Merge remote-tracking branch 'origin/main' into warn-non-spec

.github/workflows/releases.yml

@@ -55,7 +55,7 @@ jobs:
         with:
           name: releases
           path: dist
-      - uses: pypa/[email protected].2
+      - uses: pypa/[email protected].3
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}

docs/guide/index.rst

@@ -4,5 +4,6 @@ Guide
 .. toctree::
     :maxdepth: 1
 
+    whatsnew_v3
     storage
     consolidated_metadata

docs/guide/whatsnew_v3.rst

@@ -0,0 +1,14 @@
+What's new in v3
+================
+
+This page gives an overview of major changes and additions in version 3.
+
+
+Dependencies
+------------
+- The new ``remote`` dependency group can be used to install a supported version of
+  ``fsspec``, required for remote data access.
+- The new ``gpu`` dependency group can be used to install a supported version of
+  ``cuda``, required for GPU functionality.
+- The ``jupyter`` optional dependency group has been removed, since v3 contains no
+  jupyter specific functionality.

docs/release.rst

@@ -39,6 +39,8 @@ Dependency Changes
   fsspec and any relevant implementations (e.g. s3fs) before using the ``RemoteStore``.
   By :user:`Joe Hamman <jhamman>` :issue:`2391`.
 
+* ``RemoteStore`` was renamed to ``FsspecStore``.
+  By :user:`Joe Hamman <jhamman>` :issue:`2557`.
 
 .. release_3.0.0-alpha:
 

pyproject.toml

@@ -53,9 +53,14 @@ license = {text = "MIT License"}
 keywords = ["Python", "compressed", "ndimensional-arrays", "zarr"]
 
 [project.optional-dependencies]
-fsspec = [
+# User extras
+remote = [
     "fsspec>=2023.10.0",
 ]
+gpu = [
+    "cupy-cuda12x",
+]
+# Development extras
 test = [
     "coverage",
     "pytest",
@@ -68,15 +73,7 @@ test = [
     "hypothesis",
     "universal-pathlib",
 ]
-
-jupyter = [
-    'notebook',
-    'ipytree>=0.2.2',
-    'ipywidgets>=8.0.0',
-]
-gpu = [
-    "cupy-cuda12x",
-]
+optional = ["rich", "universal-pathlib"]
 docs = [
     'sphinx==8.1.3',
     'sphinx-autobuild>=2021.3.14',
@@ -87,19 +84,9 @@ docs = [
     'pydata-sphinx-theme',
     'numpydoc',
     'numcodecs[msgpack]',
-    'msgpack',
-]
-extra = [
-    'msgpack',
-]
-optional = [
-    'universal-pathlib>=0.0.22',
-    'rich'
-]
-tree = [
-    'rich',
 ]
 
+
 [project.urls]
 "Bug Tracker" = "https://github.com/zarr-developers/zarr-python/issues"
 Changelog = "https://zarr.readthedocs.io/en/stable/release.html"
@@ -129,7 +116,7 @@ dependencies = [
     "numpy~={matrix:numpy}",
     "universal_pathlib",
 ]
-features = ["test", "extra"]
+features = ["test"]
 
 [[tool.hatch.envs.test.matrix]]
 python = ["3.11", "3.12", "3.13"]
@@ -160,7 +147,7 @@ dependencies = [
     "numpy~={matrix:numpy}",
     "universal_pathlib",
 ]
-features = ["test", "extra", "gpu"]
+features = ["test", "gpu"]
 
 [[tool.hatch.envs.gputest.matrix]]
 python = ["3.11", "3.12", "3.13"]

src/zarr/storage/__init__.py

@@ -1,16 +1,16 @@
 from zarr.storage.common import StoreLike, StorePath, make_store_path
+from zarr.storage.fsspec import FsspecStore
 from zarr.storage.local import LocalStore
 from zarr.storage.logging import LoggingStore
 from zarr.storage.memory import MemoryStore
-from zarr.storage.remote import RemoteStore
 from zarr.storage.wrapper import WrapperStore
 from zarr.storage.zip import ZipStore
 
 __all__ = [
+    "FsspecStore",
     "LocalStore",
     "LoggingStore",
     "MemoryStore",
-    "RemoteStore",
     "StoreLike",
     "StorePath",
     "WrapperStore",

src/zarr/storage/common.py

@@ -281,7 +281,7 @@ async def make_store_path(
     TypeError
         If the StoreLike object is not one of the supported types.
     """
-    from zarr.storage.remote import RemoteStore  # circular import
+    from zarr.storage.fsspec import FsspecStore  # circular import
 
     used_storage_options = False
     path_normalized = normalize_path(path)
@@ -302,7 +302,7 @@ async def make_store_path(
 
             if _is_fsspec_uri(store_like):
                 used_storage_options = True
-                store = RemoteStore.from_url(
+                store = FsspecStore.from_url(
                     store_like, storage_options=storage_options, read_only=_read_only
                 )
             else:

src/zarr/storage/remote.py → src/zarr/storage/fsspec.py

@@ -22,7 +22,7 @@
 )
 
