Finish typing zarr.metadata#1880

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Merged
jhamman merged 1 commit into from
May 21, 2024
Merged

Finish typing zarr.metadata #1880

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1 change: 0 additions & 1 deletion pyproject.toml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -241,7 +241,6 @@ module = [
"zarr.array",
"zarr.common",
"zarr.group",
"zarr.metadata"
]
disallow_untyped_defs = false

Expand Down
2 changes: 2 additions & 0 deletions src/zarr/array.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -199,6 +199,8 @@ async def _create_v3(

if chunk_key_encoding is None:
chunk_key_encoding = ("default", "/")
assert chunk_key_encoding is not None

if isinstance(chunk_key_encoding, tuple):
chunk_key_encoding = (
V2ChunkKeyEncoding(separator=chunk_key_encoding[1])
Expand Down
8 changes: 4 additions & 4 deletions src/zarr/chunk_grids.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@
import itertools
from collections.abc import Iterator
from dataclasses import dataclass
from typing import TYPE_CHECKING, Any
from typing import TYPE_CHECKING

from zarr.abc.metadata import Metadata
from zarr.common import (
Expand All@@ -22,13 +22,13 @@
@dataclass(frozen=True)
class ChunkGrid(Metadata):
@classmethod
def from_dict(cls, data: dict[str, JSON]) -> ChunkGrid:
def from_dict(cls, data: dict[str, JSON] | ChunkGrid) -> ChunkGrid:

@jhammanjhammanMay 21, 2024

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your change is fine but I don't know why from_dict accepts a ChunkGrid object. 🤷

if isinstance(data, ChunkGrid):
return data

name_parsed, _ = parse_named_configuration(data)
if name_parsed == "regular":
return RegularChunkGrid.from_dict(data)
return RegularChunkGrid._from_dict(data)
raise ValueError(f"Unknown chunk grid. Got {name_parsed}.")

def all_chunk_coords(self, array_shape: ChunkCoords) -> Iterator[ChunkCoords]:
Expand All@@ -45,7 +45,7 @@ def __init__(self, *, chunk_shape: ChunkCoordsLike) -> None:
object.__setattr__(self, "chunk_shape", chunk_shape_parsed)

@classmethod
def from_dict(cls, data: dict[str, Any]) -> Self:
def _from_dict(cls, data: dict[str, JSON]) -> Self:
_, configuration_parsed = parse_named_configuration(data, "regular")

return cls(**configuration_parsed) # type: ignore[arg-type]
Expand Down
2 changes: 1 addition & 1 deletion src/zarr/chunk_key_encodings.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -34,7 +34,7 @@ def __init__(self, *, separator: SeparatorLiteral) -> None:
object.__setattr__(self, "separator", separator_parsed)

@classmethod
def from_dict(cls, data: dict[str, JSON]) -> ChunkKeyEncoding:
def from_dict(cls, data: dict[str, JSON] | ChunkKeyEncoding) -> ChunkKeyEncoding:
if isinstance(data, ChunkKeyEncoding):
return data

Expand Down
5 changes: 3 additions & 2 deletions src/zarr/common.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@
from collections.abc import Awaitable, Callable, Iterator

import numpy as np
import numpy.typing as npt

ZARR_JSON = "zarr.json"
ZARRAY_JSON = ".zarray"
Expand DownExpand Up@@ -150,7 +151,7 @@ def parse_named_configuration(
return name_parsed, configuration_parsed


def parse_shapelike(data: Any) -> tuple[int, ...]:
def parse_shapelike(data: Iterable[int]) -> tuple[int, ...]:
if not isinstance(data, Iterable):
raise TypeError(f"Expected an iterable. Got {data} instead.")
data_tuple = tuple(data)
Expand All@@ -164,7 +165,7 @@ def parse_shapelike(data: Any) -> tuple[int, ...]:
return data_tuple


def parse_dtype(data: Any) -> np.dtype[Any]:
def parse_dtype(data: npt.DTypeLike) -> np.dtype[Any]:
# todo: real validation
return np.dtype(data)

Expand Down
41 changes: 22 additions & 19 deletions src/zarr/metadata.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -22,6 +22,7 @@

from typing_extensions import Self

import numcodecs.abc

from zarr.common import (
JSON,
Expand DownExpand Up@@ -168,15 +169,15 @@ class ArrayV3Metadata(ArrayMetadata):
def __init__(
self,
*,
shape,
data_type,
chunk_grid,
chunk_key_encoding,
fill_value,
codecs,
attributes,
dimension_names,
):
shape: Iterable[int],
data_type: npt.DTypeLike,
chunk_grid: dict[str, JSON] | ChunkGrid,
chunk_key_encoding: dict[str, JSON] | ChunkKeyEncoding,
fill_value: Any,
codecs: Iterable[Codec | JSON],
attributes: None | dict[str, JSON],
dimension_names: None | Iterable[str],
) -> None:
"""
Because the class is a frozen dataclass, we set attributes using object.__setattr__
"""
Expand DownExpand Up@@ -249,14 +250,14 @@ def encode_chunk_key(self, chunk_coords: ChunkCoords) -> str:
return self.chunk_key_encoding.encode_chunk_key(chunk_coords)

def to_buffer_dict(self) -> dict[str, Buffer]:
def _json_convert(o):
def _json_convert(o: np.dtype[Any] | Enum | Codec) -> str | dict[str, Any]:
if isinstance(o, np.dtype):
return str(o)
if isinstance(o, Enum):
return o.name
# this serializes numcodecs compressors
# todo: implement to_dict for codecs
elif hasattr(o, "get_config"):
elif isinstance(o, numcodecs.abc.Codec):
return o.get_config()
raise TypeError

Expand All@@ -271,9 +272,10 @@ def from_dict(cls, data: dict[str, JSON]) -> ArrayV3Metadata:
# check that the node_type attribute is correct
_ = parse_node_type_array(data.pop("node_type"))

dimension_names = data.pop("dimension_names", None)
data["dimension_names"] = data.pop("dimension_names", None)

return cls(**data, dimension_names=dimension_names)
# TODO: Remove the ignores and use a TypedDict to type `data`
return cls(**data) # type: ignore[arg-type]

def to_dict(self) -> dict[str, Any]:
out_dict = super().to_dict()
Expand DownExpand Up@@ -367,7 +369,9 @@ def codec_pipeline(self) -> CodecPipeline:
)

def to_buffer_dict(self) -> dict[str, Buffer]:
def _json_convert(o):
def _json_convert(
o: np.dtype[Any],
) -> str | list[tuple[str, str] | tuple[str, str, tuple[int, ...]]]:
if isinstance(o, np.dtype):
if o.fields is None:
return o.str
Expand DownExpand Up@@ -399,7 +403,7 @@ def to_dict(self) -> JSON:
zarray_dict["chunks"] = self.chunk_grid.chunk_shape

