fix chunk/shard iteration (#3299)

* factor array element iteration routines into stand-alone functions, and add a failing test

* add shard_grid_shape, chunk_grid_shape

Co-authored-by: Bojidar Marinov <[email protected]>

* docstrings

* handle null shards

* use shard_grid_shape instead of cdata_shape in nchunks

* add improved set of low-level iteration routines for arrays

* correct deprecation message

* check for deprecation warnings around iter_chunk_keys

* plug tiny coverage holes

* lint

* rename chunks_initialized to shards_initialized

* add nshards, nshards_initialized

* fix doctests

* remove iter_chunk_keys

* make nchunks_initialized report the product of the number of shards and the number of chunks per shard

* changelog

* correct name of changelog entry

* add test for unsharded data

* add test for cdata_shape, shard_grid_shape, chunk_grid_shape

* add nshards

* expand nchunks_initialized test conditions

* restore memorystore

* expand test parametrization

* unbreak tests

* include asyncarray cdata_shape in test

* make new API private

* docstrings

* remove references to private API

* Update src/zarr/core/array.py

Co-authored-by: Deepak Cherian <[email protected]>

* Update src/zarr/core/indexing.py

Co-authored-by: Deepak Cherian <[email protected]>

* fix docstring

---------

Co-authored-by: Bojidar Marinov <[email protected]>
Co-authored-by: Deepak Cherian <[email protected]>

Author: 3 people

changes/3299.bugfix.rst

@@ -0,0 +1,4 @@
+Fix a bug in ``create_array`` caused by iterating over chunk-aligned regions instead of
+shard-aligned regions when writing data. Additionally, the behavior of ``nchunks_initialized``
+has been adjusted. This function consistently reports the number of chunks present in stored objects,
+even when the array uses the sharding codec.