 
-class RemoteStore(Store):
+class FsspecStore(Store):
     """
     A remote Store based on FSSpec
 
@@ -61,8 +61,8 @@ class RemoteStore(Store):
 
     See Also
     --------
-    RemoteStore.from_upath
-    RemoteStore.from_url
+    FsspecStore.from_upath
+    FsspecStore.from_url
     """
 
     # based on FSSpec
@@ -96,17 +96,17 @@ def __init__(
         if "://" in path and not path.startswith("http"):
             # `not path.startswith("http")` is a special case for the http filesystem (¯\_(ツ)_/¯)
             scheme, _ = path.split("://", maxsplit=1)
-            raise ValueError(f"path argument to RemoteStore must not include scheme ({scheme}://)")
+            raise ValueError(f"path argument to FsspecStore must not include scheme ({scheme}://)")
 
     @classmethod
     def from_upath(
         cls,
         upath: Any,
         read_only: bool = False,
         allowed_exceptions: tuple[type[Exception], ...] = ALLOWED_EXCEPTIONS,
-    ) -> RemoteStore:
+    ) -> FsspecStore:
         """
-        Create a RemoteStore from an upath object.
+        Create a FsspecStore from an upath object.
 
         Parameters
         ----------
@@ -120,7 +120,7 @@ def from_upath(
 
         Returns
         -------
-        RemoteStore
+        FsspecStore
         """
         return cls(
             fs=upath.fs,
@@ -136,9 +136,9 @@ def from_url(
         storage_options: dict[str, Any] | None = None,
         read_only: bool = False,
         allowed_exceptions: tuple[type[Exception], ...] = ALLOWED_EXCEPTIONS,
-    ) -> RemoteStore:
+    ) -> FsspecStore:
         """
-        Create a RemoteStore from a URL.
+        Create a FsspecStore from a URL.
 
         Parameters
         ----------
@@ -154,7 +154,7 @@ def from_url(
 
         Returns
         -------
-        RemoteStore
+        FsspecStore
         """
         try:
             from fsspec import url_to_fs
@@ -185,7 +185,7 @@ async def clear(self) -> None:
             pass
 
     def __repr__(self) -> str:
-        return f"<RemoteStore({type(self.fs).__name__}, {self.path})>"
+        return f"<FsspecStore({type(self.fs).__name__}, {self.path})>"
 
     def __eq__(self, other: object) -> bool:
         return (

tests/conftest.py

@@ -13,7 +13,7 @@
 from zarr.abc.store import Store
 from zarr.core.sync import sync
 from zarr.storage import LocalStore, MemoryStore, StorePath, ZipStore
-from zarr.storage.remote import RemoteStore
+from zarr.storage.fsspec import FsspecStore
 
 if TYPE_CHECKING:
     from collections.abc import Generator
@@ -25,14 +25,14 @@
 
 
 async def parse_store(
-    store: Literal["local", "memory", "remote", "zip"], path: str
-) -> LocalStore | MemoryStore | RemoteStore | ZipStore:
+    store: Literal["local", "memory", "fsspec", "zip"], path: str
+) -> LocalStore | MemoryStore | FsspecStore | ZipStore:
     if store == "local":
         return await LocalStore.open(path)
     if store == "memory":
         return await MemoryStore.open()
-    if store == "remote":
-        return await RemoteStore.open(url=path)
+    if store == "fsspec":
+        return await FsspecStore.open(url=path)
     if store == "zip":
         return await ZipStore.open(path + "/zarr.zip", mode="w")
     raise AssertionError
@@ -56,8 +56,8 @@ async def local_store(tmpdir: LEGACY_PATH) -> LocalStore:
 
 
 @pytest.fixture
-async def remote_store(url: str) -> RemoteStore:
-    return await RemoteStore.open(url)
+async def remote_store(url: str) -> FsspecStore:
+    return await FsspecStore.open(url)
 
 
 @pytest.fixture
@@ -87,7 +87,7 @@ def sync_store(request: pytest.FixtureRequest, tmp_path: LEGACY_PATH) -> Store:
 @dataclass
 class AsyncGroupRequest:
     zarr_format: ZarrFormat
-    store: Literal["local", "remote", "memory", "zip"]
+    store: Literal["local", "fsspec", "memory", "zip"]
     attributes: dict[str, Any] = field(default_factory=dict)
 
 

tests/test_store/test_core.py

@@ -7,9 +7,9 @@
 from zarr.core.common import AccessModeLiteral
 from zarr.storage._utils import normalize_path
 from zarr.storage.common import StoreLike, StorePath, make_store_path
+from zarr.storage.fsspec import FsspecStore
 from zarr.storage.local import LocalStore
 from zarr.storage.memory import MemoryStore
-from zarr.storage.remote import RemoteStore
 