_ = zarray_dict.pop("data_type")
zarray_dict["dtype"] = self.data_type
zarray_dict["dtype"] = self.data_type.str

return zarray_dict

Expand All@@ -422,7 +426,7 @@ def update_attributes(self, attributes: dict[str, JSON]) -> Self:
return replace(self, attributes=attributes)


def parse_dimension_names(data: Any) -> tuple[str, ...] | None:
def parse_dimension_names(data: None | Iterable[str]) -> tuple[str, ...] | None:
if data is None:
return data
if isinstance(data, Iterable) and all([isinstance(x, str) for x in data]):
Expand All@@ -432,12 +436,11 @@ def parse_dimension_names(data: Any) -> tuple[str, ...] | None:


# todo: real validation
def parse_attributes(data: Any) -> dict[str, JSON]:
def parse_attributes(data: None | dict[str, JSON]) -> dict[str, JSON]:
if data is None:
return {}

data_json = cast(dict[str, JSON], data)
return data_json
return data


# todo: move to its own module and drop _v3 suffix
Expand Down
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
Finish typing zarr.metadata#1880

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to your account

 Merged

jhamman
merged 1 commit into

from

May 21, 2024
 Merged


Finish typing zarr.metadata
#1880
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1 change: 0 additions & 1 deletion
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -241,7 +241,6 @@ module = [
 "zarr.array",
 "zarr.common",
 "zarr.group",
 "zarr.metadata"
]
disallow_untyped_defs = false

Expand Down

2 changes: 2 additions & 0 deletions
src/zarr/array.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -199,6 +199,8 @@ async def _create_v3(

 if chunk_key_encoding is None:
 chunk_key_encoding = ("default", "/")
 assert chunk_key_encoding is not None

 if isinstance(chunk_key_encoding, tuple):
 chunk_key_encoding = (
 V2ChunkKeyEncoding(separator=chunk_key_encoding[1])
Expand Down

8 changes: 4 additions & 4 deletions
src/zarr/chunk_grids.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@
import itertools
from collections.abc import Iterator
from dataclasses import dataclass
from typing import TYPE_CHECKING, Any
from typing import TYPE_CHECKING

from zarr.abc.metadata import Metadata
from zarr.common import (
Expand All@@ -22,13 +22,13 @@
@dataclass(frozen=True)
class ChunkGrid(Metadata):
 @classmethod
 def from_dict(cls, data: dict[str, JSON]) -> ChunkGrid:
 def from_dict(cls, data: dict[str, JSON] | ChunkGrid) -> ChunkGrid:
@jhammanjhammanMay 21, 2024

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Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

your change is fine but I don't know why from_dict accepts a ChunkGrid object. 🤷
 if isinstance(data, ChunkGrid):
 return data

 name_parsed, _ = parse_named_configuration(data)
 if name_parsed == "regular":
 return RegularChunkGrid.from_dict(data)
 return RegularChunkGrid._from_dict(data)
 raise ValueError(f"Unknown chunk grid. Got {name_parsed}.")

 def all_chunk_coords(self, array_shape: ChunkCoords) -> Iterator[ChunkCoords]:
Expand All@@ -45,7 +45,7 @@ def __init__(self, *, chunk_shape: ChunkCoordsLike) -> None:
 object.__setattr__(self, "chunk_shape", chunk_shape_parsed)

 @classmethod
 def from_dict(cls, data: dict[str, Any]) -> Self:
 def _from_dict(cls, data: dict[str, JSON]) -> Self:
 _, configuration_parsed = parse_named_configuration(data, "regular")

 return cls(**configuration_parsed) # type: ignore[arg-type]
Expand Down

2 changes: 1 addition & 1 deletion
src/zarr/chunk_key_encodings.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -34,7 +34,7 @@ def __init__(self, *, separator: SeparatorLiteral) -> None:
 object.__setattr__(self, "separator", separator_parsed)

 @classmethod
 def from_dict(cls, data: dict[str, JSON]) -> ChunkKeyEncoding:
 def from_dict(cls, data: dict[str, JSON] | ChunkKeyEncoding) -> ChunkKeyEncoding:
 if isinstance(data, ChunkKeyEncoding):
 return data

Expand Down

5 changes: 3 additions & 2 deletions
src/zarr/common.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@
 from collections.abc import Awaitable, Callable, Iterator

import numpy as np
import numpy.typing as npt

ZARR_JSON = "zarr.json"
ZARRAY_JSON = ".zarray"
Expand DownExpand Up@@ -150,7 +151,7 @@ def parse_named_configuration(
 return name_parsed, configuration_parsed


def parse_shapelike(data: Any) -> tuple[int, ...]:
def parse_shapelike(data: Iterable[int]) -> tuple[int, ...]:
 if not isinstance(data, Iterable):
 raise TypeError(f"Expected an iterable. Got {data} instead.")
 data_tuple = tuple(data)
Expand All@@ -164,7 +165,7 @@ def parse_shapelike(data: Any) -> tuple[int, ...]:
 return data_tuple


def parse_dtype(data: Any) -> np.dtype[Any]:
def parse_dtype(data: npt.DTypeLike) -> np.dtype[Any]:
 # todo: real validation
 return np.dtype(data)

Expand Down

41 changes: 22 additions & 19 deletions
src/zarr/metadata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -22,6 +22,7 @@

 from typing_extensions import Self

import numcodecs.abc

from zarr.common import (
 JSON,
Expand DownExpand Up@@ -168,15 +169,15 @@ class ArrayV3Metadata(ArrayMetadata):
 def __init__(
 self,
 *,
 shape,
 data_type,
 chunk_grid,
 chunk_key_encoding,
 fill_value,
 codecs,
 attributes,
 dimension_names,
 ):
 shape: Iterable[int],
 data_type: npt.DTypeLike,
 chunk_grid: dict[str, JSON] | ChunkGrid,
 chunk_key_encoding: dict[str, JSON] | ChunkKeyEncoding,
 fill_value: Any,
 codecs: Iterable[Codec | JSON],
 attributes: None | dict[str, JSON],
 dimension_names: None | Iterable[str],
 ) -> None:
 """
 Because the class is a frozen dataclass, we set attributes using object.__setattr__
 """
Expand DownExpand Up@@ -249,14 +250,14 @@ def encode_chunk_key(self, chunk_coords: ChunkCoords) -> str:
 return self.chunk_key_encoding.encode_chunk_key(chunk_coords)

 def to_buffer_dict(self) -> dict[str, Buffer]:
 def _json_convert(o):
 def _json_convert(o: np.dtype[Any] | Enum | Codec) -> str | dict[str, Any]:
 if isinstance(o, np.dtype):
 return str(o)
 if isinstance(o, Enum):
 return o.name
 # this serializes numcodecs compressors
 # todo: implement to_dict for codecs
 elif hasattr(o, "get_config"):
 elif isinstance(o, numcodecs.abc.Codec):
 return o.get_config()
 raise TypeError

