Zarr v3

[will-moore]

Work in progress to update to Zarr v3.
This is currently focussed on getting existing Zarr v2 tests to pass...

Most of the tests are now passing using a recent commit on main branch of zarr-python.

 = 4 failed, 384 passed, 3 skipped, 6 xfailed, 1832 warnings in 86.38s (0:01:26) =

4 failing tests are:

• TestWriter.test_writer[3D-scale-True-from_array-V01]
• TestWriter.test_writer[3D-scale-True-from_array-V02]
• TestWriter.test_writer[3D-scale-True-from_array-V03]
• TestWriter.test_writer[3D-scale-True-from_array-V04]

          # check memory is contiguous, if so flatten
          if arr.flags.c_contiguous or arr.flags.f_contiguous:
              if flatten:
                  # can flatten without copy
                  arr = arr.reshape(-1, order="A")
          else:
  >           raise ValueError("an array with contiguous memory is required")
  E           ValueError: an array with contiguous memory is required
  
  .tox/py311/lib/python3.11/site-packages/numcodecs/compat.py:113: ValueError

These tests were passing before
* 109f71f6 (HEAD) Refactors v2 codec handling (#2425) (zarr-developers/zarr-python#2425)

This PR is just reading & writing zarr v2 data.
In several places I've hard-coded zarr_version=2. This works because you can do zarr.open_group(store=self.__store, path="/", zarr_version=2) in parse_url() to create a group to write into, or find a group to read from without specifying whether you expect the group to already exist.

Without the zarr_version=2, zarr will create zarr.json if the mode of the store is w.

[will-moore]

Zarr v3 is not supported on python 3.9 or 3.10. I'll remove them from the build...

Build on python 3.12 is failing tests with:

  = 106 failed, 282 passed, 3 skipped, 6 xfailed, 2270 warnings in 75.86s (0:01:15) =

[imagesc-bot]

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/ome-zarr-py-development-status/104671/4