && Yf[α_c(i)] != α_d(Xf[i])
+    Iterators.map(i->(i, Y[α(c, i), f], α(d, X[i, f])),
+      Iterators.filter(parts(X, c)) do i
+        Y[α(c,i), f] != α(d,X[i, f])
       end))
   end
   Dict(ps)
@@ -664,8 +660,6 @@ naturality_failures(α::CSetTransformation) =
   naturality_failures(dom(α), codom(α), α.components; combinatorial=true)
 naturality_failures(α::TightACSetTransformation) =
   naturality_failures(dom(α), codom(α), α.components)
-naturality_failures(α::LooseACSetTransformation)=
-  naturality_failures(dom(α), codom(α), α.components, α.type_components)
 
 """ Pretty-print failures of transformation to be natural.
 
@@ -1358,4 +1352,29 @@ function var_reference(X::ACSet, at::Symbol, i::Int)
   error("Wandering variable $at#$p")
 end
 
+# Mark as deleted
+#################
+
+"""
+Check whether an ACSetTransformation is still valid, despite possible deletion 
+of elements in the codomain. An ACSetTransformation that isn't in bounds will 
+throw an error, rather than return `false`, if run through `is_natural`.
+"""
+function in_bounds(f::ACSetTransformation) 
+  X, Y = dom(f), codom(f)
+  S = acset_schema(X)
+  all(ob(S)) do o 
+    all(parts(X, o)) do i 
+      f[o](i) ∈ parts(Y, o)
+    end
+  end || return false
+  all(attrtypes(S)) do o 
+    all(AttrVar.(parts(X, o))) do i 
+      j = f[o](i) 
+      !(j isa AttrVar) || j.val ∈ parts(Y, o)
+    end
+  end
+end
+
+
 end # module

src/categorical_algebra/FinSets.jl

@@ -14,6 +14,7 @@ using StaticArrays: StaticVector, SVector, SizedVector, similar_type
 import Tables, PrettyTables
 
 using ACSets
+import ACSets.Columns: preimage
 @reexport using ..Sets
 using ...Theories, ...Graphs
 using ..FinCats, ..FreeDiagrams, ..Limits, ..Subobjects
@@ -187,15 +188,22 @@ FinFunction(::typeof(identity), args...) =
 FinFunction(f::AbstractDict, args...) =
   FinFunctionDict(f, (FinSet(arg) for arg in args)...)
 
-function FinFunction(f::AbstractVector{Int}, args...;
-                     index=false, known_correct = false)
-  cod = FinSet(args[end])
+function FinFunction(f::AbstractVector, args...;
+                     index=false, known_correct = false, 
+                     dom_parts=nothing, codom_parts=nothing)
+  cod = FinSet(isnothing(codom_parts) ? args[end] : codom_parts)
+  f = Vector{Int}(f) # coerce empty vectors
   if !known_correct
     for (i,t) ∈ enumerate(f)
-      t ∈ cod || error("Value $t at index $i is not in $cod.")
+      if isnothing(dom_parts) || i ∈ dom_parts
+        t ∈ cod || error("Value $t at index $i is not in $cod.")
+      end
     end
   end
   if !index
+    if !isnothing(dom_parts) 
+      args = (length(f), args[2:end]...)
+    end
     FinDomFunctionVector(f, (FinSet(arg) for arg in args)...)
   else
     index = index == true ? nothing : index
@@ -501,10 +509,8 @@ Sets.do_compose(f::Union{FinFunctionVector,IndexedFinFunctionVector},
   FinDomFunctionVector(g.func[f.func], codom(g))
 
 # These could be made to fail early if ever used in performance-critical areas
-is_epic(f::FinFunction) =
-length(codom(f)) == length(Set(values(collect(f))))
-is_monic(f::FinFunction)  =
-length(dom(f)) == length(Set(values(collect(f))))
+is_epic(f::FinFunction) = length(codom(f)) == length(Set(values(collect(f))))
+is_monic(f::FinFunction) = length(dom(f)) == length(Set(values(collect(f))))
 
 # Dict-based functions
 #---------------------

src/categorical_algebra/HomSearch.jl

@@ -234,18 +234,18 @@ function backtracking_search(f, X::ACSet, Y::ACSet;
   end
 
   pred_nt = NamedTuple{Ob}(let dic = get(predicates, c, Dict()); 
-    Union{Set{Int}, Nothing}[haskey(dic, p) ? Set(dic[p]) : nothing for p in parts(X,c)] 
+    Union{Set{Int}, Nothing}[haskey(dic, p) ? Set(dic[p]) : nothing for p in 1:maxpart(X,c)] 
   end for c in Ob)
 
