Merge branch 'main' into dep/stores

.github/workflows/python-package.yml

@@ -80,11 +80,8 @@ jobs:
         mkdir ~/blob_emulator
         azurite -l ~/blob_emulator --debug debug.log 2>&1 > stdouterr.log &
         pytest --cov=zarr --cov-config=pyproject.toml --doctest-plus --cov-report xml --cov=./ --timeout=300
-    - uses: codecov/codecov-action@v3
+    - uses: codecov/codecov-action@v4
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       with:
-        token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
-          #files: ./coverage1.xml,./coverage2.xml # optional
-          #flags: unittests # optional
-          #name: codecov-umbrella # optional
-          #fail_ci_if_error: true # optional (default = false)
         verbose: true # optional (default = false)

.pre-commit-config.yaml

@@ -8,19 +8,19 @@ default_language_version:
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.3.5'
+    rev: 'v0.4.1'
     hooks:
     - id: ruff
   - repo: https://github.com/psf/black
-    rev: 24.3.0
+    rev: 24.4.0
     hooks:
     - id: black
   - repo: https://github.com/codespell-project/codespell
     rev: v2.2.6
     hooks:
       - id: codespell
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     - id: check-yaml
   - repo: https://github.com/pre-commit/mirrors-mypy

docs/release.rst

@@ -20,6 +20,8 @@ Unreleased
 
 Enhancements
 ~~~~~~~~~~~~
+* Performance improvement for reading and writing chunks if any of the dimensions is size 1. :issue:`1730`
+  By :user:`Deepak Cherian <dcherian>`.
 
 
 Docs
@@ -37,22 +39,38 @@ Maintenance
 
 Enhancements
 ~~~~~~~~~~~~
+
 * [v3] Dramatically reduce number of ``__contains__`` requests in favor of optimistically calling `__getitem__`
   and handling any error that may arise.
-  By :user:`Deepak Cherian <dcherian>`.
+  By :user:`Deepak Cherian <dcherian>` :issue:`1741`.
 
 * [v3] Reuse the downloaded array metadata when creating an ``Array``.
-  By :user:`Deepak Cherian <dcherian>`.
+  By :user:`Deepak Cherian <dcherian>` :issue:`1734`.
 
 * Optimize ``Array.info`` so that it calls `getsize` only once.
-  By :user:`Deepak Cherian <dcherian>`.
+  By :user:`Deepak Cherian <dcherian>` :issue:`1733`.
 
 * Override IPython ``_repr_*_`` methods to avoid expensive lookups against object stores.
   By :user:`Deepak Cherian <dcherian>` :issue:`1716`.
 
 * FSStore now raises rather than return bad data.
   By :user:`Martin Durant <martindurant>` and :user:`Ian Carroll <itcarroll>` :issue:`1604`.
 