Expand All@@ -271,9 +272,10 @@ def from_dict(cls, data: dict[str, JSON]) -> ArrayV3Metadata:
 # check that the node_type attribute is correct
 _ = parse_node_type_array(data.pop("node_type"))

 dimension_names = data.pop("dimension_names", None)
data["dimension_names"] = data.pop("dimension_names", None)

 return cls(**data, dimension_names=dimension_names)
 # TODO: Remove the ignores and use a TypedDict to type `data`
 return cls(**data) # type: ignore[arg-type]

 def to_dict(self) -> dict[str, Any]:
 out_dict = super().to_dict()
Expand DownExpand Up@@ -367,7 +369,9 @@ def codec_pipeline(self) -> CodecPipeline:
 )

 def to_buffer_dict(self) -> dict[str, Buffer]:
 def _json_convert(o):
 def _json_convert(
 o: np.dtype[Any],
 ) -> str | list[tuple[str, str] | tuple[str, str, tuple[int, ...]]]:
 if isinstance(o, np.dtype):
 if o.fields is None:
 return o.str
Expand DownExpand Up@@ -399,7 +403,7 @@ def to_dict(self) -> JSON:
 zarray_dict["chunks"] = self.chunk_grid.chunk_shape

 _ = zarray_dict.pop("data_type")
 zarray_dict["dtype"] = self.data_type
 zarray_dict["dtype"] = self.data_type.str

 return zarray_dict

Expand All@@ -422,7 +426,7 @@ def update_attributes(self, attributes: dict[str, JSON]) -> Self:
 return replace(self, attributes=attributes)


def parse_dimension_names(data: Any) -> tuple[str, ...] | None:
def parse_dimension_names(data: None | Iterable[str]) -> tuple[str, ...] | None:
 if data is None:
 return data
 if isinstance(data, Iterable) and all([isinstance(x, str) for x in data]):
Expand All@@ -432,12 +436,11 @@ def parse_dimension_names(data: Any) -> tuple[str, ...] | None:


# todo: real validation
def parse_attributes(data: Any) -> dict[str, JSON]:
def parse_attributes(data: None | dict[str, JSON]) -> dict[str, JSON]:
 if data is None:
 return {}

 data_json = cast(dict[str, JSON], data)
 return data_json
 return data


# todo: move to its own module and drop _v3 suffix
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Finish typing zarr.metadata#1880

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
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to your account

 Merged

jhamman
merged 1 commit into

from

May 21, 2024
 Merged


Finish typing zarr.metadata
#1880
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1 change: 0 additions & 1 deletion
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -241,7 +241,6 @@ module = [
 "zarr.array",
 "zarr.common",
 "zarr.group",
 "zarr.metadata"
]
disallow_untyped_defs = false

Expand Down

2 changes: 2 additions & 0 deletions
src/zarr/array.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -199,6 +199,8 @@ async def _create_v3(

 if chunk_key_encoding is None:
 chunk_key_encoding = ("default", "/")
 assert chunk_key_encoding is not None

 if isinstance(chunk_key_encoding, tuple):
 chunk_key_encoding = (
 V2ChunkKeyEncoding(separator=chunk_key_encoding[1])
Expand Down

8 changes: 4 additions & 4 deletions
src/zarr/chunk_grids.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@
import itertools
from collections.abc import Iterator
from dataclasses import dataclass
from typing import TYPE_CHECKING, Any
from typing import TYPE_CHECKING

from zarr.abc.metadata import Metadata
from zarr.common import (
Expand All@@ -22,13 +22,13 @@
@dataclass(frozen=True)
class ChunkGrid(Metadata):
 @classmethod
 def from_dict(cls, data: dict[str, JSON]) -> ChunkGrid:
 def from_dict(cls, data: dict[str, JSON] | ChunkGrid) -> ChunkGrid:
@jhammanjhammanMay 21, 2024

Copy link


Copy Markdown

Member
Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

your change is fine but I don't know why from_dict accepts a ChunkGrid object. 🤷
 if isinstance(data, ChunkGrid):
 return data

 name_parsed, _ = parse_named_configuration(data)
 if name_parsed == "regular":
 return RegularChunkGrid.from_dict(data)
 return RegularChunkGrid._from_dict(data)
 raise ValueError(f"Unknown chunk grid. Got {name_parsed}.")

 def all_chunk_coords(self, array_shape: ChunkCoords) -> Iterator[ChunkCoords]:
Expand All@@ -45,7 +45,7 @@ def __init__(self, *, chunk_shape: ChunkCoordsLike) -> None:
 object.__setattr__(self, "chunk_shape", chunk_shape_parsed)

 @classmethod
 def from_dict(cls, data: dict[str, Any]) -> Self:
 def _from_dict(cls, data: dict[str, JSON]) -> Self:
 _, configuration_parsed = parse_named_configuration(data, "regular")

 return cls(**configuration_parsed) # type: ignore[arg-type]
Expand Down

2 changes: 1 addition & 1 deletion
src/zarr/chunk_key_encodings.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -34,7 +34,7 @@ def __init__(self, *, separator: SeparatorLiteral) -> None:
 object.__setattr__(self, "separator", separator_parsed)

 @classmethod
 def from_dict(cls, data: dict[str, JSON]) -> ChunkKeyEncoding:
 def from_dict(cls, data: dict[str, JSON] | ChunkKeyEncoding) -> ChunkKeyEncoding:
 if isinstance(data, ChunkKeyEncoding):
 return data

Expand Down

5 changes: 3 additions & 2 deletions
src/zarr/common.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@
 from collections.abc import Awaitable, Callable, Iterator

import numpy as np
import numpy.typing as npt

ZARR_JSON = "zarr.json"
ZARRAY_JSON = ".zarray"
Expand DownExpand Up@@ -150,7 +151,7 @@ def parse_named_configuration(
 return name_parsed, configuration_parsed


def parse_shapelike(data: Any) -> tuple[int, ...]:
def parse_shapelike(data: Iterable[int]) -> tuple[int, ...]:
 if not isinstance(data, Iterable):
 raise TypeError(f"Expected an iterable. Got {data} instead.")
 data_tuple = tuple(data)
Expand All@@ -164,7 +165,7 @@ def parse_shapelike(data: Any) -> tuple[int, ...]:
 return data_tuple


def parse_dtype(data: Any) -> np.dtype[Any]:
def parse_dtype(data: npt.DTypeLike) -> np.dtype[Any]:
 # todo: real validation
 return np.dtype(data)

