fix: update compat entires, reduce method ambiguities

SciML · Dec 19, 2023 · 54e7b48 · 54e7b48
1 parent 094c2bb
commit 54e7b48
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Showing 7 changed files with 71 additions and 110 deletions.
diff --git a/Project.toml b/Project.toml
@@ -12,6 +12,7 @@ IteratorInterfaceExtensions = "82899510-4779-5014-852e-03e436cf321d"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 SymbolicIndexingInterface = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
@@ -39,14 +40,15 @@ GPUArraysCore = "0.1"
 IteratorInterfaceExtensions = "1"
 LabelledArrays = "1"
 LinearAlgebra = "1"
-Measurements = "2"
-MonteCarloMeasurements = "1"
+Measurements = "2.3"
+MonteCarloMeasurements = "1.1"
 NLsolve = "4"
 Pkg = "1"
 Random = "1"
 RecipesBase = "0.7, 0.8, 1.0"
 Requires = "1.0"
 SafeTestsets = "0.1"
+SparseArrays = "1"
 StaticArrays = "0.12"
 StaticArraysCore = "1.1"
 Statistics = "1"

diff --git a/src/RecursiveArrayTools.jl b/src/RecursiveArrayTools.jl
@@ -8,6 +8,7 @@ using DocStringExtensions
 using RecipesBase, StaticArraysCore, Statistics,
     ArrayInterface, LinearAlgebra
 using SymbolicIndexingInterface
+using SparseArrays
 
 import Adapt
 

diff --git a/src/array_partition.jl b/src/array_partition.jl
@@ -176,14 +176,16 @@ Base.all(f, A::ArrayPartition) = all(f, (all(f, x) for x in A.x))
 Base.all(f::Function, A::ArrayPartition) = all((all(f, x) for x in A.x))
 Base.all(A::ArrayPartition) = all(identity, A)
 
-function Base.copyto!(dest::AbstractArray, A::ArrayPartition)
-    @assert length(dest) == length(A)
-    cur = 1
-    @inbounds for i in 1:length(A.x)
-        dest[cur:(cur + length(A.x[i]) - 1)] .= vec(A.x[i])
-        cur += length(A.x[i])
+for type in [AbstractArray, SparseArrays.AbstractCompressedVector, PermutedDimsArray]
+    @eval function Base.copyto!(dest::$(type), A::ArrayPartition)
+        @assert length(dest) == length(A)
+        cur = 1
+        @inbounds for i in 1:length(A.x)
+            dest[cur:(cur + length(A.x[i]) - 1)] .= vec(A.x[i])
+            cur += length(A.x[i])
+        end
+        dest
     end
-    dest
 end
 
 function Base.copyto!(A::ArrayPartition, src::ArrayPartition)
@@ -419,30 +421,38 @@ end
 
 ArrayInterface.zeromatrix(A::ArrayPartition) = ArrayInterface.zeromatrix(Vector(A))
 
-function LinearAlgebra.ldiv!(A::Factorization, b::ArrayPartition)
-    (x = ldiv!(A, Array(b)); copyto!(b, x))
+function __get_subtypes_in_module(mod, supertype; include_supertype = true, all=false, except=[])
+    return filter([getproperty(mod, name) for name in names(mod; all) if !in(name, except)]) do value
+            return value isa Type && (value <: supertype) && (include_supertype || value != supertype) && !in(value, except)
+        end
 end
 
-@static if VERSION >= v"1.9"
-    function LinearAlgebra.ldiv!(A::LinearAlgebra.SVD{T, Tr, M},
-        b::ArrayPartition) where {Tr, T, M <: AbstractArray{T}}
+for factorization in vcat(__get_subtypes_in_module(LinearAlgebra, Factorization; include_supertype = false, all=true, except=[:LU, :LAPACKFactorizations]), LDLt{T,<:SymTridiagonal{T,V} where {V<:AbstractVector{T}}} where {T})
+    @eval function LinearAlgebra.ldiv!(A::T, b::ArrayPartition) where {T<:$factorization}
         (x = ldiv!(A, Array(b)); copyto!(b, x))
     end
+end
 
-    function LinearAlgebra.ldiv!(A::LinearAlgebra.QRCompactWY{T, M, C},
-        b::ArrayPartition) where {
-        T <: Union{Float32, Float64, ComplexF64, ComplexF32},
-        M <: AbstractMatrix{T},
-        C <: AbstractMatrix{T},
-    }
-        (x = ldiv!(A, Array(b)); copyto!(b, x))
-    end
+function LinearAlgebra.ldiv!(A::LinearAlgebra.SVD{T, Tr, M},
+    b::ArrayPartition) where {Tr, T, M <: AbstractArray{T}}
+    (x = ldiv!(A, Array(b)); copyto!(b, x))
 end
 