+* Avoid redundant ``__contains__``.
+  By :user:`Deepak Cherian <dcherian>` :issue:`1739`.
+
+Docs
+~~~~
+
+* Fix link to GCSMap in ``tutorial.rst``.
+  By :user:`Daniel Jahn <dahnj>` :issue:`1689`.
+
+* Endorse `SPEC0000 <https://scientific-python.org/specs/spec-0000/>`_ and state version support policy in ``installation.rst``.
+  By :user:`Sanket Verma <msankeys963>` :issue:`1665`.
+
+* Migrate v1 and v2 specification to `Zarr-Specs <https://zarr-specs.readthedocs.io/en/latest/specs.html>`_.
+  By :user:`Sanket Verma <msankeys963>` :issue:`1582`.
+
 Maintenance
 ~~~~~~~~~~~
 
@@ -61,7 +79,12 @@ Maintenance
 
 * Bump minimum supported NumPy version to 1.23 (per spec 0000)
   By :user:`Joe Hamman <jhamman>` :issue:`1719`.
-
+
+* Minor fixes: Using ``is`` instead of ``type`` and removing unnecessary ``None``.
+  By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1737`.
+
+* Fix tests failure related to Pytest 8.
+  By :user:`David Stansby <dstansby>` :issue:`1714`.
 
 .. _release_2.17.1:
 

pyproject.toml

@@ -138,6 +138,7 @@ filterwarnings = [
     "ignore:PY_SSIZE_T_CLEAN will be required.*:DeprecationWarning",
     "ignore:The loop argument is deprecated since Python 3.8.*:DeprecationWarning",
     "ignore:The .* is deprecated and will be removed in a Zarr-Python version 3*:FutureWarning",
+    "ignore:The experimental Zarr V3 implementation in this version .*:FutureWarning",
 ]
 
 

zarr/_storage/store.py

@@ -1,5 +1,6 @@
 import abc
 import os
+import warnings
 from collections import defaultdict
 from collections.abc import MutableMapping
 from copy import copy
@@ -23,6 +24,7 @@
 DEFAULT_ZARR_VERSION: ZARR_VERSION = 2
 
 v3_api_available = os.environ.get("ZARR_V3_EXPERIMENTAL_API", "0").lower() not in ["0", "false"]
+_has_warned_about_v3 = False  # to avoid printing the warning multiple times
 
 V3_DEPRECATION_MESSAGE = (
     "The {store} is deprecated and will be removed in a Zarr-Python version 3, see "
@@ -31,6 +33,17 @@
 
 
 def assert_zarr_v3_api_available():
+    # we issue a warning about the experimental v3 implementation when it is first used
+    global _has_warned_about_v3
+    if v3_api_available and not _has_warned_about_v3:
+        warnings.warn(
+            "The experimental Zarr V3 implementation in this version of Zarr-Python is not "
+            "in alignment with the final V3 specification. This version will be removed in "
+            "Zarr-Python 3 in favor of a spec compliant version.",
+            FutureWarning,
+            stacklevel=1,
+        )
+        _has_warned_about_v3 = True
     if not v3_api_available:
         raise NotImplementedError(
             "# V3 reading and writing is experimental! To enable support, set:\n"

zarr/tests/test_storage_v3.py

@@ -4,12 +4,18 @@
 import inspect
 import os
 import tempfile
+import warnings
 
 import numpy as np
 import pytest
 
 import zarr
-from zarr._storage.store import _get_hierarchy_metadata, v3_api_available, StorageTransformer
+from zarr._storage.store import (
+    _get_hierarchy_metadata,
+    assert_zarr_v3_api_available,
+    v3_api_available,
+    StorageTransformer,
+)
 from zarr._storage.v3_storage_transformers import ShardingStorageTransformer, v3_sharding_available
 from zarr.core import Array
 from zarr.meta import _default_entry_point_metadata_v3
@@ -668,6 +674,18 @@ def test_top_level_imports():
             assert not hasattr(zarr, store_name)  # pragma: no cover
 
 
+def test_assert_zarr_v3_api_available_warns_once():
+    import zarr._storage.store
+
+    zarr._storage.store._has_warned_about_v3 = False
+    warnings.resetwarnings()
+    with pytest.warns() as record:
+        assert_zarr_v3_api_available()
+        assert_zarr_v3_api_available()
+    assert len(record) == 1
+    assert "The experimental Zarr V3 implementation" in str(record[0].message)
+
+
 def _get_public_and_dunder_methods(some_class):
     return set(
         name

zarr/tests/test_util.py

@@ -89,6 +89,15 @@ def test_is_total_slice():
     assert not is_total_slice((slice(0, 50), slice(0, 50)), (100, 100))
     assert not is_total_slice((slice(0, 100, 2), slice(0, 100)), (100, 100))
 
+    # size-1 dimension edge-case
+    # https://github.com/zarr-developers/zarr-python/issues/1730
+    assert is_total_slice((slice(0, 1),), (1,))
+    # this is an equivalent selection (without a slice)
+    assert is_total_slice((0,), (1,))
+    # same for multidimensional selection
+    assert is_total_slice((slice(0, 1), slice(0, 10)), (1, 10))
+    assert is_total_slice((0, slice(0, 10)), (1, 10))
+
     with pytest.raises(TypeError):
         is_total_slice("foo", (100,))
 

zarr/util.py

@@ -234,8 +234,17 @@ def is_total_slice(item, shape: Tuple[int]) -> bool:
     if isinstance(item, tuple):
         return all(
             (
-                isinstance(it, slice)
-                and ((it == slice(None)) or ((it.stop - it.start == sh) and (it.step in [1, None])))
+                (
+                    isinstance(it, slice)
+                    and (
+                        (it == slice(None))
+                        or ((it.stop - it.start == sh) and (it.step in [1, None]))
+                    )
+                )
+                # The only scalar edge case, indexing with int 0 along a size-1 dimension
+                # is identical to a total slice
+                # https://github.com/zarr-developers/zarr-python/issues/1730
+                or (isinstance(it, int) and it == 0 and sh == 1)
             )
             for it, sh in zip(item, shape)
         )