Expand Down

41 changes: 22 additions & 19 deletions
src/zarr/metadata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -22,6 +22,7 @@

 from typing_extensions import Self

import numcodecs.abc

from zarr.common import (
 JSON,
Expand DownExpand Up@@ -168,15 +169,15 @@ class ArrayV3Metadata(ArrayMetadata):
 def __init__(
 self,
 *,
 shape,
 data_type,
 chunk_grid,
 chunk_key_encoding,
 fill_value,
 codecs,
 attributes,
 dimension_names,
 ):
 shape: Iterable[int],
 data_type: npt.DTypeLike,
 chunk_grid: dict[str, JSON] | ChunkGrid,
 chunk_key_encoding: dict[str, JSON] | ChunkKeyEncoding,
 fill_value: Any,
 codecs: Iterable[Codec | JSON],
 attributes: None | dict[str, JSON],
 dimension_names: None | Iterable[str],
 ) -> None:
 """
 Because the class is a frozen dataclass, we set attributes using object.__setattr__
 """
Expand DownExpand Up@@ -249,14 +250,14 @@ def encode_chunk_key(self, chunk_coords: ChunkCoords) -> str:
 return self.chunk_key_encoding.encode_chunk_key(chunk_coords)

 def to_buffer_dict(self) -> dict[str, Buffer]:
 def _json_convert(o):
 def _json_convert(o: np.dtype[Any] | Enum | Codec) -> str | dict[str, Any]:
 if isinstance(o, np.dtype):
 return str(o)
 if isinstance(o, Enum):
 return o.name
 # this serializes numcodecs compressors
 # todo: implement to_dict for codecs
 elif hasattr(o, "get_config"):
 elif isinstance(o, numcodecs.abc.Codec):
 return o.get_config()
 raise TypeError

Expand All@@ -271,9 +272,10 @@ def from_dict(cls, data: dict[str, JSON]) -> ArrayV3Metadata:
 # check that the node_type attribute is correct
 _ = parse_node_type_array(data.pop("node_type"))

 dimension_names = data.pop("dimension_names", None)
data["dimension_names"] = data.pop("dimension_names", None)

 return cls(**data, dimension_names=dimension_names)
 # TODO: Remove the ignores and use a TypedDict to type `data`
 return cls(**data) # type: ignore[arg-type]

 def to_dict(self) -> dict[str, Any]:
 out_dict = super().to_dict()
Expand DownExpand Up@@ -367,7 +369,9 @@ def codec_pipeline(self) -> CodecPipeline:
 )

 def to_buffer_dict(self) -> dict[str, Buffer]:
 def _json_convert(o):
 def _json_convert(
 o: np.dtype[Any],
 ) -> str | list[tuple[str, str] | tuple[str, str, tuple[int, ...]]]:
 if isinstance(o, np.dtype):
 if o.fields is None:
 return o.str
Expand DownExpand Up@@ -399,7 +403,7 @@ def to_dict(self) -> JSON:
 zarray_dict["chunks"] = self.chunk_grid.chunk_shape

 _ = zarray_dict.pop("data_type")
 zarray_dict["dtype"] = self.data_type
 zarray_dict["dtype"] = self.data_type.str

 return zarray_dict

Expand All@@ -422,7 +426,7 @@ def update_attributes(self, attributes: dict[str, JSON]) -> Self:
 return replace(self, attributes=attributes)


def parse_dimension_names(data: Any) -> tuple[str, ...] | None:
def parse_dimension_names(data: None | Iterable[str]) -> tuple[str, ...] | None:
 if data is None:
 return data
 if isinstance(data, Iterable) and all([isinstance(x, str) for x in data]):
Expand All@@ -432,12 +436,11 @@ def parse_dimension_names(data: Any) -> tuple[str, ...] | None:


# todo: real validation
def parse_attributes(data: Any) -> dict[str, JSON]:
def parse_attributes(data: None | dict[str, JSON]) -> dict[str, JSON]:
 if data is None:
 return {}

 data_json = cast(dict[str, JSON], data)
 return data_json
 return data


# todo: move to its own module and drop _v3 suffix
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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 Merged

jhamman
merged 1 commit into

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May 21, 2024
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Finish typing zarr.metadata
#1880
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1 change: 0 additions & 1 deletion
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -241,7 +241,6 @@ module = [
 "zarr.array",
 "zarr.common",
 "zarr.group",
 "zarr.metadata"
]
disallow_untyped_defs = false

Expand Down

2 changes: 2 additions & 0 deletions
src/zarr/array.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -199,6 +199,8 @@ async def _create_v3(

 if chunk_key_encoding is None:
 chunk_key_encoding = ("default", "/")
 assert chunk_key_encoding is not None

 if isinstance(chunk_key_encoding, tuple):
 chunk_key_encoding = (
 V2ChunkKeyEncoding(separator=chunk_key_encoding[1])
Expand Down

8 changes: 4 additions & 4 deletions
src/zarr/chunk_grids.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@
import itertools
from collections.abc import Iterator
from dataclasses import dataclass
from typing import TYPE_CHECKING, Any
from typing import TYPE_CHECKING

from zarr.abc.metadata import Metadata
from zarr.common import (
Expand All@@ -22,13 +22,13 @@
@dataclass(frozen=True)
class ChunkGrid(Metadata):
 @classmethod
 def from_dict(cls, data: dict[str, JSON]) -> ChunkGrid:
 def from_dict(cls, data: dict[str, JSON] | ChunkGrid) -> ChunkGrid:
@jhammanjhammanMay 21, 2024

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Choose a reason for hiding this comment

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your change is fine but I don't know why from_dict accepts a ChunkGrid object. 🤷
 if isinstance(data, ChunkGrid):
 return data

 name_parsed, _ = parse_named_configuration(data)
 if name_parsed == "regular":
 return RegularChunkGrid.from_dict(data)
 return RegularChunkGrid._from_dict(data)
 raise ValueError(f"Unknown chunk grid. Got {name_parsed}.")

 def all_chunk_coords(self, array_shape: ChunkCoords) -> Iterator[ChunkCoords]:
Expand All@@ -45,7 +45,7 @@ def __init__(self, *, chunk_shape: ChunkCoordsLike) -> None:
 object.__setattr__(self, "chunk_shape", chunk_shape_parsed)

