Merge branch 'main' of https://github.com/zarr-developers/zarr-python …

…into feature/slim-zarr
zarr-developers · Oct 17, 2024 · 5daa82a · 5daa82a
2 parents 002b805 + 4d663cc
commit 5daa82a
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Showing 14 changed files with 311 additions and 147 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -18,15 +18,18 @@ maintainers = [
     { name = "Juan Nunez-Iglesias", email = "juan.nunez-iglesias@monash.edu" },
     { name = "Martin Durant", email = "mdurant@anaconda.com" },
     { name = "Norman Rzepka" },
-    { name = "Ryan Abernathey" }
+    { name = "Ryan Abernathey" },
+    { name = "David Stansby" },
+    { name = "Tom Augspurger", email = "tom.w.augspurger@gmail.com" },
+    { name = "Deepak Cherian" }
 ]
 requires-python = ">=3.11"
 # If you add a new dependency here, please also add it to .pre-commit-config.yml
 dependencies = [
     'numpy>=1.25',
     'numcodecs>=0.12',
-    'typing_extensions',
-    'donfig',
+    'typing_extensions>=4.9',
+    'donfig>=0.8.1',
 ]
 dynamic = [
   "version",
@@ -49,10 +52,10 @@ keywords = ["Python", "compressed", "ndimensional-arrays", "zarr"]
 
 [project.optional-dependencies]
 remote = [
-    "fsspec",
+    "fsspec>=2023.10.0",
 ]
 sharding = [
-    "crc32c",
+    "crc32c>=2.4",
 ]
 test = [
     "coverage",
@@ -205,34 +208,33 @@ extend-exclude = [
 
 [tool.ruff.lint]
 extend-select = [
-    "ANN", # flake8-annotations
-    "B",   # flake8-bugbear
-    "C4",  # flake8-comprehensions
-    "FLY", # flynt
-    "G",   # flake8-logging-format
-    "I",   # isort
-    "ISC", # flake8-implicit-str-concat
-    "PGH", # pygrep-hooks
-    "PT",  # flake8-pytest-style
-    "PYI", # flake8-pyi
-    "RSE", # flake8-raise
-    "RET", # flake8-return
+    "ANN",  # flake8-annotations
+    "B",    # flake8-bugbear
+    "C4",   # flake8-comprehensions
+    "FLY",  # flynt
+    "G",    # flake8-logging-format
+    "I",    # isort
+    "ISC",  # flake8-implicit-str-concat
+    "PERF", # Perflint
+    "PGH",  # pygrep-hooks
+    "PT",   # flake8-pytest-style
+    "PYI",  # flake8-pyi
+    "RSE",  # flake8-raise
+    "RET",  # flake8-return
     "RUF",
-    "TCH", # flake8-type-checking
-    "TRY", # tryceratops
-    "UP",  # pyupgrade
-    "W",   # pycodestyle warnings
+    "TCH",  # flake8-type-checking
+    "TRY",  # tryceratops
+    "UP",   # pyupgrade
+    "W",    # pycodestyle warnings
 ]
 ignore = [
-    "ANN003",
-    "ANN101",
-    "ANN102",
+    "ANN101", # deprecated
+    "ANN102", # deprecated
     "ANN401",
     "PT004",  # deprecated
     "PT005",  # deprecated
     "PT011",  # TODO: apply this rule
     "PT012",  # TODO: apply this rule
-    "PYI013",
     "RET505",
     "RET506",
     "RUF005",

diff --git a/src/zarr/abc/codec.py b/src/zarr/abc/codec.py
@@ -156,20 +156,14 @@ async def encode(
 class ArrayArrayCodec(BaseCodec[NDBuffer, NDBuffer]):
     """Base class for array-to-array codecs."""
 
-    ...
-
 
 class ArrayBytesCodec(BaseCodec[NDBuffer, Buffer]):
     """Base class for array-to-bytes codecs."""
 
-    ...
-
 
 class BytesBytesCodec(BaseCodec[Buffer, Buffer]):
     """Base class for bytes-to-bytes codecs."""
 
