Merge branch 'main' into improve-dtype-docs

Author: d-v-b

changes/2819.chore.rst

@@ -167,8 +167,17 @@ def skip_submodules(
 # documentation.
 html_theme_options = {
     "github_url": "https://github.com/zarr-developers/zarr-python",
-    "twitter_url": "https://twitter.com/zarr_dev",
     "icon_links": [
+        {
+            "name": "Bluesky",
+            "url": "https://bsky.app/profile/zarr.dev",
+            "icon": "fa-brands fa-bluesky",
+        },
+        {
+            "name": "Mastodon",
+            "url": "https://fosstodon.org/@zarr",
+            "icon": "fa-brands fa-mastodon",
+        },
         {
             "name": "Zarr Dev",
             "url": "https://zarr.dev/",
@@ -178,7 +187,6 @@ def skip_submodules(
     ],
     "collapse_navigation": True,
     "navigation_with_keys": False,
-    "announcement": "Zarr-Python 3 is here! Check out the release announcement <a href='https://zarr.dev/blog/zarr-python-3-release/'>here.</a>",
 }
 
 # Add any paths that contain custom themes here, relative to this directory.

docs/conf.py

@@ -8,7 +8,24 @@ Release notes
 
 Features
 ~~~~~~~~
-
+- Ensure that invocations of ``create_array`` use consistent keyword arguments, with consistent defaults.
+
+  ``zarr.api.synchronous.create_array`` now takes a ``write_data`` keyword argument
+  The ``Group.create_array`` method takes ``data`` and ``write_data`` keyword arguments.
+  The functions ``api.asynchronous.create``, ``api.asynchronous.create_array``
+  and the methods ``Group.create_array``, ``Group.array``, had the default
+  ``fill_value`` changed from ``0`` to the ``DEFAULT_FILL_VALUE`` value, which instructs Zarr to
+  use the default scalar value associated with the array's data type as the fill value. These are
+  all functions or methods for array creation that mirror, wrap or are wrapped by, another function
+  that already has a default ``fill_value`` set to ``DEFAULT_FILL_VALUE``. This change is necessary
+  to make these functions consistent across the entire codebase, but as this changes default values,
+  new data might have a different fill value than expected after this change.
+
+  For data types where 0 is meaningful, like integers or floats, the default scalar is 0, so this
+  change should not be noticeable. For data types where 0 is ambiguous, like fixed-length unicode
+  strings, the default fill value might be different after this change. Users who were relying on how
+  Zarr interpreted ``0`` as a non-numeric scalar value should set their desired fill value explicitly
+  after this change.
 - Added public API for Buffer ABCs and implementations.
 
   Use :mod:`zarr.buffer` to access buffer implementations, and

docs/release-notes.rst

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any, Literal, Self
+from typing import TYPE_CHECKING
 
 import numpy as np
 import numpy.typing as npt
@@ -14,7 +14,7 @@
 
 if TYPE_CHECKING:
     from collections.abc import Iterable
-    from typing import ClassVar, Literal
+    from typing import Any, ClassVar, Literal, Self
 
     from zarr.core.array_spec import ArraySpec
     from zarr.core.common import ZarrFormat

tests/package_with_entrypoint/__init__.py

@@ -1,16 +1,15 @@
 from __future__ import annotations
 
 import inspect
-import pathlib
 import re
 from typing import TYPE_CHECKING
 
 import zarr.codecs
 import zarr.storage
 
 if TYPE_CHECKING:
-    import pathlib
     from collections.abc import Callable
+    from pathlib import Path
 
     from zarr.abc.store import Store
     from zarr.core.common import JSON, MemoryOrder, ZarrFormat
@@ -45,10 +44,6 @@
 from zarr.storage._utils import normalize_path
 from zarr.testing.utils import gpu_test
 
-if TYPE_CHECKING:
-    from collections.abc import Callable
-    from pathlib import Path
