Fix handling of datasets with shape (0,0,...)

[rly]

Fix #76.

For an HDF5 dataset with shape (0,0,0), no chunks should be written. This was the previous behavior before #68 and seems reasonable.

For an HDF5 dataset with shape (0,0,0), the chunks key in .zarray was being set to (0,0,0). However, that is not allowed in Zarr. Accessing an array with such chunking results in a ZeroDivisionError: division by zero when trying to access the array. I set it to (1,1,1) instead which is what Zarr does for an array of that shape.

>>> import zarr
>>> a = zarr.empty(shape=(0,0,0))
>>> a.shape
(0, 0, 0)
>>> a.chunks
(1, 1, 1)
>>> a[:]
array([], shape=(0, 0, 0), dtype=float64)
>>> a = zarr.empty(shape=(0,0,0), chunks=(0,0,0))
>>> a.chunks
(0, 0, 0)
>>> a[:]
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/rly/mambaforge/envs/test4/lib/python3.11/site-packages/zarr/core.py", line 800, in __getitem__
    result = self.get_basic_selection(pure_selection, fields=fields)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/rly/mambaforge/envs/test4/lib/python3.11/site-packages/zarr/core.py", line 926, in get_basic_selection
    return self._get_basic_selection_nd(selection=selection, out=out, fields=fields)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/rly/mambaforge/envs/test4/lib/python3.11/site-packages/zarr/core.py", line 966, in _get_basic_selection_nd
    indexer = BasicIndexer(selection, self)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/rly/mambaforge/envs/test4/lib/python3.11/site-packages/zarr/indexing.py", line 339, in __init__
    dim_indexer = SliceDimIndexer(dim_sel, dim_len, dim_chunk_len)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/rly/mambaforge/envs/test4/lib/python3.11/site-packages/zarr/indexing.py", line 181, in __init__
    self.nchunks = ceildiv(self.dim_len, self.dim_chunk_len)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/rly/mambaforge/envs/test4/lib/python3.11/site-packages/zarr/indexing.py", line 167, in ceildiv
    return math.ceil(a / b)
                     ~~^~~
ZeroDivisionError: division by zero

I also fixed an issue flagged by pyright in LindiReferenceFileSystemStore.__contains__:

error: Method "__contains__" overrides class "Mapping" in an incompatible manner
    Parameter 2 type mismatch: base parameter is type "object", override parameter is type "str"`

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 91.66667% with 1 lines in your changes are missing coverage. Please review.

Project coverage is 79.47%. Comparing base (731fcb5) to head (ffea54a).

Files	Patch %	Lines
...ndi/LindiH5pyFile/LindiReferenceFileSystemStore.py	66.66%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #77      +/-   ##
==========================================
+ Coverage   79.43%   79.47%   +0.03%     
==========================================
  Files          30       30              
  Lines        2256     2265       +9     
==========================================
+ Hits         1792     1800       +8     
- Misses        464      465       +1     

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[magland]

Looks good to me!

[rly]

Thanks. Released in version 0.3.9.