fix(storage): remove VerboseModule to make zarr.storage picklable (gh-4029)

[NIK-TIGER-BILL]

Description of PR

Fixes #4029.

The VerboseModule subclass prevented zarr.storage from being pickled by cloudpickle (and therefore by Dask). The only purpose of the subclass was to emit a deprecation warning when setting zarr.storage.default_compressor, which has been deprecated for a long time.

TODO:

• Add unit tests and/or doctests in docstrings
• Add docstrings and API docs for any new/modified user-facing classes and functions
• New/modified features documented in docs/user-guide/*.md
• Changes documented as a new file in changes/
• GitHub Actions have all passed
• Test coverage is 100% (Codecov passes)

[maxrjones]

We likely want to also remove

zarr-python/src/zarr/core/config.py

Lines 71 to 88 in 036ede7

	# these keys were removed from the config as part of the 3.1.0 release.
	# these deprecations should be removed in 3.1.1 or thereabouts.
	deprecations = {
	"array.v2_default_compressor.numeric": None,
	"array.v2_default_compressor.string": None,
	"array.v2_default_compressor.bytes": None,
	"array.v2_default_filters.string": None,
	"array.v2_default_filters.bytes": None,
	"array.v3_default_filters.numeric": None,
	"array.v3_default_filters.raw": None,
	"array.v3_default_filters.bytes": None,
	"array.v3_default_serializer.numeric": None,
	"array.v3_default_serializer.string": None,
	"array.v3_default_serializer.bytes": None,
	"array.v3_default_compressors.string": None,
	"array.v3_default_compressors.bytes": None,
	"array.v3_default_compressors": None,
	}

and the tests in

zarr-python/tests/test_config.py

Lines 448 to 475 in 036ede7

	@pytest.mark.parametrize(
	"key",
	[
	"array.v2_default_compressor.numeric",
	"array.v2_default_compressor.string",
	"array.v2_default_compressor.bytes",
	"array.v2_default_filters.string",
	"array.v2_default_filters.bytes",
	"array.v3_default_filters.numeric",
	"array.v3_default_filters.raw",
	"array.v3_default_filters.bytes",
	"array.v3_default_serializer.numeric",
	"array.v3_default_serializer.string",
	"array.v3_default_serializer.bytes",
	"array.v3_default_compressors.string",
	"array.v3_default_compressors.bytes",
	"array.v3_default_compressors",
	],
	)
	def test_deprecated_config(key: str) -> None:
	"""
	Test that a valuerror is raised when setting the default chunk encoding for a given
	data type category
	"""
	with pytest.raises(ValueError):
	with zarr.config.set({key: "foo"}):
	pass

to complete the deprecation cycle. What do you think @d-v-b @chuckwondo?

[d-v-b]

What do you think @d-v-b @chuckwondo?

Sounds good to me! And we should consider building up a bit more tooling around deprecations. It's not great that we flag stuff as deprecated and the fragments linger for a long time in the codebase.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.25%. Comparing base (036ede7) to head (6ddae03).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4030      +/-   ##
==========================================
- Coverage   93.50%   93.25%   -0.25%     
==========================================
  Files          90       90              
  Lines       11981    11970      -11     
==========================================
- Hits        11203    11163      -40     
- Misses        778      807      +29     

Files with missing lines	Coverage Δ
src/zarr/storage/__init__.py	100.00% <ø> (+5.00%)	⬆️

... and 7 files with indirect coverage changes

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[maxrjones]

What do you think @d-v-b @chuckwondo?

Sounds good to me! And we should consider building up a bit more tooling around deprecations. It's not great that we flag stuff as deprecated and the fragments linger for a long time in the codebase.

Sounds good, thanks for confirming. I agree with the tooling directly, let's handle that separately. @NIK-TIGER-BILL are you up for removing the components mentioned in #4030 (comment) as part of this PR?