-function LinearAlgebra.ldiv!(A::LU, b::ArrayPartition)
-    LinearAlgebra._ipiv_rows!(A, 1:length(A.ipiv), b)
-    ldiv!(UpperTriangular(A.factors), ldiv!(UnitLowerTriangular(A.factors), b))
-    return b
+function LinearAlgebra.ldiv!(A::LinearAlgebra.QRCompactWY{T, M, C},
+    b::ArrayPartition) where {
+    T <: Union{Float32, Float64, ComplexF64, ComplexF32},
+    M <: AbstractMatrix{T},
+    C <: AbstractMatrix{T},
+}
+    (x = ldiv!(A, Array(b)); copyto!(b, x))
+end
+
+for type in [LU, LU{T,Tridiagonal{T,V}} where {T,V}]
+    @eval function LinearAlgebra.ldiv!(A::$type, b::ArrayPartition)
+        LinearAlgebra._ipiv_rows!(A, 1:length(A.ipiv), b)
+        ldiv!(UpperTriangular(A.factors), ldiv!(UnitLowerTriangular(A.factors), b))
+        return b
+    end
 end
 
 # block matrix indexing
@@ -458,78 +468,31 @@ end
 # [U11  U12  U13]   [ b1 ]
 # [ 0   U22  U23] \ [ b2 ]
 # [ 0    0   U33]   [ b3 ]
-function LinearAlgebra.ldiv!(A::UnitUpperTriangular, bb::ArrayPartition)
-    A = A.data
-    n = npartitions(bb)
-    b = bb.x
-    lens = map(length, b)
-    @inbounds for j in n:-1:1
-        Ajj = UnitUpperTriangular(getblock(A, lens, j, j))
-        xj = ldiv!(Ajj, vec(b[j]))
-        for i in (j - 1):-1:1
-            Aij = getblock(A, lens, i, j)
-            # bi = -Aij * xj + bi
-            mul!(vec(b[i]), Aij, xj, -1, true)
-        end
-    end
-    return bb
-end
-
-function LinearAlgebra.ldiv!(A::UpperTriangular, bb::ArrayPartition)
-    A = A.data
-    n = npartitions(bb)
-    b = bb.x
-    lens = map(length, b)
-    @inbounds for j in n:-1:1
-        Ajj = UpperTriangular(getblock(A, lens, j, j))
-        xj = ldiv!(Ajj, vec(b[j]))
-        for i in (j - 1):-1:1
-            Aij = getblock(A, lens, i, j)
-            # bi = -Aij * xj + bi
-            mul!(vec(b[i]), Aij, xj, -1, true)
-        end
-    end
-    return bb
-end
-
-function LinearAlgebra.ldiv!(A::UnitLowerTriangular, bb::ArrayPartition)
-    A = A.data
-    n = npartitions(bb)
-    b = bb.x
-    lens = map(length, b)
-    @inbounds for j in 1:n
-        Ajj = UnitLowerTriangular(getblock(A, lens, j, j))
-        xj = ldiv!(Ajj, vec(b[j]))
-        for i in (j + 1):n
-            Aij = getblock(A, lens, i, j)
-            # bi = -Aij * xj + b[i]
-            mul!(vec(b[i]), Aij, xj, -1, true)
+for basetype in [UnitUpperTriangular, UpperTriangular, UnitLowerTriangular, LowerTriangular]
+    for type in [basetype, basetype{T, <:Adjoint{T}} where {T}, basetype{T, <:Transpose{T}} where {T}]
+        j_iter, i_iter = if basetype <: UnitUpperTriangular || basetype <: UpperTriangular
+            (:(n:-1:1), :(j-1:-1:1))
+        else
+            (:(1:n), :((j+1):n))
         end
-    end
-    return bb
-end
-function _ldiv!(A::LowerTriangular, bb::ArrayPartition)
-    A = A.data
-    n = npartitions(bb)
-    b = bb.x
-    lens = map(length, b)
-    @inbounds for j in 1:n
-        Ajj = LowerTriangular(getblock(A, lens, j, j))
-        xj = ldiv!(Ajj, vec(b[j]))
-        for i in (j + 1):n
-            Aij = getblock(A, lens, i, j)
-            # bi = -Aij * xj + b[i]
-            mul!(vec(b[i]), Aij, xj, -1, true)
+        @eval function LinearAlgebra.ldiv!(A::$type, bb::ArrayPartition)
+            A = A.data
+            n = npartitions(bb)
+            b = bb.x
+            lens = map(length, b)
+            @inbounds for j in $j_iter
+                Ajj = $basetype(getblock(A, lens, j, j))
+                xj = ldiv!(Ajj, vec(b[j]))
+                for i in $i_iter
+                    Aij = getblock(A, lens, i, j)
+                    # bi = -Aij * xj + bi
+                    mul!(vec(b[i]), Aij, xj, -1, true)
+                end
+            end
+            return bb
         end
     end
-    return bb
-end
-
-function LinearAlgebra.ldiv!(A::LowerTriangular{T, <:LinearAlgebra.Adjoint{T}},
-    bb::ArrayPartition) where {T}
-    _ldiv!(A, bb)
 end
-LinearAlgebra.ldiv!(A::LowerTriangular, bb::ArrayPartition) = _ldiv!(A, bb)
 
