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Merge pull request #17 from JuliaAstro/quality
chore: Julia v12 updates
2 parents f961c03 + fa1e21b commit 63fb577

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‎.github/workflows/CI.yml‎

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@@ -27,6 +27,8 @@ jobs:
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- uses: julia-actions/cache@v2
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- uses: julia-actions/julia-buildpkg@v1
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- uses: julia-actions/julia-runtest@v1
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with:
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test_args: '--verbose'
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- uses: julia-actions/julia-processcoverage@v1
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- uses: codecov/codecov-action@v5
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with:

‎Project.toml‎

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name = "ASDF"
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uuid = "686f71d1-807d-59a4-a860-28280ea06d7b"
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authors = ["Erik Schnetter <schnetter@gmail.com>"]
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version = "2.0.0"
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authors = ["Erik Schnetter <schnetter@gmail.com>"]
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[workspace]
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projects = ["test", "docs"]
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[deps]
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BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e"
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ChunkCodecLibBlosc = "c6a955be-ab7f-4fbb-b38f-caf93db6b928"
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ChunkCodecLibBzip2 = "2b723af9-f480-4e8d-a1e4-4a9f5a906122"
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ChunkCodecLibLz4 = "7e9cc85e-5614-42a3-ad86-b78f920b38a5"
@@ -17,7 +19,6 @@ StridedViews = "4db3bf67-4bd7-4b4e-b153-31dc3fb37143"
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YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
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[compat]
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BlockArrays = "0.16.43, 1"
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ChunkCodecLibBlosc = "0.2.0, 0.3"
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ChunkCodecLibBzip2 = "0.2.0, 1.0"
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ChunkCodecLibLz4 = "0.2.1, 1.0"

‎src/ASDF.jl‎

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@@ -1,16 +1,15 @@
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module ASDF
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3-
using BlockArrays
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using CodecXz
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using ChunkCodecLibBlosc
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using ChunkCodecLibBzip2
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using ChunkCodecLibLz4
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using ChunkCodecLibZlib
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using ChunkCodecLibZstd
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using MD5
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using PkgVersion
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using StridedViews
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using YAML
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using ChunkCodecLibBlosc: BloscCodec, BloscEncodeOptions
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using ChunkCodecLibBzip2: BZ2Codec, BZ2EncodeOptions
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using ChunkCodecLibLz4: LZ4FrameCodec, LZ4FrameEncodeOptions
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using ChunkCodecLibZlib: ZlibCodec, ZlibEncodeOptions
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using ChunkCodecLibZstd: ZstdCodec, ZstdEncodeOptions, decode, encode
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using CodecXz: XzCompressor, XzDecompressor
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using MD5: md5
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using PkgVersion: PkgVersion
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using StridedViews: StridedView
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using YAML: YAML
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################################################################################
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‎test/Project.toml‎

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[deps]
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ASDF = "686f71d1-807d-59a4-a860-28280ea06d7b"
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Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
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ParallelTestRunner = "d3525ed8-44d0-4b2c-a655-542cee43accc"
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Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
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YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"

‎test/runtests.jl‎

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using ParallelTestRunner: runtests, find_tests, parse_args
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using ASDF
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using Test
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using YAML
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5-
map_tree(f, x) = f(x)
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map_tree(f, vec::AbstractVector) = [map_tree(f, elem) for elem in vec]
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map_tree(f, dict::AbstractDict) = Dict(key => map_tree(f, val) for (key, val) in dict)
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output(x) = nothing
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function output(arr::ASDF.NDArray)
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println("source: $(arr.source)")
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data = arr[]
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println(" type: $(typeof(data))")
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return println(" size: $(size(data))")
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end
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################################################################################
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@testset "Read ASDF file" begin
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asdf = ASDF.load_file("blue_upchan_gain.00000000.asdf")
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println(YAML.write(asdf.metadata))
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map_tree(output, asdf.metadata)
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buffer = asdf.metadata[0]["buffer"][]
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@test eltype(buffer) == Float16
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@test size(buffer) == (256,)
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@test buffer == fill(1, 256)
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dish_index = asdf.metadata[0]["dish_index"][]
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@test eltype(dish_index) == Int32
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@test size(dish_index) == (3, 2)
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@test dish_index == [
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-1 -1
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]
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end
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################################################################################
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@testset "Read ASDF file with chunked arrays" begin
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asdf = ASDF.load_file("chunking.asdf")
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println(YAML.write(asdf.metadata))
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46-
map_tree(output, asdf.metadata)
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chunky = asdf.metadata["chunky"][]
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@test eltype(chunky) == Float16
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@test size(chunky) == (4, 4)
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@test chunky == [
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11 21 31 41
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12 22 32 42
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13 23 33 43
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14 24 34 44
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]
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const init_code = quote
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using ASDF
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using Test
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using YAML
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9+
map_tree(f, x) = f(x)
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map_tree(f, vec::AbstractVector) = [map_tree(f, elem) for elem in vec]
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map_tree(f, dict::AbstractDict) = Dict(key => map_tree(f, val) for (key, val) in dict)
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output(x) = nothing
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function output(arr::ASDF.NDArray)
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println("source: $(arr.source)")
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data = arr[]
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println(" type: $(typeof(data))")
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return println(" size: $(size(data))")
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end
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end
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################################################################################
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@testset "Write ASDF file" begin
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dirname = mktempdir(; cleanup=true)
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filename = joinpath(dirname, "output.asdf")
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array = Float64[1/(i+j+k-2) for i in 1:50, j in 1:51, k in 1:52]
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doc = Dict{Any,Any}(
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"data1" => ASDF.NDArrayWrapper([1 2; 3 4]; inline=false),
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"data2" => ASDF.NDArrayWrapper([1 2; 3 4]; inline=true),
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"group" => Dict{Any,Any}(
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"element1" => ASDF.NDArrayWrapper(array; compression=ASDF.C_None),
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"element2" => ASDF.NDArrayWrapper(array; compression=ASDF.C_Blosc),
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"element3" => ASDF.NDArrayWrapper(array; compression=ASDF.C_Bzip2),
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"element4" => ASDF.NDArrayWrapper(array; compression=ASDF.C_Lz4),
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"element5" => ASDF.NDArrayWrapper(array; compression=ASDF.C_Xz),
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"element6" => ASDF.NDArrayWrapper(array; compression=ASDF.C_Zlib),
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"element7" => ASDF.NDArrayWrapper(array; compression=ASDF.C_Zstd),
77-
),
78-
)
79-
ASDF.write_file(filename, doc)
22+
args = parse_args(Base.ARGS)
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testsuite = find_tests(@__DIR__)
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81-
doc′ = ASDF.load_file(filename)
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map_tree(output, doc′.metadata)
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84-
data1 = doc["data1"][]
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data1′ = doc′.metadata["data1"][]
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@test eltype(data1′) == eltype(data1)
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@test size(data1′) == size(data1)
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@test data1′ == data1
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90-
data2 = doc["data2"][]
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data2′ = doc′.metadata["data2"][]
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@test eltype(data2′) == eltype(data2)
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@test size(data2′) == size(data2)
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@test data2′ == data2
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for n in 1:7
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element = doc["group"]["element$n"][]
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element′ = doc′.metadata["group"]["element$n"][]
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@test eltype(element′) == eltype(element)
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@test size(element′) == size(element)
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@test element′ == element
102-
end
103-
end
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runtests(ASDF, args; testsuite, init_code)