 
 @pytest.mark.parametrize("path", [None, "", "bar"])
@@ -73,7 +73,7 @@ async def test_make_store_path_invalid() -> None:
 async def test_make_store_path_fsspec(monkeypatch) -> None:
     pytest.importorskip("fsspec")
     store_path = await make_store_path("http://foo.com/bar")
-    assert isinstance(store_path.store, RemoteStore)
+    assert isinstance(store_path.store, FsspecStore)
 
 
 @pytest.mark.parametrize(

tests/test_store/test_remote.py → tests/test_store/test_fsspec.py

@@ -10,7 +10,7 @@
 import zarr.api.asynchronous
 from zarr.core.buffer import Buffer, cpu, default_buffer_prototype
 from zarr.core.sync import _collect_aiterator, sync
-from zarr.storage import RemoteStore
+from zarr.storage import FsspecStore
 from zarr.testing.store import StoreTests
 
 if TYPE_CHECKING:
@@ -84,7 +84,7 @@ def s3(s3_base: None) -> Generator[s3fs.S3FileSystem, None, None]:
 
 
 async def test_basic() -> None:
-    store = RemoteStore.from_url(
+    store = FsspecStore.from_url(
         f"s3://{test_bucket_name}/foo/spam/",
         storage_options={"endpoint_url": endpoint_url, "anon": False},
     )
@@ -102,8 +102,8 @@ async def test_basic() -> None:
     assert out[0].to_bytes() == data[1:]
 
 
-class TestRemoteStoreS3(StoreTests[RemoteStore, cpu.Buffer]):
-    store_cls = RemoteStore
+class TestFsspecStoreS3(StoreTests[FsspecStore, cpu.Buffer]):
+    store_cls = FsspecStore
     buffer_cls = cpu.Buffer
 
     @pytest.fixture
@@ -114,36 +114,36 @@ def store_kwargs(self, request) -> dict[str, str | bool]:
         return {"fs": fs, "path": path}
 
     @pytest.fixture
-    def store(self, store_kwargs: dict[str, str | bool]) -> RemoteStore:
+    def store(self, store_kwargs: dict[str, str | bool]) -> FsspecStore:
         return self.store_cls(**store_kwargs)
 
-    async def get(self, store: RemoteStore, key: str) -> Buffer:
+    async def get(self, store: FsspecStore, key: str) -> Buffer:
         #  make a new, synchronous instance of the filesystem because this test is run in sync code
         new_fs = fsspec.filesystem(
             "s3", endpoint_url=store.fs.endpoint_url, anon=store.fs.anon, asynchronous=False
         )
         return self.buffer_cls.from_bytes(new_fs.cat(f"{store.path}/{key}"))
 
-    async def set(self, store: RemoteStore, key: str, value: Buffer) -> None:
+    async def set(self, store: FsspecStore, key: str, value: Buffer) -> None:
         #  make a new, synchronous instance of the filesystem because this test is run in sync code
         new_fs = fsspec.filesystem(
             "s3", endpoint_url=store.fs.endpoint_url, anon=store.fs.anon, asynchronous=False
         )
         new_fs.write_bytes(f"{store.path}/{key}", value.to_bytes())
 
-    def test_store_repr(self, store: RemoteStore) -> None:
-        assert str(store) == "<RemoteStore(S3FileSystem, test)>"
+    def test_store_repr(self, store: FsspecStore) -> None:
+        assert str(store) == "<FsspecStore(S3FileSystem, test)>"
 
-    def test_store_supports_writes(self, store: RemoteStore) -> None:
+    def test_store_supports_writes(self, store: FsspecStore) -> None:
         assert store.supports_writes
 
-    def test_store_supports_partial_writes(self, store: RemoteStore) -> None:
+    def test_store_supports_partial_writes(self, store: FsspecStore) -> None:
         assert not store.supports_partial_writes
 
-    def test_store_supports_listing(self, store: RemoteStore) -> None:
+    def test_store_supports_listing(self, store: FsspecStore) -> None:
         assert store.supports_listing
 
-    async def test_remote_store_from_uri(self, store: RemoteStore):
+    async def test_fsspec_store_from_uri(self, store: FsspecStore) -> None:
         storage_options = {
             "endpoint_url": endpoint_url,
             "anon": False,
@@ -188,7 +188,7 @@ def test_from_upath(self) -> None:
             anon=False,
             asynchronous=True,
         )
-        result = RemoteStore.from_upath(path)
+        result = FsspecStore.from_upath(path)
         assert result.fs.endpoint_url == endpoint_url
         assert result.fs.asynchronous
         assert result.path == f"{test_bucket_name}/foo/bar"
@@ -197,7 +197,7 @@ def test_init_raises_if_path_has_scheme(self, store_kwargs) -> None:
         # regression test for https://github.com/zarr-developers/zarr-python/issues/2342
         store_kwargs["path"] = "s3://" + store_kwargs["path"]
         with pytest.raises(
-            ValueError, match="path argument to RemoteStore must not include scheme .*"
+            ValueError, match="path argument to FsspecStore must not include scheme .*"
         ):
             self.store_cls(**store_kwargs)