Apply Repo-Review suggestions to zarr-python?

[DimitriPapadopoulos]

Would you agree to an effort to apply Repo-Review suggestions from the Scientific Python Development Guide? Many of them make sense to me.

https://learn.scientific-python.org/development/guides/repo-review/?repo=zarr-developers%2Fzarr-python&branch=main

[d-v-b]

I would! if any of the changes would affect development, then we should get them into the v3 branch

[DimitriPapadopoulos]

They would affect development in the sense that these new constraints might require to change the code in some places. However, the changes are usually quite simple, I believe they wouldn't imply complex merges down the road. Does this sound acceptable?

Issues reported by "ruff check --select B"

zarr/_storage/absstore.py:147:13: B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
zarr/_storage/absstore.py:160:13: B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
zarr/_storage/v3_storage_transformers.py:187:17: B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
zarr/_storage/v3_storage_transformers.py:269:17: B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
zarr/core.py:200:13: B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
zarr/creation.py:300:9: B028 No explicit `stacklevel` keyword argument found
zarr/hierarchy.py:191:17: B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
zarr/hierarchy.py:198:21: B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
zarr/hierarchy.py:522:13: B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
zarr/indexing.py:935:13: B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
zarr/meta.py:314:17: B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
zarr/meta.py:521:13: B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
zarr/meta_v1.py:26:9: B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
zarr/n5.py:128:21: B028 No explicit `stacklevel` keyword argument found
zarr/n5.py:330:13: B028 No explicit `stacklevel` keyword argument found
zarr/n5.py:414:21: B028 No explicit `stacklevel` keyword argument found
zarr/n5.py:601:9: B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
zarr/n5.py:710:13: B028 No explicit `stacklevel` keyword argument found
zarr/storage.py:587:17: B028 No explicit `stacklevel` keyword argument found
zarr/storage.py:595:9: B028 No explicit `stacklevel` keyword argument found
zarr/storage.py:872:13: B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
zarr/storage.py:891:17: B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
zarr/storage.py:1139:21: B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
zarr/tests/test_meta.py:602:9: B007 Loop control variable `key` not used within loop body
zarr/tests/test_storage_v3.py:283:9: B015 Pointless comparison. Did you mean to assign a value? Otherwise, prepend `assert` or remove it.
zarr/util.py:202:21: B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
zarr/util.py:323:13: B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
zarr/util.py:488:9: B904 Within an `except` clause, raise exceptions with `raise ... from err` or `raise ... from None` to distinguish them from errors in exception handling
Found 28 errors.

Issues reported by "ruff check --select UP"