 @classmethod
 def from_dict(cls, data: dict[str, Any]) -> Self:
 def _from_dict(cls, data: dict[str, JSON]) -> Self:
 _, configuration_parsed = parse_named_configuration(data, "regular")

 return cls(**configuration_parsed) # type: ignore[arg-type]
Expand Down

2 changes: 1 addition & 1 deletion
src/zarr/chunk_key_encodings.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -34,7 +34,7 @@ def __init__(self, *, separator: SeparatorLiteral) -> None:
 object.__setattr__(self, "separator", separator_parsed)

 @classmethod
 def from_dict(cls, data: dict[str, JSON]) -> ChunkKeyEncoding:
 def from_dict(cls, data: dict[str, JSON] | ChunkKeyEncoding) -> ChunkKeyEncoding:
 if isinstance(data, ChunkKeyEncoding):
 return data

Expand Down

5 changes: 3 additions & 2 deletions
src/zarr/common.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@
 from collections.abc import Awaitable, Callable, Iterator

import numpy as np
import numpy.typing as npt

ZARR_JSON = "zarr.json"
ZARRAY_JSON = ".zarray"
Expand DownExpand Up@@ -150,7 +151,7 @@ def parse_named_configuration(
 return name_parsed, configuration_parsed


def parse_shapelike(data: Any) -> tuple[int, ...]:
def parse_shapelike(data: Iterable[int]) -> tuple[int, ...]:
 if not isinstance(data, Iterable):
 raise TypeError(f"Expected an iterable. Got {data} instead.")
 data_tuple = tuple(data)
Expand All@@ -164,7 +165,7 @@ def parse_shapelike(data: Any) -> tuple[int, ...]:
 return data_tuple


def parse_dtype(data: Any) -> np.dtype[Any]:
def parse_dtype(data: npt.DTypeLike) -> np.dtype[Any]:
 # todo: real validation
 return np.dtype(data)

Expand Down

41 changes: 22 additions & 19 deletions
src/zarr/metadata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -22,6 +22,7 @@

 from typing_extensions import Self

import numcodecs.abc

from zarr.common import (
 JSON,
Expand DownExpand Up@@ -168,15 +169,15 @@ class ArrayV3Metadata(ArrayMetadata):
 def __init__(
 self,
 *,
 shape,
 data_type,
 chunk_grid,
 chunk_key_encoding,
 fill_value,
 codecs,
 attributes,
 dimension_names,
 ):
 shape: Iterable[int],
 data_type: npt.DTypeLike,
 chunk_grid: dict[str, JSON] | ChunkGrid,
 chunk_key_encoding: dict[str, JSON] | ChunkKeyEncoding,
 fill_value: Any,
 codecs: Iterable[Codec | JSON],
 attributes: None | dict[str, JSON],
 dimension_names: None | Iterable[str],
 ) -> None:
 """
 Because the class is a frozen dataclass, we set attributes using object.__setattr__
 """
Expand DownExpand Up@@ -249,14 +250,14 @@ def encode_chunk_key(self, chunk_coords: ChunkCoords) -> str:
 return self.chunk_key_encoding.encode_chunk_key(chunk_coords)

 def to_buffer_dict(self) -> dict[str, Buffer]:
 def _json_convert(o):
 def _json_convert(o: np.dtype[Any] | Enum | Codec) -> str | dict[str, Any]:
 if isinstance(o, np.dtype):
 return str(o)
 if isinstance(o, Enum):
 return o.name
 # this serializes numcodecs compressors
 # todo: implement to_dict for codecs
 elif hasattr(o, "get_config"):
 elif isinstance(o, numcodecs.abc.Codec):
 return o.get_config()
 raise TypeError

Expand All@@ -271,9 +272,10 @@ def from_dict(cls, data: dict[str, JSON]) -> ArrayV3Metadata:
 # check that the node_type attribute is correct
 _ = parse_node_type_array(data.pop("node_type"))

 dimension_names = data.pop("dimension_names", None)
data["dimension_names"] = data.pop("dimension_names", None)

 return cls(**data, dimension_names=dimension_names)
 # TODO: Remove the ignores and use a TypedDict to type `data`
 return cls(**data) # type: ignore[arg-type]

 def to_dict(self) -> dict[str, Any]:
 out_dict = super().to_dict()
Expand DownExpand Up@@ -367,7 +369,9 @@ def codec_pipeline(self) -> CodecPipeline:
 )

 def to_buffer_dict(self) -> dict[str, Buffer]:
 def _json_convert(o):
 def _json_convert(
 o: np.dtype[Any],
 ) -> str | list[tuple[str, str] | tuple[str, str, tuple[int, ...]]]:
 if isinstance(o, np.dtype):
 if o.fields is None:
 return o.str
Expand DownExpand Up@@ -399,7 +403,7 @@ def to_dict(self) -> JSON:
 zarray_dict["chunks"] = self.chunk_grid.chunk_shape

 _ = zarray_dict.pop("data_type")
 zarray_dict["dtype"] = self.data_type
 zarray_dict["dtype"] = self.data_type.str

 return zarray_dict

Expand All@@ -422,7 +426,7 @@ def update_attributes(self, attributes: dict[str, JSON]) -> Self:
 return replace(self, attributes=attributes)


def parse_dimension_names(data: Any) -> tuple[str, ...] | None:
def parse_dimension_names(data: None | Iterable[str]) -> tuple[str, ...] | None:
 if data is None:
 return data
 if isinstance(data, Iterable) and all([isinstance(x, str) for x in data]):
Expand All@@ -432,12 +436,11 @@ def parse_dimension_names(data: Any) -> tuple[str, ...] | None:


# todo: real validation
def parse_attributes(data: Any) -> dict[str, JSON]:
def parse_attributes(data: None | dict[str, JSON]) -> dict[str, JSON]:
 if data is None:
 return {}

 data_json = cast(dict[str, JSON], data)
 return data_json
 return data


# todo: move to its own module and drop _v3 suffix
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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Finish typing zarr.metadata#1880

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 Merged

jhamman
merged 1 commit into

from

May 21, 2024
 Merged


Finish typing zarr.metadata
#1880
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1 change: 0 additions & 1 deletion
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -241,7 +241,6 @@ module = [
 "zarr.array",
 "zarr.common",
 "zarr.group",
 "zarr.metadata"
]
disallow_untyped_defs = false