-    ...
-
 
 Codec = ArrayArrayCodec | ArrayBytesCodec | BytesBytesCodec
 

diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py
@@ -170,10 +170,7 @@ async def consolidate_metadata(
         The group, with the ``consolidated_metadata`` field set to include
         the metadata of each child node.
     """
-    store_path = await make_store_path(store)
-
-    if path is not None:
-        store_path = store_path / path
+    store_path = await make_store_path(store, path=path)
 
     group = await AsyncGroup.open(store_path, zarr_format=zarr_format, use_consolidated=False)
     group.store_path.store._check_writable()
@@ -291,10 +288,7 @@ async def open(
     """
     zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format)
 
-    store_path = await make_store_path(store, mode=mode, storage_options=storage_options)
-
-    if path is not None:
-        store_path = store_path / path
+    store_path = await make_store_path(store, mode=mode, path=path, storage_options=storage_options)
 
     if "shape" not in kwargs and mode in {"a", "w", "w-"}:
         try:
@@ -401,9 +395,7 @@ async def save_array(
     )
 
     mode = kwargs.pop("mode", None)
-    store_path = await make_store_path(store, mode=mode, storage_options=storage_options)
-    if path is not None:
-        store_path = store_path / path
+    store_path = await make_store_path(store, path=path, mode=mode, storage_options=storage_options)
     new = await AsyncArray.create(
         store_path,
         zarr_format=zarr_format,
@@ -582,9 +574,7 @@ async def group(
 
     mode = None if isinstance(store, Store) else cast(AccessModeLiteral, "a")
 
-    store_path = await make_store_path(store, mode=mode, storage_options=storage_options)
-    if path is not None:
-        store_path = store_path / path
+    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)
@@ -697,9 +687,7 @@ async def open_group(
     if chunk_store is not None:
         warnings.warn("chunk_store is not yet implemented", RuntimeWarning, stacklevel=2)
 
-    store_path = await make_store_path(store, mode=mode, storage_options=storage_options)
-    if path is not None:
-        store_path = store_path / path
+    store_path = await make_store_path(store, mode=mode, storage_options=storage_options, path=path)
 
     if attributes is None:
         attributes = {}
@@ -883,9 +871,7 @@ async def create(
         if not isinstance(store, Store | StorePath):
             mode = "a"
 
-    store_path = await make_store_path(store, mode=mode, storage_options=storage_options)
-    if path is not None:
-        store_path = store_path / path
+    store_path = await make_store_path(store, path=path, mode=mode, storage_options=storage_options)
 
     return await AsyncArray.create(
         store_path,
@@ -925,6 +911,7 @@ async def empty(
     retrieve data from an empty Zarr array, any values may be returned,
     and these are not guaranteed to be stable from one access to the next.
     """
+
     return await create(shape=shape, fill_value=None, **kwargs)
 
 
@@ -1044,7 +1031,7 @@ async def open_array(
     store: StoreLike | None = None,
     zarr_version: ZarrFormat | None = None,  # deprecated
     zarr_format: ZarrFormat | None = None,
-    path: PathLike | None = None,
+    path: PathLike = "",
     storage_options: dict[str, Any] | None = None,
     **kwargs: Any,  # TODO: type kwargs as valid args to save
 ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]:
@@ -1071,9 +1058,7 @@ async def open_array(
     """
 
     mode = kwargs.pop("mode", None)
-    store_path = await make_store_path(store, mode=mode)
-    if path is not None:
-        store_path = store_path / path
+    store_path = await make_store_path(store, path=path, mode=mode)
 
     zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format)
 

diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py
@@ -2873,13 +2873,7 @@ def chunks_initialized(
     store_contents = list(
         collect_aiterator(array.store_path.store.list_prefix(prefix=array.store_path.path))
     )
-    out: list[str] = []
-
-    for chunk_key in array._iter_chunk_keys():
-        if chunk_key in store_contents:
-            out.append(chunk_key)
-
-    return tuple(out)
+    return tuple(chunk_key for chunk_key in array._iter_chunk_keys() if chunk_key in store_contents)
 
 
 def _build_parents(