   # Initialize state variables for search.
   assignment = merge(
-    NamedTuple{Ob}(zeros(Int, nparts(X, c)) for c in Ob),
+    NamedTuple{Ob}(zeros(Int, maxpart(X, c)) for c in Ob),
     NamedTuple{Attr}(Pair{Int,Union{AttrVar,attrtype_type(X,c)}}[
-      0 => AttrVar(0) for _ in parts(X,c)] for c in Attr)
+      0 => AttrVar(0) for _ in 1:maxpart(X,c)] for c in Attr)
   )
   assignment_depth = map(copy, assignment)
   inv_assignment = NamedTuple{ObAttr}(
-    (c in monic ? zeros(Int, nparts(Y, c)) : nothing) for c in ObAttr)
+    (c in monic ? zeros(Int, maxpart(Y, c)) : nothing) for c in ObAttr)
   loosefuns = NamedTuple{Attr}(
     isnothing(type_components) ? identity : get(type_components, c, identity) for c in Attr)
   state = BacktrackingState(assignment, assignment_depth, 
@@ -305,8 +305,8 @@ function find_mrv_elem(state::BacktrackingState, depth)
   S = acset_schema(state.dom)
   mrv, mrv_elem = Inf, nothing
   Y = state.codom
-  for c in ob(S), (x, y) in enumerate(state.assignment[c])
-    y == 0 || continue
+  for c in ob(S), x in parts(state.dom, c)
+    state.assignment[c][x] == 0 || continue
     n = count(can_assign_elem(state, depth, c, x, y) for y in parts(Y, c))
     if n < mrv
       mrv, mrv_elem = n, (c, x)

test/categorical_algebra/CSets.jl

@@ -532,11 +532,20 @@ end
 ##########
 
 const WG = WeightedGraph
-A = @acset WG{Bool} begin V=1;E=2;Weight=2;src=1;tgt=1;weight=[AttrVar(1),true] end
-B = @acset WG{Bool} begin V=1;E=2;Weight=1;src=1;tgt=1;weight=[true, false] end
+A = @acset WG{Bool} begin V=1; E=2; Weight=2;
+  src=1; tgt=1; weight=[AttrVar(1), true] 
+end
+B = @acset WG{Bool} begin V=1; E=2; Weight=1;
+  src=1; tgt=1; weight=[true, false] 
+end
 
 @test VarFunction(A,:weight) == VarFunction{Bool}([AttrVar(1), true], FinSet(2))
 
+f = ACSetTransformation(
+  Dict(:V=>[1],:E=>[1,2],:Weight=>[AttrVar(2), AttrVar(1)]), A, A
+)
+@test !is_natural(f) # this should not be true, bug in is_natural
+
 f = ACSetTransformation(Dict(:V=>[1],:E=>[2,1],:Weight=>[false, AttrVar(1)]), A,B)
 @test is_natural(f)
 @test force(id(A) ⋅ f) == force(f) == force(f ⋅ id(B))
@@ -761,10 +770,30 @@ end
 @test is_isomorphic(apex(ABC),expected)
 
 # 3. Apply commutative monoid to attrs
-ABC = pullback(AC,BC; attrfun=(weight=prod,))
+ABC = pullback(AC, BC; attrfun=(weight=prod,))
 expected = @acset WeightedGraph{Float64} begin V=6; E=7;
   src=[1,1,2,3,3,4,5]; tgt=[2,3,4,4,5,6,6]; weight=[-5,-2,-2,-5,-3,-3,-5]
 end
 @test is_isomorphic(apex(ABC),expected)
 
+# Mark as deleted
+#################
+
+@acset_type AbsMADGraph(SchWeightedGraph, part_type=BitSetParts) <: AbstractGraph
+const MADGraph = AbsMADGraph{Symbol}
+p2, p3 = path_graph.(MADGraph, 3:4)
+p2[:weight] = [:y,AttrVar(add_part!(p2, :Weight))]
+p3[:weight] = [AttrVar(add_part!(p3, :Weight)), :y, AttrVar(add_part!(p3, :Weight))]
+f = homomorphism(p2, p3)
+@test in_bounds(f) && is_natural(f)
+rem_part!(p3, :Weight, 2)
+p3[3, :weight] = :z
+@test !in_bounds(f) 
+
+f = homomorphism(p2, p3)
+@test in_bounds(f) && is_natural(f)
+rem_part!(p3, :E, 3)
+rem_part!(p3, :V, 4)
+@test !in_bounds(f)
+
 end

test/categorical_algebra/HomSearch.jl

@@ -241,4 +241,16 @@ results = first(is_iso1) ? results : reverse(results)
 exp = @acset WG begin V=3; E=1; src=1; tgt=2; weight=[false] end
 @test first(first(maximum_common_subobject(g1, g2; abstract=false))) == exp
 
+# Mark as deleted
+#################
+@acset_type AbsMADGraph(SchWeightedGraph, part_type=BitSetParts) <: AbstractGraph
+const MADGraph = AbsMADGraph{Symbol}
+
+v1, v2 = MADGraph.(1:2)
+@test !is_isomorphic(v1,v2)
+rem_part!(v2, :V, 1)
+@test is_isomorphic(v1,v2)
+@test is_isomorphic(v2,v1)
+
+
 end # module