Expand Down

2 changes: 2 additions & 0 deletions
src/zarr/array.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -199,6 +199,8 @@ async def _create_v3(

 if chunk_key_encoding is None:
 chunk_key_encoding = ("default", "/")
 assert chunk_key_encoding is not None

 if isinstance(chunk_key_encoding, tuple):
 chunk_key_encoding = (
 V2ChunkKeyEncoding(separator=chunk_key_encoding[1])
Expand Down

8 changes: 4 additions & 4 deletions
src/zarr/chunk_grids.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@
import itertools
from collections.abc import Iterator
from dataclasses import dataclass
from typing import TYPE_CHECKING, Any
from typing import TYPE_CHECKING

from zarr.abc.metadata import Metadata
from zarr.common import (
Expand All@@ -22,13 +22,13 @@
@dataclass(frozen=True)
class ChunkGrid(Metadata):
 @classmethod
 def from_dict(cls, data: dict[str, JSON]) -> ChunkGrid:
 def from_dict(cls, data: dict[str, JSON] | ChunkGrid) -> ChunkGrid:
@jhammanjhammanMay 21, 2024

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Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

your change is fine but I don't know why from_dict accepts a ChunkGrid object. 🤷
 if isinstance(data, ChunkGrid):
 return data

 name_parsed, _ = parse_named_configuration(data)
 if name_parsed == "regular":
 return RegularChunkGrid.from_dict(data)
 return RegularChunkGrid._from_dict(data)
 raise ValueError(f"Unknown chunk grid. Got {name_parsed}.")

 def all_chunk_coords(self, array_shape: ChunkCoords) -> Iterator[ChunkCoords]:
Expand All@@ -45,7 +45,7 @@ def __init__(self, *, chunk_shape: ChunkCoordsLike) -> None:
 object.__setattr__(self, "chunk_shape", chunk_shape_parsed)

 @classmethod
 def from_dict(cls, data: dict[str, Any]) -> Self:
 def _from_dict(cls, data: dict[str, JSON]) -> Self:
 _, configuration_parsed = parse_named_configuration(data, "regular")

 return cls(**configuration_parsed) # type: ignore[arg-type]
Expand Down

2 changes: 1 addition & 1 deletion
src/zarr/chunk_key_encodings.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -34,7 +34,7 @@ def __init__(self, *, separator: SeparatorLiteral) -> None:
 object.__setattr__(self, "separator", separator_parsed)

 @classmethod
 def from_dict(cls, data: dict[str, JSON]) -> ChunkKeyEncoding:
 def from_dict(cls, data: dict[str, JSON] | ChunkKeyEncoding) -> ChunkKeyEncoding:
 if isinstance(data, ChunkKeyEncoding):
 return data

Expand Down

5 changes: 3 additions & 2 deletions
src/zarr/common.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@
 from collections.abc import Awaitable, Callable, Iterator

import numpy as np
import numpy.typing as npt

ZARR_JSON = "zarr.json"
ZARRAY_JSON = ".zarray"
Expand DownExpand Up@@ -150,7 +151,7 @@ def parse_named_configuration(
 return name_parsed, configuration_parsed


def parse_shapelike(data: Any) -> tuple[int, ...]:
def parse_shapelike(data: Iterable[int]) -> tuple[int, ...]:
 if not isinstance(data, Iterable):
 raise TypeError(f"Expected an iterable. Got {data} instead.")
 data_tuple = tuple(data)
Expand All@@ -164,7 +165,7 @@ def parse_shapelike(data: Any) -> tuple[int, ...]:
 return data_tuple


def parse_dtype(data: Any) -> np.dtype[Any]:
def parse_dtype(data: npt.DTypeLike) -> np.dtype[Any]:
 # todo: real validation
 return np.dtype(data)

Expand Down

41 changes: 22 additions & 19 deletions
src/zarr/metadata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -22,6 +22,7 @@

 from typing_extensions import Self

import numcodecs.abc

from zarr.common import (
 JSON,
Expand DownExpand Up@@ -168,15 +169,15 @@ class ArrayV3Metadata(ArrayMetadata):
 def __init__(
 self,
 *,
 shape,
 data_type,
 chunk_grid,
 chunk_key_encoding,
 fill_value,
 codecs,
 attributes,
 dimension_names,
 ):
 shape: Iterable[int],
 data_type: npt.DTypeLike,
 chunk_grid: dict[str, JSON] | ChunkGrid,
 chunk_key_encoding: dict[str, JSON] | ChunkKeyEncoding,
 fill_value: Any,
 codecs: Iterable[Codec | JSON],
 attributes: None | dict[str, JSON],
 dimension_names: None | Iterable[str],
 ) -> None:
 """
 Because the class is a frozen dataclass, we set attributes using object.__setattr__
 """
Expand DownExpand Up@@ -249,14 +250,14 @@ def encode_chunk_key(self, chunk_coords: ChunkCoords) -> str:
 return self.chunk_key_encoding.encode_chunk_key(chunk_coords)

 def to_buffer_dict(self) -> dict[str, Buffer]:
 def _json_convert(o):
 def _json_convert(o: np.dtype[Any] | Enum | Codec) -> str | dict[str, Any]:
 if isinstance(o, np.dtype):
 return str(o)
 if isinstance(o, Enum):
 return o.name
 # this serializes numcodecs compressors
 # todo: implement to_dict for codecs
 elif hasattr(o, "get_config"):
 elif isinstance(o, numcodecs.abc.Codec):
 return o.get_config()
 raise TypeError

Expand All@@ -271,9 +272,10 @@ def from_dict(cls, data: dict[str, JSON]) -> ArrayV3Metadata:
 # check that the node_type attribute is correct
 _ = parse_node_type_array(data.pop("node_type"))

 dimension_names = data.pop("dimension_names", None)
data["dimension_names"] = data.pop("dimension_names", None)

 return cls(**data, dimension_names=dimension_names)
 # TODO: Remove the ignores and use a TypedDict to type `data`
 return cls(**data) # type: ignore[arg-type]

 def to_dict(self) -> dict[str, Any]:
 out_dict = super().to_dict()
Expand DownExpand Up@@ -367,7 +369,9 @@ def codec_pipeline(self) -> CodecPipeline:
 )

 def to_buffer_dict(self) -> dict[str, Buffer]:
 def _json_convert(o):
 def _json_convert(
 o: np.dtype[Any],
 ) -> str | list[tuple[str, str] | tuple[str, str, tuple[int, ...]]]:
 if isinstance(o, np.dtype):
 if o.fields is None:
 return o.str
Expand DownExpand Up@@ -399,7 +403,7 @@ def to_dict(self) -> JSON:
 zarray_dict["chunks"] = self.chunk_grid.chunk_shape

