cleanup Project.toml and fix imports

Project.toml

@@ -4,23 +4,32 @@ authors = ["Marek Kaluba <kalmar@amu.edu.pl>"]
 version = "0.3.2"
 
 [deps]
-Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+Groups = "5d8bd718-bd84-11e8-3b40-ad14f4a32557"
 IntervalArithmetic = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253"
 JuMP = "4076af6c-e467-56ae-b986-b466b2749572"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-SCS = "c946c3f1-0d1f-5ce8-9dea-7daa1f7e2d13"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 SymbolicWedderburn = "858aa9a9-4c7c-4c62-b466-2421203962a2"
 
 [compat]
-IntervalArithmetic = "^0.16.0"
+COSMO = "0.8"
-JuMP = "^0.20.0"
+Groups = "0.7"
-SCS = "^0.7.0"
+IntervalArithmetic = "0.20"
-julia = "^1.3.0"
+JuMP = "1.3"
+SCS = "1.1.0"
+StaticArrays = "1"
+SymbolicWedderburn = "0.3.1"
+julia = "1.6"
 
 [extras]
+COSMO = "1e616198-aa4e-51ec-90a2-23f7fbd31d8d"
+Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 SCS = "c946c3f1-0d1f-5ce8-9dea-7daa1f7e2d13"
+Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "SCS"]
+scripts = ["Dates", "Logging", "Serialization", "SCS", "COSMO"]
+test = ["Test", "SCS", "COSMO"]

src/PropertyT.jl

@@ -3,14 +3,15 @@ module PropertyT
 
 using LinearAlgebra
 using SparseArrays
-using Dates
 
 using IntervalArithmetic
 using JuMP
 
 using Groups
-using StarAlgebras
+import Groups.GroupsCore
 using SymbolicWedderburn
+import SymbolicWedderburn.StarAlgebras
+import SymbolicWedderburn.PermutationGroups
 
 include("constraint_matrix.jl")
 include("sos_sdps.jl")

src/actions/actions.jl

@@ -1,5 +1,5 @@
 import SymbolicWedderburn.action
-StarAlgebras.star(g::GroupElement) = inv(g)
+StarAlgebras.star(g::Groups.GroupElement) = inv(g)
 
 include("alphabet_permutation.jl")
 

src/actions/alphabet_permutation.jl

@@ -1,7 +1,9 @@
 ## action induced from permuting letters of an alphabet
 
+import Groups: Constructions
+
 struct AlphabetPermutation{GEl,I} <: SymbolicWedderburn.ByPermutations
-    perms::Dict{GEl,Perm{I}}
+    perms::Dict{GEl,PermutationGroups.Perm{I}}
 end
 
 function AlphabetPermutation(
@@ -10,14 +12,14 @@ function AlphabetPermutation(
     op,
 )
     return AlphabetPermutation(
-        Dict(γ => inv(Perm([A[op(l, γ)] for l in A])) for γ in Γ),
+        Dict(γ => inv(PermutationGroups.Perm([A[op(l, γ)] for l in A])) for γ in Γ),
     )
 end
 
 function AlphabetPermutation(A::Alphabet, W::Constructions.WreathProduct, op)
     return AlphabetPermutation(
         Dict(
-            w => inv(Perm([A[op(op(l, w.p), w.n)] for l in A])) for
+            w => inv(PermutationGroups.Perm([A[op(op(l, w.p), w.n)] for l in A])) for
             w in W
         ),
     )
@@ -25,7 +27,7 @@ end
 
 function SymbolicWedderburn.action(
     act::AlphabetPermutation,
-    γ::GroupElement,
+    γ::Groups.GroupElement,
     w::Groups.AbstractWord,
 )
     return w^(act.perms[γ])
@@ -33,7 +35,7 @@ end
 
 function SymbolicWedderburn.action(
     act::AlphabetPermutation,
-    γ::GroupElement,
+    γ::Groups.GroupElement,
     g::Groups.AbstractFPGroupElement,
 )
     G = parent(g)

