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Merged
merged 6 commits into from
Nov 27, 2023
Merged

Add extension for PDMats #303

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259fa24
Add extension for PDMats
devmotion Oct 23, 2023
8d6f033
Fix typo
devmotion Oct 23, 2023
d5dada1
Merge branch 'master' into dw/pdmats
devmotion Nov 21, 2023
e661a20
Make PDMats a dependency on Julia < 1.9
devmotion Nov 21, 2023
853e5ae
Revert changes to Aqua tests
devmotion Nov 21, 2023
4380a97
Fix imports
devmotion Nov 21, 2023
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10 changes: 8 additions & 2 deletions Project.toml
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Original file line number Diff line number Diff line change
@@ -1,33 +1,39 @@
name = "FillArrays"
uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
version = "1.7.0"
version = "1.8.0"

[deps]
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
Requires = "ae029012-a4dd-5104-9daa-d747884805df"
SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

[weakdeps]
PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150"
SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

[extensions]
FillArraysPDMatsExt = "PDMats"
FillArraysSparseArraysExt = "SparseArrays"
FillArraysStatisticsExt = "Statistics"

[compat]
Aqua = "0.5, 0.6, 0.7"
PDMats = "0.11.17"
Requires = "1"
julia = "1.6"

[extras]
Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
Base64 = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150"
ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[targets]
test = ["Aqua", "Test", "Base64", "ReverseDiff", "SparseArrays", "StaticArrays", "Statistics"]
test = ["Aqua", "Test", "Base64", "PDMats", "ReverseDiff", "SparseArrays", "StaticArrays", "Statistics"]
18 changes: 18 additions & 0 deletions ext/FillArraysPDMatsExt.jl
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@@ -0,0 +1,18 @@
module FillArraysPDMatsExt

if isdefined(Base, :get_extension)
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@jishnub jishnub Oct 31, 2023

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This style seems a bit unusual to me. Would it not be possible to import the packages directly, or is the namespace specification necessary?

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@devmotion devmotion Oct 31, 2023

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The branch is necessary, Requires needs relative imports (as shown also in the docs: https://github.com/JuliaPackaging/Requires.jl and https://pkgdocs.julialang.org/v1/creating-packages/#Requires.jl).

Moreover, in an extension one should import only the package itself and its weak dependency, and even stdlibs should be loaded indirectly: JuliaStats/LogExpFunctions.jl#63

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@jishnub jishnub Oct 31, 2023

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Oh, interesting, I had no idea about this transitive loading issue. Looks fine to me then

import FillArrays
import FillArrays.LinearAlgebra
import PDMats
else
import ..FillArrays
import ..FillArrays.LinearAlgebra
import ..PDMats
end

function PDMats.AbstractPDMat(a::LinearAlgebra.Diagonal{T,<:FillArrays.AbstractFill{T,1}}) where {T<:Real}
dim = size(a, 1)
return PDMats.ScalMat(dim, FillArrays.getindex_value(a.diag))
end

end # module
10 changes: 9 additions & 1 deletion src/FillArrays.jl
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Expand Up @@ -669,10 +669,18 @@ include("fillalgebra.jl")
include("fillbroadcast.jl")
include("trues.jl")

@static if !isdefined(Base, :get_extension)
if !isdefined(Base, :get_extension)
import Requires
include("../ext/FillArraysSparseArraysExt.jl")
include("../ext/FillArraysStatisticsExt.jl")
end
@static if !isdefined(Base, :get_extension)
function __init__()
Requires.@require PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150" begin
include("../ext/FillArraysPDMatsExt.jl")
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@devmotion devmotion Oct 23, 2023

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This codecov annotation is wrong - the line is hit since otherwise tests on Julia 1.6 would fail.

end
end
end

##
# print
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14 changes: 13 additions & 1 deletion test/runtests.jl
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
using FillArrays, LinearAlgebra, SparseArrays, StaticArrays, ReverseDiff, Random, Base64, Test, Statistics
using FillArrays, LinearAlgebra, PDMats, SparseArrays, StaticArrays, ReverseDiff, Random, Base64, Test, Statistics
import FillArrays: AbstractFill, RectDiagonal, SquareEye

using Aqua
Expand All @@ -7,6 +7,8 @@ using Aqua
# only test formatting on VERSION >= v1.7
# https://github.com/JuliaTesting/Aqua.jl/issues/105#issuecomment-1551405866
project_toml_formatting = VERSION >= v"1.7",
# Requires is only loaded on Julia < 1.9
stale_deps = (ignore = VERSION < v"1.9-" ? Symbol[] : [:Requires],),
)
end

Expand Down Expand Up @@ -2194,3 +2196,13 @@ end
@test ReverseDiff.gradient(x -> sum(abs2.((Zeros{eltype(x)}(5) .+ zeros(5)) ./ x)), rand(5)) == zeros(5)
@test ReverseDiff.gradient(x -> sum(abs2.((zeros(5) .+ Zeros{eltype(x)}(5)) ./ x)), rand(5)) == zeros(5)
end

@testset "FillArraysPDMatsExt" begin
for diag in (Ones(5), Fill(4.1, 8))
a = @inferred(AbstractPDMat(Diagonal(diag)))
@test a isa ScalMat
@test a.dim == length(diag)
@test a.value == first(diag)
end
end