 _ = zarray_dict.pop("data_type")
 zarray_dict["dtype"] = self.data_type
 zarray_dict["dtype"] = self.data_type.str

 return zarray_dict

Expand All@@ -422,7 +426,7 @@ def update_attributes(self, attributes: dict[str, JSON]) -> Self:
 return replace(self, attributes=attributes)


def parse_dimension_names(data: Any) -> tuple[str, ...] | None:
def parse_dimension_names(data: None | Iterable[str]) -> tuple[str, ...] | None:
 if data is None:
 return data
 if isinstance(data, Iterable) and all([isinstance(x, str) for x in data]):
Expand All@@ -432,12 +436,11 @@ def parse_dimension_names(data: Any) -> tuple[str, ...] | None:


# todo: real validation
def parse_attributes(data: Any) -> dict[str, JSON]:
def parse_attributes(data: None | dict[str, JSON]) -> dict[str, JSON]:
 if data is None:
 return {}

 data_json = cast(dict[str, JSON], data)
 return data_json
 return data


# todo: move to its own module and drop _v3 suffix
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Finish typing zarr.metadata#1880

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

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Already on GitHub?
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to your account

 Merged

jhamman
merged 1 commit into

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May 21, 2024
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Finish typing zarr.metadata
#1880
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1 change: 0 additions & 1 deletion
pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -241,7 +241,6 @@ module = [
 "zarr.array",
 "zarr.common",
 "zarr.group",
 "zarr.metadata"
]
disallow_untyped_defs = false

Expand Down

2 changes: 2 additions & 0 deletions
src/zarr/array.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -199,6 +199,8 @@ async def _create_v3(

 if chunk_key_encoding is None:
 chunk_key_encoding = ("default", "/")
 assert chunk_key_encoding is not None

 if isinstance(chunk_key_encoding, tuple):
 chunk_key_encoding = (
 V2ChunkKeyEncoding(separator=chunk_key_encoding[1])
Expand Down

8 changes: 4 additions & 4 deletions
src/zarr/chunk_grids.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@
import itertools
from collections.abc import Iterator
from dataclasses import dataclass
from typing import TYPE_CHECKING, Any
from typing import TYPE_CHECKING

from zarr.abc.metadata import Metadata
from zarr.common import (
Expand All@@ -22,13 +22,13 @@
@dataclass(frozen=True)
class ChunkGrid(Metadata):
 @classmethod
 def from_dict(cls, data: dict[str, JSON]) -> ChunkGrid:
 def from_dict(cls, data: dict[str, JSON] | ChunkGrid) -> ChunkGrid:
@jhammanjhammanMay 21, 2024

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your change is fine but I don't know why from_dict accepts a ChunkGrid object. 🤷
 if isinstance(data, ChunkGrid):
 return data

 name_parsed, _ = parse_named_configuration(data)
 if name_parsed == "regular":
 return RegularChunkGrid.from_dict(data)
 return RegularChunkGrid._from_dict(data)
 raise ValueError(f"Unknown chunk grid. Got {name_parsed}.")

 def all_chunk_coords(self, array_shape: ChunkCoords) -> Iterator[ChunkCoords]:
Expand All@@ -45,7 +45,7 @@ def __init__(self, *, chunk_shape: ChunkCoordsLike) -> None:
 object.__setattr__(self, "chunk_shape", chunk_shape_parsed)

 @classmethod
 def from_dict(cls, data: dict[str, Any]) -> Self:
 def _from_dict(cls, data: dict[str, JSON]) -> Self:
 _, configuration_parsed = parse_named_configuration(data, "regular")

 return cls(**configuration_parsed) # type: ignore[arg-type]
Expand Down

2 changes: 1 addition & 1 deletion
src/zarr/chunk_key_encodings.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -34,7 +34,7 @@ def __init__(self, *, separator: SeparatorLiteral) -> None:
 object.__setattr__(self, "separator", separator_parsed)

 @classmethod
 def from_dict(cls, data: dict[str, JSON]) -> ChunkKeyEncoding:
 def from_dict(cls, data: dict[str, JSON] | ChunkKeyEncoding) -> ChunkKeyEncoding:
 if isinstance(data, ChunkKeyEncoding):
 return data

Expand Down

5 changes: 3 additions & 2 deletions
src/zarr/common.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@
 from collections.abc import Awaitable, Callable, Iterator

import numpy as np
import numpy.typing as npt

ZARR_JSON = "zarr.json"
ZARRAY_JSON = ".zarray"
Expand DownExpand Up@@ -150,7 +151,7 @@ def parse_named_configuration(
 return name_parsed, configuration_parsed


def parse_shapelike(data: Any) -> tuple[int, ...]:
def parse_shapelike(data: Iterable[int]) -> tuple[int, ...]:
 if not isinstance(data, Iterable):
 raise TypeError(f"Expected an iterable. Got {data} instead.")
 data_tuple = tuple(data)
Expand All@@ -164,7 +165,7 @@ def parse_shapelike(data: Any) -> tuple[int, ...]:
 return data_tuple


def parse_dtype(data: Any) -> np.dtype[Any]:
def parse_dtype(data: npt.DTypeLike) -> np.dtype[Any]:
 # todo: real validation
 return np.dtype(data)

Expand Down

41 changes: 22 additions & 19 deletions
src/zarr/metadata.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -22,6 +22,7 @@

 from typing_extensions import Self

import numcodecs.abc

from zarr.common import (
 JSON,
Expand DownExpand Up@@ -168,15 +169,15 @@ class ArrayV3Metadata(ArrayMetadata):
 def __init__(
 self,
 *,
 shape,
 data_type,
 chunk_grid,
 chunk_key_encoding,
 fill_value,
 codecs,
 attributes,
 dimension_names,
 ):
 shape: Iterable[int],
 data_type: npt.DTypeLike,
 chunk_grid: dict[str, JSON] | ChunkGrid,
 chunk_key_encoding: dict[str, JSON] | ChunkKeyEncoding,
 fill_value: Any,
 codecs: Iterable[Codec | JSON],
 attributes: None | dict[str, JSON],
 dimension_names: None | Iterable[str],
 ) -> None:
 """
 Because the class is a frozen dataclass, we set attributes using object.__setattr__
 """
Expand DownExpand Up@@ -249,14 +250,14 @@ def encode_chunk_key(self, chunk_coords: ChunkCoords) -> str:
 return self.chunk_key_encoding.encode_chunk_key(chunk_coords)

 def to_buffer_dict(self) -> dict[str, Buffer]:
 def _json_convert(o):
 def _json_convert(o: np.dtype[Any] | Enum | Codec) -> str | dict[str, Any]:
 if isinstance(o, np.dtype):
 return str(o)
 if isinstance(o, Enum):
 return o.name
 # this serializes numcodecs compressors
 # todo: implement to_dict for codecs
 elif hasattr(o, "get_config"):
 elif isinstance(o, numcodecs.abc.Codec):
 return o.get_config()
 raise TypeError