src/certify.jl

@@ -34,7 +34,7 @@ function _fma_SOS_thr!(
     return result
 end
 
-function _cnstr_sos!(res::AlgebraElement, Q::AbstractMatrix, cnstrs)
+function _cnstr_sos!(res::StarAlgebras.AlgebraElement, Q::AbstractMatrix, cnstrs)
     StarAlgebras.zero!(res)
     Q² = Q' * Q
     for (g, A_g) in cnstrs
@@ -43,7 +43,7 @@ function _cnstr_sos!(res::AlgebraElement, Q::AbstractMatrix, cnstrs)
     return res
 end
 
-function _augmented_sos!(res::AlgebraElement, Q::AbstractMatrix)
+function _augmented_sos!(res::StarAlgebras.AlgebraElement, Q::AbstractMatrix)
     A = parent(res)
     StarAlgebras.zero!(res)
     Q² = Q' * Q
@@ -64,10 +64,10 @@ function _augmented_sos!(res::AlgebraElement, Q::AbstractMatrix)
     return res
 end
 
-function compute_sos(A::StarAlgebra, Q::AbstractMatrix; augmented::Bool)
+function compute_sos(A::StarAlgebras.StarAlgebra, Q::AbstractMatrix; augmented::Bool)
     if augmented
         z = zeros(eltype(Q), length(basis(A)))
-        res = AlgebraElement(z, A)
+        res = StarAlgebras.AlgebraElement(z, A)
         return _augmented_sos!(res, Q)
         cnstrs = constraints(basis(A), A.mstructure; augmented=true)
         return _cnstr_sos!(res, Q, cnstrs)
@@ -77,11 +77,11 @@ function compute_sos(A::StarAlgebra, Q::AbstractMatrix; augmented::Bool)
 
         _fma_SOS_thr!(z, A.mstructure, Q)
 
-        return AlgebraElement(z, A)
+        return StarAlgebras.AlgebraElement(z, A)
     end
 end
 
-function sufficient_λ(residual::AlgebraElement, λ; halfradius)
+function sufficient_λ(residual::StarAlgebras.AlgebraElement, λ; halfradius)
     L1_norm = norm(residual, 1)
     suff_λ = λ - 2.0^(2ceil(log2(halfradius))) * L1_norm
 
@@ -97,7 +97,7 @@ function sufficient_λ(residual::AlgebraElement, λ; halfradius)
 
     info_strs = [
         "Numerical metrics of the obtained SOS:",
-        "ɛ(elt - λu - ∑ξᵢ*ξᵢ) $eq_sign $(aug(residual))",
+        "ɛ(elt - λu - ∑ξᵢ*ξᵢ) $eq_sign $(StarAlgebras.aug(residual))",
         "‖elt - λu - ∑ξᵢ*ξᵢ‖₁ $eq_sign $(L1_norm)",
         " λ $eq_sign $suff_λ",
     ]
@@ -107,10 +107,10 @@ function sufficient_λ(residual::AlgebraElement, λ; halfradius)
 end
 
 function sufficient_λ(
-    elt::AlgebraElement,
+    elt::StarAlgebras.AlgebraElement,
-    order_unit::AlgebraElement,
+    order_unit::StarAlgebras.AlgebraElement,
     λ,
-    sos::AlgebraElement;
+    sos::StarAlgebras.AlgebraElement;
     halfradius
 )
 
@@ -121,15 +121,15 @@ function sufficient_λ(
 end
 
 function certify_solution(
-    elt::AlgebraElement,
+    elt::StarAlgebras.AlgebraElement,
-    orderunit::AlgebraElement,
+    orderunit::StarAlgebras.AlgebraElement,
     λ,
     Q::AbstractMatrix{<:AbstractFloat};
     halfradius,
-    augmented=iszero(aug(elt)) && iszero(aug(orderunit))
+    augmented=iszero(StarAlgebras.aug(elt)) && iszero(StarAlgebras.aug(orderunit))
 )
 
