CompatHelper: add new compat entry for "Blosc" at version "0.5"

Project.toml

@@ -5,11 +5,12 @@ version = "0.12.5"
 [deps]
 BinaryProvider = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
 Blosc = "a74b3585-a348-5f62-a45c-50e91977d574"
+CMakeWrapper = "d5fb7624-851a-54ee-a528-d3f3bac0b4a0"
 Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 Mmap = "a63ad114-7e13-5084-954f-fe012c677804"
-CMakeWrapper = "d5fb7624-851a-54ee-a528-d3f3bac0b4a0"
 
 [compat]
+Blosc = "0.5"
 julia = "0.7, 1"
 
 [extras]

src/HDF5.jl

@@ -19,7 +19,7 @@ export
     d_create, d_create_external, d_open, d_read, d_write,
     dataspace, datatype, exists, file, filename,
     g_create, g_open, get_chunk, get_create_properties, get_datasets,
-    h5open, h5read, h5rewrite, h5writeattr, h5readattr, h5write,
+    h5open, h5read, h5read_compound, h5rewrite, h5writeattr, h5readattr, h5write,
     has, iscontiguous, ishdf5, ismmappable, name,
     o_copy, o_delete, o_open, p_create,
     readmmap, @read, @write, root, set_dims!, t_create, t_commit
@@ -733,6 +733,33 @@ function h5read(filename, name::String, indices::Tuple{Vararg{Union{AbstractRang
     dat
 end
 
+"""
+    function h5read_compound(dset::HDF5.HDF5Dataset, T::DataType)
+
+Reads a dataset directly using the given datatype and returns a `Vector{T}`.
+The implementation is based on @damiendr's post in HDF5.jl Issue#408.
+"""
+function h5read_compound(dset::HDF5Dataset, T::DataType)
+    filetype = datatype(dset)  # packed layout on disk
+    memtype_id = h5t_get_native_type(filetype.id)  # padded layout in memory
+    @assert sizeof(T) == h5t_get_size(memtype_id) "Type sizes mismatch!"
+    out = Vector{T}(undef, length(dset))
+    h5d_read(dset.id, memtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, out)
+    h5t_close(memtype_id)
+    out
+end
+
+function h5read_compound(h5f::HDF5File, h5loc::AbstractString, T::DataType)
+    h5read_compound(h5f[h5loc], T)
+end
+
+function h5read_compound(filename::AbstractString, h5loc::AbstractString, T::DataType)
+    h5f = h5open(filename, "r")
+    out = h5read_compound(h5f[h5loc], T)
+    close(h5f)
+    out
+end
+
 function h5writeattr(filename, name::String, data::Dict)
     fid = h5open(filename, "r+")
     try

test/plain.jl

@@ -2,6 +2,20 @@ using HDF5
 using CRC32c
 using Test
 
+# Structures for the compound.h5 file
+struct Vec3
+    a::Float64
+    b::Float64
+    c::Float64
+end
+struct Data
+    wgt::Float64
+    xyz::Vec3
+    uvw::Vec3
+    E::Float64
+end
+
+
 @testset "plain" begin
 
 # Create a new file
@@ -390,6 +404,19 @@ if !isempty(HDF5.libhdf5_hl)
     rm(fn)
 end
 
+# Test h5read_compound
+function test_data(data)
+    @test 2 == length(data)
+    @test -2.45590412 ≈ data[1].xyz.a
+end
+fn = joinpath(test_files, "compound.h5")
+test_data(HDF5.h5read_compound(fn, "/data", Data))
+h5open(fn, "r") do f
+    test_data(HDF5.h5read_compound(f, "/data", Data))
+    test_data(HDF5.h5read_compound(f["/data"], Data))
+end
+
+
 # Test that switching time tracking off results in identical files
 h5open("tt1.h5", "w") do f
     f["x", "track_times", false] = [1, 2, 3]