zarr/_storage/store.py:7:1: UP035 [*] Import from `collections.abc` instead: `Mapping`, `Sequence`
zarr/_storage/store.py:7:1: UP035 `typing.Dict` is deprecated, use `dict` instead
zarr/_storage/store.py:7:1: UP035 `typing.List` is deprecated, use `list` instead
zarr/_storage/store.py:7:1: UP035 `typing.Tuple` is deprecated, use `tuple` instead
zarr/_storage/store.py:173:42: UP006 Use `list` instead of `List` for type annotation
zarr/_storage/store.py:297:36: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/_storage/store.py:297:47: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/_storage/store.py:298:10: UP006 Use `list` instead of `List` for type annotation
zarr/_storage/store.py:308:18: UP006 Use `list` instead of `List` for type annotation
zarr/_storage/store.py:309:32: UP006 Use `dict` instead of `Dict` for type annotation
zarr/_storage/store.py:309:42: UP006 Use `list` instead of `List` for type annotation
zarr/_storage/store.py:309:47: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/_storage/store.py:309:58: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/_storage/store.py:651:73: UP006 Use `list` instead of `List` for type annotation
zarr/_storage/v3.py:6:1: UP035 `typing.Dict` is deprecated, use `dict` instead
zarr/_storage/v3.py:515:30: UP006 Use `dict` instead of `Dict` for type annotation
zarr/_storage/v3.py:516:29: UP006 Use `dict` instead of `Dict` for type annotation
zarr/_storage/v3_storage_transformers.py:4:1: UP035 [*] Import from `collections.abc` instead: `Iterator`
zarr/_storage/v3_storage_transformers.py:4:1: UP035 `typing.Tuple` is deprecated, use `tuple` instead
zarr/_storage/v3_storage_transformers.py:33:41: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/_storage/v3_storage_transformers.py:33:61: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/_storage/v3_storage_transformers.py:41:38: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/_storage/v3_storage_transformers.py:49:38: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/_storage/v3_storage_transformers.py:134:48: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/_storage/v3_storage_transformers.py:134:59: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/_storage/v3_storage_transformers.py:161:64: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/creation.py:2:1: UP035 [*] Import from `collections.abc` instead: `Sequence`
zarr/creation.py:2:1: UP035 `typing.Tuple` is deprecated, use `tuple` instead
zarr/creation.py:32:23: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/creation.py:33:24: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/meta.py:12:1: UP035 [*] Import from `collections.abc` instead: `Mapping`
zarr/meta.py:12:1: UP035 `typing.List` is deprecated, use `list` instead
zarr/meta.py:183:40: UP006 Use `list` instead of `List` for type annotation
zarr/n5.py:7:1: UP035 `typing.Dict` is deprecated, use `dict` instead
zarr/n5.py:235:44: UP006 Use `dict` instead of `Dict` for type annotation
zarr/n5.py:573:42: UP006 Use `dict` instead of `Dict` for type annotation
zarr/n5.py:573:61: UP006 Use `dict` instead of `Dict` for type annotation
zarr/n5.py:581:44: UP006 Use `dict` instead of `Dict` for type annotation
zarr/n5.py:581:63: UP006 Use `dict` instead of `Dict` for type annotation
zarr/n5.py:589:42: UP006 Use `dict` instead of `Dict` for type annotation
zarr/n5.py:589:78: UP006 Use `dict` instead of `Dict` for type annotation
zarr/n5.py:639:21: UP006 Use `dict` instead of `Dict` for type annotation
zarr/n5.py:640:6: UP006 Use `dict` instead of `Dict` for type annotation
zarr/n5.py:669:26: UP006 Use `dict` instead of `Dict` for type annotation
zarr/n5.py:669:45: UP006 Use `dict` instead of `Dict` for type annotation
zarr/n5.py:681:57: UP006 Use `dict` instead of `Dict` for type annotation
zarr/n5.py:681:77: UP006 Use `dict` instead of `Dict` for type annotation
zarr/n5.py:741:50: UP006 Use `dict` instead of `Dict` for type annotation
zarr/n5.py:741:78: UP006 Use `dict` instead of `Dict` for type annotation
zarr/storage.py:36:1: UP035 [*] Import from `collections.abc` instead: `Sequence`, `Mapping`
zarr/storage.py:36:1: UP035 `typing.List` is deprecated, use `list` instead
zarr/storage.py:36:1: UP035 `typing.Tuple` is deprecated, use `tuple` instead
zarr/storage.py:36:1: UP035 `typing.Dict` is deprecated, use `dict` instead
zarr/storage.py:320:23: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/storage.py:321:30: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/storage.py:743:25: UP006 Use `dict` instead of `Dict` for type annotation
zarr/storage.py:914:45: UP006 Use `list` instead of `List` for type annotation
zarr/storage.py:1544:15: UP033 [*] Use `@functools.cache` instead of `@functools.lru_cache(maxsize=None)`
zarr/storage.py:2411:31: UP006 Use `dict` instead of `Dict` for type annotation
zarr/storage.py:2412:30: UP006 Use `dict` instead of `Dict` for type annotation
zarr/storage.py:2413:29: UP006 Use `dict` instead of `Dict` for type annotation
zarr/tests/test_core.py:6:1: UP035 [*] Import from `collections.abc` instead: `Sequence`
zarr/tests/test_core.py:6:1: UP035 `typing.Tuple` is deprecated, use `tuple` instead
zarr/tests/test_core.py:102:27: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/tests/test_core.py:111:61: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/tests/test_core.py:111:82: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/tests/test_core.py:114:55: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/tests/test_core.py:117:46: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/tests/test_core.py:2164:55: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/tests/test_core.py:2997:53: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/tests/test_core.py:3059:53: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/tests/test_core.py:3079:53: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/tests/test_n5.py:8:1: UP035 `typing.Tuple` is deprecated, use `tuple` instead
zarr/tests/test_n5.py:31:44: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/tests/util.py:4:1: UP035 [*] Import from `collections.abc` instead: `Mapping`, `Sequence`
zarr/util.py:8:1: UP035 [*] Import from `collections.abc` instead: `Iterator`, `Mapping`, `Iterable`
zarr/util.py:8:1: UP035 `typing.Dict` is deprecated, use `dict` instead
zarr/util.py:8:1: UP035 `typing.Tuple` is deprecated, use `tuple` instead
zarr/util.py:74:41: UP006 Use `dict` instead of `Dict` for type annotation
zarr/util.py:79:39: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/util.py:79:66: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/util.py:90:18: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/util.py:102:25: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/util.py:102:60: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/util.py:148:42: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/util.py:148:77: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/util.py:183:67: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/util.py:221:33: UP006 Use `tuple` instead of `Tuple` for type annotation
zarr/util.py:378:29: UP006 Use `dict` instead of `Dict` for type annotation
zarr/util.py:668:17: UP006 Use `tuple` instead of `Tuple` for type annotation
Found 90 errors.

[d-v-b]

by "affect development" I was thinking of pretty big changes like using a src layout (not sure if repo-review catches this). But for things that don't move code around, I'm all for getting those in main

[DimitriPapadopoulos]

I have started implementing the required changes in #1702, #1703, #1704, #1705, #1707, #1708.

Once most of the issues are fixed, I plan on adding a GitHub Action to automatically run repo-review on the repository, typically using sp-repo-review.