-    should_we_augment = !augmented && aug(elt) == aug(orderunit) == 0
+    should_we_augment = !augmented && StarAlgebras.aug(elt) == StarAlgebras.aug(orderunit) == 0
 
     Q = should_we_augment ? augment_columns!(Q) : Q
     @time sos = compute_sos(parent(elt), Q, augmented=augmented)

src/gradings.jl

@@ -46,7 +46,7 @@ function _groupby(keys::AbstractVector{K}, vals::AbstractVector{V}) where {K,V}
     return d
 end
 
-function laplacians(RG::StarAlgebra, S, grading)
+function laplacians(RG::StarAlgebras.StarAlgebra, S, grading)
     d = _groupby(grading, S)
     Δs = Dict(α => RG(length(Sα)) - sum(RG(s) for s in Sα) for (α, Sα) in d)
     return Δs
@@ -61,7 +61,7 @@ function Adj(rootsystem::AbstractDict, subtype::Symbol)
         +,
         (
             Δα * Δβ for (α, Δα) in rootsystem for (β, Δβ) in rootsystem if
-            PropertyT_new.Roots.classify_sub_root_system(
+            Roots.classify_sub_root_system(
                 roots,
                 first(α),
                 first(β),

src/sos_sdps.jl

@@ -5,8 +5,8 @@ Formulate the dual to the sum of squares decomposition problem for `X - λ·u`.
 See also [sos_problem_primal](@ref).
 """
 function sos_problem_dual(
-    elt::AlgebraElement,
+    elt::StarAlgebras.AlgebraElement,
-    order_unit::AlgebraElement=zero(elt);
+    order_unit::StarAlgebras.AlgebraElement=zero(elt);
     lower_bound=-Inf
 )
     @assert parent(elt) == parent(order_unit)
@@ -70,7 +70,7 @@ function constraints(
             a, b = basis[i], basis[j]
 
             push!(cnstrs[basis[one(a)]], k)
-            push!(cnstrs[basis[star(a)]], -k)
+            push!(cnstrs[basis[StarAlgebras.star(a)]], -k)
             push!(cnstrs[basis[b]], -k)
         end
     end
@@ -80,7 +80,7 @@ function constraints(
     )
 end
 
-function constraints(A::StarAlgebra; augmented::Bool, twisted::Bool)
+function constraints(A::StarAlgebras.StarAlgebra; augmented::Bool, twisted::Bool)
     mstructure = if StarAlgebras._istwisted(A.mstructure) == twisted
         A.mstructure
     else
@@ -108,10 +108,10 @@ be added to the model. This may improve the accuracy of the solution if
 The default `u = zero(X)` formulates a simple feasibility problem.
 """
 function sos_problem_primal(
-    elt::AlgebraElement,
+    elt::StarAlgebras.AlgebraElement,
-    order_unit::AlgebraElement=zero(elt);
+    order_unit::StarAlgebras.AlgebraElement=zero(elt);
     upper_bound=Inf,
-    augmented::Bool=iszero(aug(elt)) && iszero(aug(order_unit))
+    augmented::Bool=iszero(StarAlgebras.aug(elt)) && iszero(StarAlgebras.aug(order_unit))
 )
     @assert parent(elt) === parent(order_unit)
 
@@ -168,23 +168,26 @@ function isorth_projection(ds::SymbolicWedderburn.DirectSummand)
 end
 
 sos_problem_primal(
-    elt::AlgebraElement,
+    elt::StarAlgebras.AlgebraElement,
     wedderburn::WedderburnDecomposition;
     kwargs...
 ) = sos_problem_primal(elt, zero(elt), wedderburn; kwargs...)
 