-
 
 def test_create(memory_store: Store) -> None:
     store = memory_store
@@ -209,9 +204,7 @@ async def test_open_group(memory_store: MemoryStore) -> None:
 
 
 @pytest.mark.parametrize("zarr_format", [None, 2, 3])
-async def test_open_group_unspecified_version(
-    tmpdir: pathlib.Path, zarr_format: ZarrFormat
-) -> None:
+async def test_open_group_unspecified_version(tmpdir: Path, zarr_format: ZarrFormat) -> None:
     """Regression test for https://github.com/zarr-developers/zarr-python/issues/2175"""
 
     # create a group with specified zarr format (could be 2, 3, or None)
@@ -272,7 +265,7 @@ def test_save_errors() -> None:
         zarr.save("data/example.zarr", a, mode="w")
 
 
-def test_open_with_mode_r(tmp_path: pathlib.Path) -> None:
+def test_open_with_mode_r(tmp_path: Path) -> None:
     # 'r' means read only (must exist)
     with pytest.raises(FileNotFoundError):
         zarr.open(store=tmp_path, mode="r")
@@ -288,7 +281,7 @@ def test_open_with_mode_r(tmp_path: pathlib.Path) -> None:
         z2[:] = 3
 
 
-def test_open_with_mode_r_plus(tmp_path: pathlib.Path) -> None:
+def test_open_with_mode_r_plus(tmp_path: Path) -> None:
     # 'r+' means read/write (must exist)
     with pytest.raises(FileNotFoundError):
         zarr.open(store=tmp_path, mode="r+")
@@ -301,7 +294,7 @@ def test_open_with_mode_r_plus(tmp_path: pathlib.Path) -> None:
     z2[:] = 3
 
 
-async def test_open_with_mode_a(tmp_path: pathlib.Path) -> None:
+async def test_open_with_mode_a(tmp_path: Path) -> None:
     # Open without shape argument should default to group
     g = zarr.open(store=tmp_path, mode="a")
     assert isinstance(g, Group)
@@ -319,7 +312,7 @@ async def test_open_with_mode_a(tmp_path: pathlib.Path) -> None:
     z2[:] = 3
 
 
-def test_open_with_mode_w(tmp_path: pathlib.Path) -> None:
+def test_open_with_mode_w(tmp_path: Path) -> None:
     # 'w' means create (overwrite if exists);
     arr = zarr.open(store=tmp_path, mode="w", shape=(3, 3))
     assert isinstance(arr, Array)
@@ -333,7 +326,7 @@ def test_open_with_mode_w(tmp_path: pathlib.Path) -> None:
     z2[:] = 3
 
 
-def test_open_with_mode_w_minus(tmp_path: pathlib.Path) -> None:
+def test_open_with_mode_w_minus(tmp_path: Path) -> None:
     # 'w-' means create  (fail if exists)
     arr = zarr.open(store=tmp_path, mode="w-", shape=(3, 3))
     assert isinstance(arr, Array)
@@ -405,7 +398,7 @@ def test_load_array(sync_store: Store) -> None:
 
 @pytest.mark.parametrize("path", ["data", None])
 @pytest.mark.parametrize("load_read_only", [True, False, None])
-def test_load_zip(tmp_path: pathlib.Path, path: str | None, load_read_only: bool | None) -> None:
+def test_load_zip(tmp_path: Path, path: str | None, load_read_only: bool | None) -> None:
     file = tmp_path / "test.zip"
     data = np.arange(100).reshape(10, 10)
 
@@ -423,7 +416,7 @@ def test_load_zip(tmp_path: pathlib.Path, path: str | None, load_read_only: bool
 
 @pytest.mark.parametrize("path", ["data", None])
 @pytest.mark.parametrize("load_read_only", [True, False])
-def test_load_local(tmp_path: pathlib.Path, path: str | None, load_read_only: bool) -> None:
+def test_load_local(tmp_path: Path, path: str | None, load_read_only: bool) -> None:
     file = tmp_path / "test.zip"
     data = np.arange(100).reshape(10, 10)
 
@@ -1139,7 +1132,7 @@ async def test_open_falls_back_to_open_group_async(zarr_format: ZarrFormat) -> N
 
 
 @pytest.mark.parametrize("mode", ["r", "r+", "w", "a"])
-def test_open_modes_creates_group(tmp_path: pathlib.Path, mode: str) -> None:
+def test_open_modes_creates_group(tmp_path: Path, mode: str) -> None:
     # https://github.com/zarr-developers/zarr-python/issues/2490
     zarr_dir = tmp_path / f"mode-{mode}-test.zarr"
     if mode in ["r", "r+"]: