Merge branch 'main' into remove-fsspec-path-check

Author: d-v-b

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ ci:
 default_stages: [pre-commit, pre-push]
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.2
+    rev: v0.12.7
     hooks:
       - id: ruff-check
         args: ["--fix", "--show-fixes"]
@@ -22,7 +22,7 @@ repos:
       - id: check-yaml
       - id: trailing-whitespace
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.16.1
+    rev: v1.17.1
     hooks:
       - id: mypy
         files: src|tests

changes/3098.misc.rst

@@ -0,0 +1,3 @@
+Define Zarr-specific warning classes that subclass the Python built-in warnings.
+These classes makes it easier to control the visibility of warnings emitted by Zarr Python.
+See `zarr.errors` for these warning classes.

changes/3144.bugfix.rst

@@ -0,0 +1 @@
+Ensure that -0.0 is not considered equal to 0.0 when checking if all the values in a chunk are equal to an array's fill value.```

codecov.yml

@@ -3,6 +3,7 @@ coverage:
     patch:
       default:
         target: auto
+        informational: true
     project:
       default:
         target: auto

docs/user-guide/arrays.rst

@@ -238,6 +238,8 @@ built-in delta filter::
 
    >>> import lzma
    >>> from numcodecs.zarr3 import LZMA
+   >>> import warnings
+   >>> warnings.filterwarnings("ignore", category=UserWarning)
    >>>
    >>> lzma_filters = [dict(id=lzma.FILTER_DELTA, dist=4), dict(id=lzma.FILTER_LZMA2, preset=1)]
    >>> compressors = LZMA(filters=lzma_filters)

docs/user-guide/consolidated_metadata.rst

@@ -27,6 +27,8 @@ In Python, the consolidated metadata is available on the ``.consolidated_metadat
 attribute of the ``GroupMetadata`` object.
 
    >>> import zarr
+   >>> import warnings
+   >>> warnings.filterwarnings("ignore", category=UserWarning)
    >>>
    >>> store = zarr.storage.MemoryStore()
    >>> group = zarr.create_group(store=store)

pyproject.toml

@@ -389,16 +389,6 @@ addopts = [
 ]
 filterwarnings = [
     "error",
-    # TODO: explicitly filter or catch the warnings below where we expect them to be emitted in the tests
-    "ignore:Consolidated metadata is currently not part in the Zarr format 3 specification.*:UserWarning",
-    "ignore:Creating a zarr.buffer.gpu.Buffer with an array that does not support the __cuda_array_interface__.*:UserWarning",
-    "ignore:Automatic shard shape inference is experimental and may change without notice.*:UserWarning",
-    "ignore:The codec .* is currently not part in the Zarr format 3 specification.*:UserWarning",
-    "ignore:The dtype .* is currently not part in the Zarr format 3 specification.*:UserWarning",
-    "ignore:Use zarr.create_array instead.:DeprecationWarning",
-    "ignore:Duplicate name.*:UserWarning",
-    "ignore:The `compressor` argument is deprecated. Use `compressors` instead.:UserWarning",
-    "ignore:Numcodecs codecs are not in the Zarr version 3 specification and may not be supported by other zarr implementations.:UserWarning",
     "ignore:Unclosed client session <aiohttp.client.ClientSession.*:ResourceWarning"
 ]
 markers = [

src/zarr/_compat.py

@@ -4,6 +4,8 @@
 from inspect import Parameter, signature
 from typing import Any, TypeVar
 
+from zarr.errors import ZarrFutureWarning
+
 T = TypeVar("T")
 
 # Based off https://github.com/scikit-learn/scikit-learn/blob/e87b32a81c70abed8f2e97483758eb64df8255e9/sklearn/utils/validation.py#L63
@@ -54,7 +56,7 @@ def inner_f(*args: Any, **kwargs: Any) -> T:
                     f"{version} passing these as positional arguments "
                     "will result in an error"
                 ),
-                FutureWarning,
+                ZarrFutureWarning,
                 stacklevel=2,
             )
             kwargs.update(zip(sig.parameters, args, strict=False))

src/zarr/api/asynchronous.py

@@ -39,7 +39,13 @@
     create_hierarchy,
 )
 from zarr.core.metadata import ArrayMetadataDict, ArrayV2Metadata, ArrayV3Metadata
-from zarr.errors import GroupNotFoundError, NodeTypeValidationError
+from zarr.errors import (
+    GroupNotFoundError,
+    NodeTypeValidationError,
+    ZarrDeprecationWarning,
+    ZarrRuntimeWarning,
+    ZarrUserWarning,
+)
 from zarr.storage import StorePath
 from zarr.storage._common import make_store_path
 
@@ -141,7 +147,7 @@ def _like_args(a: ArrayLike, kwargs: dict[str, Any]) -> dict[str, Any]:
         else:
             # TODO: Remove type: ignore statement when type inference improves.
             # mypy cannot correctly infer the type of a.metadata here for some reason.
-            new["codecs"] = a.metadata.codecs  # type: ignore[unreachable]
+            new["codecs"] = a.metadata.codecs
 
     else:
         # TODO: set default values compressor/codecs
@@ -162,7 +168,7 @@ def _handle_zarr_version_or_format(
         )
     if zarr_version is not None:
         warnings.warn(
-            "zarr_version is deprecated, use zarr_format", DeprecationWarning, stacklevel=2
+            "zarr_version is deprecated, use zarr_format", ZarrDeprecationWarning, stacklevel=2
         )
         return zarr_version
     return zarr_format
@@ -228,7 +234,7 @@ async def consolidate_metadata(
         warnings.warn(
             "Consolidated metadata is currently not part in the Zarr format 3 specification. It "
             "may not be supported by other zarr implementations and may change in the future.",
-            category=UserWarning,
+            category=ZarrUserWarning,
             stacklevel=1,
         )
 
@@ -536,7 +542,7 @@ async def save_group(
     await asyncio.gather(*aws)
 
 
-@deprecated("Use AsyncGroup.tree instead.")
+@deprecated("Use AsyncGroup.tree instead.", category=ZarrDeprecationWarning)
 async def tree(grp: AsyncGroup, expand: bool | None = None, level: int | None = None) -> Any:
     """Provide a rich display of the hierarchy.
 