 function sos_problem_primal(
-    elt::AlgebraElement,
+    elt::StarAlgebras.AlgebraElement,
-    orderunit::AlgebraElement,
+    orderunit::StarAlgebras.AlgebraElement,
     wedderburn::WedderburnDecomposition;
     upper_bound=Inf,
-    augmented=iszero(aug(elt)) && iszero(aug(orderunit))
+    augmented=iszero(StarAlgebras.aug(elt)) && iszero(StarAlgebras.aug(orderunit)),
+    check_orthogonality=true
 )
 
     @assert parent(elt) === parent(orderunit)
+    if check_orthogonality
         if any(!isorth_projection, direct_summands(wedderburn))
             error("Wedderburn decomposition contains a non-orthogonal projection")
         end
+    end
 
     feasibility_problem = iszero(orderunit)
 
@@ -215,8 +218,8 @@ function sos_problem_primal(
         tmps = SymbolicWedderburn._tmps(wedderburn)
     end
 
-    X = convert(Vector{T}, coeffs(elt))
+    X = convert(Vector{T}, StarAlgebras.coeffs(elt))
-    U = convert(Vector{T}, coeffs(orderunit))
+    U = convert(Vector{T}, StarAlgebras.coeffs(orderunit))
 
     # defining constraints based on the multiplicative structure
     cnstrs = constraints(parent(elt), augmented=augmented, twisted=true)
@@ -278,7 +281,7 @@ function reconstruct!(
         if eltype(res) <: AbstractFloat
             SymbolicWedderburn.zerotol!(tmp2, atol=1e-12)
         end
-        tmp2 .*= degree(ds)
+        tmp2 .*= SymbolicWedderburn.degree(ds)
 
         @assert size(tmp2) == size(res)
 
@@ -291,7 +294,7 @@ function reconstruct!(
             end
         end
     end
-    res ./= order(Int, G)
+    res ./= Groups.order(Int, G)
 
     return res
 end

src/sqadjop.jl

@@ -1,4 +1,4 @@
-import PermutationGroups.AbstractPerm
+import SymbolicWedderburn.PermutationGroups.AbstractPerm
 
 # move to Groups
 Base.keys(a::Alphabet) = keys(1:length(a))
@@ -15,7 +15,7 @@ isadjacent(σ::AbstractPerm, τ::AbstractPerm, i=1, j=2) =
     (j^σ == i^τ && i^σ ≠ j^τ)    # second σ equal to first τ
 
 function _ncycle(start, length, n=start + length - 1)
-    p = Perm(Int8(n))
+    p = PermutationGroups.Perm(Int8(n))
     @assert n ≥ start + length - 1
     for k in start:start+length-2
         p[k] = k + 1
@@ -24,7 +24,7 @@ function _ncycle(start, length, n=start + length - 1)
     return p
 end
 
-alternating_group(n::Integer) = PermGroup([_ncycle(i, 3) for i in 1:n-2])
+alternating_group(n::Integer) = PermutationGroups.PermGroup([_ncycle(i, 3) for i in 1:n-2])
 
 function small_gens(G::MatrixGroups.SpecialLinearGroup)
     A = alphabet(G)
@@ -46,13 +46,13 @@ function small_gens(G::Groups.AutomorphismGroup{<:FreeGroup})
     return union!(S, inv.(S))
 end
 
-function small_laplacian(RG::StarAlgebra)
+function small_laplacian(RG::StarAlgebras.StarAlgebra)
     G = StarAlgebras.object(RG)
     S₂ = small_gens(G)
     return length(S₂) * one(RG) - sum(RG(s) for s in S₂)
 end
 
-function SqAdjOp(A::StarAlgebra, n::Integer, Δ₂=small_laplacian(A))
+function SqAdjOp(A::StarAlgebras.StarAlgebra, n::Integer, Δ₂=small_laplacian(A))
     @assert parent(Δ₂) === A
 
     alt_n = alternating_group(n)