‎test/test-aqua.jl‎

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@testset "Aqua" begin
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using ASDF, Aqua
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Aqua.test_all(ASDF)
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end

‎test/test-read.jl‎

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@testset "Read ASDF file" begin
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asdf = ASDF.load_file("blue_upchan_gain.00000000.asdf")
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println(YAML.write(asdf.metadata))
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5+
map_tree(output, asdf.metadata)
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7+
buffer = asdf.metadata[0]["buffer"][]
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@test eltype(buffer) == Float16
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@test size(buffer) == (256,)
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@test buffer == fill(1, 256)
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dish_index = asdf.metadata[0]["dish_index"][]
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@test eltype(dish_index) == Int32
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@test size(dish_index) == (3, 2)
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@test dish_index == [
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-1 -1
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42 53
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43 54
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]
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end

‎test/test-read_chunked.jl‎

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@testset "Read ASDF file with chunked arrays" begin
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asdf = ASDF.load_file("chunking.asdf")
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println(YAML.write(asdf.metadata))
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5+
map_tree(output, asdf.metadata)
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chunky = asdf.metadata["chunky"][]
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@test eltype(chunky) == Float16
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@test size(chunky) == (4, 4)
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@test chunky == [
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11 21 31 41
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12 22 32 42
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13 23 33 43
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14 24 34 44
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]
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end

‎test/test-write.jl‎

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@testset "Write ASDF file" begin
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dirname = mktempdir(; cleanup=true)
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filename = joinpath(dirname, "output.asdf")
4+
5+
array = Float64[1/(i+j+k-2) for i in 1:50, j in 1:51, k in 1:52]
6+
doc = Dict{Any,Any}(
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"data1" => ASDF.NDArrayWrapper([1 2; 3 4]; inline=false),
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"data2" => ASDF.NDArrayWrapper([1 2; 3 4]; inline=true),
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"group" => Dict{Any,Any}(
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"element1" => ASDF.NDArrayWrapper(array; compression=ASDF.C_None),
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"element2" => ASDF.NDArrayWrapper(array; compression=ASDF.C_Blosc),
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"element3" => ASDF.NDArrayWrapper(array; compression=ASDF.C_Bzip2),
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"element4" => ASDF.NDArrayWrapper(array; compression=ASDF.C_Lz4),
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"element5" => ASDF.NDArrayWrapper(array; compression=ASDF.C_Xz),
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"element6" => ASDF.NDArrayWrapper(array; compression=ASDF.C_Zlib),
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"element7" => ASDF.NDArrayWrapper(array; compression=ASDF.C_Zstd),
17+
),
18+
)
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ASDF.write_file(filename, doc)
20+
21+
doc′ = ASDF.load_file(filename)
22+
map_tree(output, doc′.metadata)
23+
24+
data1 = doc["data1"][]
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data1′ = doc′.metadata["data1"][]
26+
@test eltype(data1′) == eltype(data1)
27+
@test size(data1′) == size(data1)
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@test data1′ == data1
29+
30+
data2 = doc["data2"][]
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data2′ = doc′.metadata["data2"][]
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@test eltype(data2′) == eltype(data2)
33+
@test size(data2′) == size(data2)
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@test data2′ == data2
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for n in 1:7
37+
element = doc["group"]["element$n"][]
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element′ = doc′.metadata["group"]["element$n"][]
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@test eltype(element′) == eltype(element)
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@test size(element′) == size(element)
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@test element′ == element
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end
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end

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