@@ -674,13 +680,13 @@ async def group(
     store_path = await make_store_path(store, path=path, mode=mode, storage_options=storage_options)
 
     if chunk_store is not None:
-        warnings.warn("chunk_store is not yet implemented", RuntimeWarning, stacklevel=2)
+        warnings.warn("chunk_store is not yet implemented", ZarrRuntimeWarning, stacklevel=2)
     if cache_attrs is not None:
-        warnings.warn("cache_attrs is not yet implemented", RuntimeWarning, stacklevel=2)
+        warnings.warn("cache_attrs is not yet implemented", ZarrRuntimeWarning, stacklevel=2)
     if synchronizer is not None:
-        warnings.warn("synchronizer is not yet implemented", RuntimeWarning, stacklevel=2)
+        warnings.warn("synchronizer is not yet implemented", ZarrRuntimeWarning, stacklevel=2)
     if meta_array is not None:
-        warnings.warn("meta_array is not yet implemented", RuntimeWarning, stacklevel=2)
+        warnings.warn("meta_array is not yet implemented", ZarrRuntimeWarning, stacklevel=2)
 
     if attributes is None:
         attributes = {}
@@ -827,13 +833,13 @@ async def open_group(
     zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format)
 
     if cache_attrs is not None:
-        warnings.warn("cache_attrs is not yet implemented", RuntimeWarning, stacklevel=2)
+        warnings.warn("cache_attrs is not yet implemented", ZarrRuntimeWarning, stacklevel=2)
     if synchronizer is not None:
-        warnings.warn("synchronizer is not yet implemented", RuntimeWarning, stacklevel=2)
+        warnings.warn("synchronizer is not yet implemented", ZarrRuntimeWarning, stacklevel=2)
     if meta_array is not None:
-        warnings.warn("meta_array is not yet implemented", RuntimeWarning, stacklevel=2)
+        warnings.warn("meta_array is not yet implemented", ZarrRuntimeWarning, stacklevel=2)
     if chunk_store is not None:
-        warnings.warn("chunk_store is not yet implemented", RuntimeWarning, stacklevel=2)
+        warnings.warn("chunk_store is not yet implemented", ZarrRuntimeWarning, stacklevel=2)
 
     store_path = await make_store_path(store, mode=mode, storage_options=storage_options, path=path)
     if attributes is None:
@@ -1011,19 +1017,19 @@ async def create(
     )
 
     if synchronizer is not None:
-        warnings.warn("synchronizer is not yet implemented", RuntimeWarning, stacklevel=2)
+        warnings.warn("synchronizer is not yet implemented", ZarrRuntimeWarning, stacklevel=2)
     if chunk_store is not None:
-        warnings.warn("chunk_store is not yet implemented", RuntimeWarning, stacklevel=2)
+        warnings.warn("chunk_store is not yet implemented", ZarrRuntimeWarning, stacklevel=2)
     if cache_metadata is not None:
-        warnings.warn("cache_metadata is not yet implemented", RuntimeWarning, stacklevel=2)
+        warnings.warn("cache_metadata is not yet implemented", ZarrRuntimeWarning, stacklevel=2)
     if cache_attrs is not None:
-        warnings.warn("cache_attrs is not yet implemented", RuntimeWarning, stacklevel=2)
+        warnings.warn("cache_attrs is not yet implemented", ZarrRuntimeWarning, stacklevel=2)
     if object_codec is not None:
-        warnings.warn("object_codec is not yet implemented", RuntimeWarning, stacklevel=2)
+        warnings.warn("object_codec is not yet implemented", ZarrRuntimeWarning, stacklevel=2)
     if read_only is not None:
-        warnings.warn("read_only is not yet implemented", RuntimeWarning, stacklevel=2)
+        warnings.warn("read_only is not yet implemented", ZarrRuntimeWarning, stacklevel=2)
     if meta_array is not None:
-        warnings.warn("meta_array is not yet implemented", RuntimeWarning, stacklevel=2)
+        warnings.warn("meta_array is not yet implemented", ZarrRuntimeWarning, stacklevel=2)
 
     if write_empty_chunks is not None:
         _warn_write_empty_chunks_kwarg()
@@ -1042,7 +1048,7 @@ async def create(
                 "This is redundant. When both are set, write_empty_chunks will be used instead "
                 "of the value in config."
             )
-            warnings.warn(UserWarning(msg), stacklevel=1)
+            warnings.warn(ZarrUserWarning(msg), stacklevel=1)
         config_parsed = dataclasses.replace(config_parsed, write_empty_chunks=write_empty_chunks)
 
     return await AsyncArray._create(

src/zarr/api/synchronous.py

@@ -10,6 +10,7 @@
 from zarr.core.group import Group
 from zarr.core.sync import sync
 from zarr.core.sync_group import create_hierarchy
+from zarr.errors import ZarrDeprecationWarning
 
 if TYPE_CHECKING:
     from collections.abc import Iterable
@@ -339,7 +340,7 @@ def save_group(
     )
 
 
-@deprecated("Use Group.tree instead.")
+@deprecated("Use Group.tree instead.", category=ZarrDeprecationWarning)
 def tree(grp: Group, expand: bool | None = None, level: int | None = None) -> Any:
     """Provide a rich display of the hierarchy.