 # TODO: optimize
 function LinearAlgebra._ipiv_rows!(A::LU, order::OrdinalRange, B::ArrayPartition)

diff --git a/src/vector_of_array.jl b/src/vector_of_array.jl
@@ -139,7 +139,7 @@ function VectorOfArray(vec::AbstractVector{VT}) where {T, N, VT <: AbstractArray
 end
 
 function DiffEqArray(vec::AbstractVector{T},
-    ts,
+    ts::AbstractVector,
     ::NTuple{N, Int},
     p = nothing,
     sys = nothing) where {T, N}
@@ -532,7 +532,7 @@ function Base.CartesianIndices(VA::AbstractVectorOfArray)
 end
 
 # Tools for creating similar objects
-Base.eltype(::VectorOfArray{T}) where {T} = T
+Base.eltype(::Type{<:AbstractVectorOfArray{T}}) where {T} = T
 # TODO: Is there a better way to do this?
 @inline function Base.similar(VA::AbstractVectorOfArray, args...)
     if args[end] isa Type

diff --git a/test/qa.jl b/test/qa.jl
@@ -1,7 +1,9 @@
 using RecursiveArrayTools, Aqua
 @testset "Aqua" begin
     Aqua.find_persistent_tasks_deps(RecursiveArrayTools)
-    Aqua.test_ambiguities(RecursiveArrayTools, recursive = false, broken = true)
+    ambs = Aqua.detect_ambiguities(RecursiveArrayTools; recursive = true)
+    @warn "Number of method ambiguities: $(length(ambs))"
+    @test length(ambs) <= 2
     Aqua.test_deps_compat(RecursiveArrayTools)
     Aqua.test_piracies(RecursiveArrayTools)
     Aqua.test_project_extras(RecursiveArrayTools)

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -51,7 +51,7 @@ end
         @time @safetestset "Upstream Tests" begin
             include("upstream.jl")
         end
-        # @time @safetestset "Adjoint Tests" begin include("adjoints.jl") end
+        @time @safetestset "Adjoint Tests" begin include("adjoints.jl") end
         @time @safetestset "Measurement Tests" begin
             include("measurements.jl")
         end
@@ -65,7 +65,7 @@ end
         @time @safetestset "Event Tests with ArrayPartition" begin
             include("downstream/downstream_events.jl")
         end
-        VERSION >= v"1.9" && @time @safetestset "Measurements and Units" begin
+        @time @safetestset "Measurements and Units" begin
             include("downstream/measurements_and_units.jl")
         end
         @time @safetestset "TrackerExt" begin

diff --git a/test/upstream.jl b/test/upstream.jl
@@ -41,14 +41,7 @@ end
             ArrayPartition(zeros(1), [0.75])),
         (0.0, 1.0)), AutoTsit5(Rodas5())).retcode == ReturnCode.Success
 
-if VERSION < v"1.7"
-    @test solve(ODEProblem(dyn,
-            ArrayPartition(ArrayPartition(zeros(1), [-1.0]),
-                ArrayPartition(zeros(1), [0.75])),
-            (0.0, 1.0)), Rodas5()).retcode == ReturnCode.Success
-else
-    @test_broken solve(ODEProblem(dyn,
-            ArrayPartition(ArrayPartition(zeros(1), [-1.0]),
-                ArrayPartition(zeros(1), [0.75])),
-            (0.0, 1.0)), Rodas5()).retcode == ReturnCode.Success
-end
+@test_broken solve(ODEProblem(dyn,
+        ArrayPartition(ArrayPartition(zeros(1), [-1.0]),
+            ArrayPartition(zeros(1), [0.75])),
+        (0.0, 1.0)), Rodas5()).retcode == ReturnCode.Success