Empty (extensible) dataset cannot be read back

[tamasgal]

I just stumbled upon the issue that HDF5.jl chokes on datasets which were initialised to 0-size but never resized or populated later.
A workaround is of course to not create datasets which are empty but currently I set-up my data processing in a homogenous way, so that each HDF5 file has the same structure and sometimes a dataset is empty.

Maybe I am doing something wrong and this is not the way to initialise datasets which might be empty, but that's what I found in the HDF5 docs and also in examples.

Here is a MWE, just uncomment the two lines and the error disappears:

using HDF5

fname = tempname()
groupname = "a_group"
dsetname = "foo"

h5open(fname, "w") do fid
    create_group(fid, groupname)
    create_dataset(fid[groupname], dsetname, datatype(Float32), ((0,), (-1,)), chunk=(100,))
    
    # Uncomment these otherwise the datasets are unreadable
    #dset = fid[groupname][dsetname]
    #HDF5.set_extent_dims(dset, (100,))
end
    
h5open(fname, "r") do fid
    fid[groupname][dsetname][:]
end

Here is the error which indicates that the binary parsing loses track:

UInt64[0x0000000000000000]
UInt64[0x0000000000000001]
UInt64[0x0000000000000000]
(0,)
index out of range

Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:33
  [2] hyperslab(dspace::HDF5.Dataspace, I::Base.Slice{Base.OneTo{Int64}})
    @ HDF5 ~/.julia/packages/HDF5/0iEnL/src/HDF5.jl:1691
  [3] generic_read(obj::HDF5.Dataset, filetype::HDF5.Datatype, #unused#::Type{Float32}, I::Function)
    @ HDF5 ~/.julia/packages/HDF5/0iEnL/src/HDF5.jl:1252
  [4] getindex(dset::HDF5.Dataset, I::Function)
    @ HDF5 ~/.julia/packages/HDF5/0iEnL/src/HDF5.jl:1188
  [5] (::var"#77#78")(fid::HDF5.File)
    @ Main ./In[28]:17
  [6] h5open(::var"#77#78", ::String, ::Vararg{String, N} where N; swmr::Bool, pv::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ HDF5 ~/.julia/packages/HDF5/0iEnL/src/HDF5.jl:458
  [7] h5open(::Function, ::String, ::String)
    @ HDF5 ~/.julia/packages/HDF5/0iEnL/src/HDF5.jl:456
  [8] top-level scope
    @ In[28]:16
  [9] eval
    @ ./boot.jl:360 [inlined]
 [10] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:1094

[simonbyrne]

Fixed by #1011