Expand All@@ -271,9 +272,10 @@ def from_dict(cls, data: dict[str, JSON]) -> ArrayV3Metadata:
 # check that the node_type attribute is correct
 _ = parse_node_type_array(data.pop("node_type"))

 dimension_names = data.pop("dimension_names", None)
data["dimension_names"] = data.pop("dimension_names", None)

 return cls(**data, dimension_names=dimension_names)
 # TODO: Remove the ignores and use a TypedDict to type `data`
 return cls(**data) # type: ignore[arg-type]

 def to_dict(self) -> dict[str, Any]:
 out_dict = super().to_dict()
Expand DownExpand Up@@ -367,7 +369,9 @@ def codec_pipeline(self) -> CodecPipeline:
 )

 def to_buffer_dict(self) -> dict[str, Buffer]:
 def _json_convert(o):
 def _json_convert(
 o: np.dtype[Any],
 ) -> str | list[tuple[str, str] | tuple[str, str, tuple[int, ...]]]:
 if isinstance(o, np.dtype):
 if o.fields is None:
 return o.str
Expand DownExpand Up@@ -399,7 +403,7 @@ def to_dict(self) -> JSON:
 zarray_dict["chunks"] = self.chunk_grid.chunk_shape

 _ = zarray_dict.pop("data_type")
 zarray_dict["dtype"] = self.data_type
 zarray_dict["dtype"] = self.data_type.str

 return zarray_dict

Expand All@@ -422,7 +426,7 @@ def update_attributes(self, attributes: dict[str, JSON]) -> Self:
 return replace(self, attributes=attributes)


def parse_dimension_names(data: Any) -> tuple[str, ...] | None:
def parse_dimension_names(data: None | Iterable[str]) -> tuple[str, ...] | None:
 if data is None:
 return data
 if isinstance(data, Iterable) and all([isinstance(x, str) for x in data]):
Expand All@@ -432,12 +436,11 @@ def parse_dimension_names(data: Any) -> tuple[str, ...] | None:


# todo: real validation
def parse_attributes(data: Any) -> dict[str, JSON]:
def parse_attributes(data: None | dict[str, JSON]) -> dict[str, JSON]:
 if data is None:
 return {}

 data_json = cast(dict[str, JSON], data)
 return data_json
 return data


# todo: move to its own module and drop _v3 suffix
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Finish typing zarr.metadata#1880

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to your account

 Merged

jhamman
merged 1 commit into

from

May 21, 2024
 Merged


Finish typing zarr.metadata
#1880
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1 change: 0 additions & 1 deletion
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -241,7 +241,6 @@ module = [
 "zarr.array",
 "zarr.common",
 "zarr.group",
 "zarr.metadata"
]
disallow_untyped_defs = false

Expand Down

2 changes: 2 additions & 0 deletions
src/zarr/array.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -199,6 +199,8 @@ async def _create_v3(

 if chunk_key_encoding is None:
 chunk_key_encoding = ("default", "/")
 assert chunk_key_encoding is not None

 if isinstance(chunk_key_encoding, tuple):
 chunk_key_encoding = (
 V2ChunkKeyEncoding(separator=chunk_key_encoding[1])
Expand Down

8 changes: 4 additions & 4 deletions
src/zarr/chunk_grids.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@
import itertools
from collections.abc import Iterator
from dataclasses import dataclass
from typing import TYPE_CHECKING, Any
from typing import TYPE_CHECKING

from zarr.abc.metadata import Metadata
from zarr.common import (
Expand All@@ -22,13 +22,13 @@
@dataclass(frozen=True)
class ChunkGrid(Metadata):
 @classmethod
 def from_dict(cls, data: dict[str, JSON]) -> ChunkGrid:
 def from_dict(cls, data: dict[str, JSON] | ChunkGrid) -> ChunkGrid:
@jhammanjhammanMay 21, 2024

Copy link


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Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

your change is fine but I don't know why from_dict accepts a ChunkGrid object. 🤷
 if isinstance(data, ChunkGrid):
 return data

 name_parsed, _ = parse_named_configuration(data)
 if name_parsed == "regular":
 return RegularChunkGrid.from_dict(data)
 return RegularChunkGrid._from_dict(data)
 raise ValueError(f"Unknown chunk grid. Got {name_parsed}.")

 def all_chunk_coords(self, array_shape: ChunkCoords) -> Iterator[ChunkCoords]:
Expand All@@ -45,7 +45,7 @@ def __init__(self, *, chunk_shape: ChunkCoordsLike) -> None:
 object.__setattr__(self, "chunk_shape", chunk_shape_parsed)

 @classmethod
 def from_dict(cls, data: dict[str, Any]) -> Self:
 def _from_dict(cls, data: dict[str, JSON]) -> Self:
 _, configuration_parsed = parse_named_configuration(data, "regular")

 return cls(**configuration_parsed) # type: ignore[arg-type]
Expand Down

2 changes: 1 addition & 1 deletion
src/zarr/chunk_key_encodings.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -34,7 +34,7 @@ def __init__(self, *, separator: SeparatorLiteral) -> None:
 object.__setattr__(self, "separator", separator_parsed)

 @classmethod
 def from_dict(cls, data: dict[str, JSON]) -> ChunkKeyEncoding:
 def from_dict(cls, data: dict[str, JSON] | ChunkKeyEncoding) -> ChunkKeyEncoding:
 if isinstance(data, ChunkKeyEncoding):
 return data

Expand Down

5 changes: 3 additions & 2 deletions
src/zarr/common.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@
 from collections.abc import Awaitable, Callable, Iterator

import numpy as np
import numpy.typing as npt

ZARR_JSON = "zarr.json"
ZARRAY_JSON = ".zarray"
Expand DownExpand Up@@ -150,7 +151,7 @@ def parse_named_configuration(
 return name_parsed, configuration_parsed


def parse_shapelike(data: Any) -> tuple[int, ...]:
def parse_shapelike(data: Iterable[int]) -> tuple[int, ...]:
 if not isinstance(data, Iterable):
 raise TypeError(f"Expected an iterable. Got {data} instead.")
 data_tuple = tuple(data)
Expand All@@ -164,7 +165,7 @@ def parse_shapelike(data: Any) -> tuple[int, ...]:
 return data_tuple


def parse_dtype(data: Any) -> np.dtype[Any]:
def parse_dtype(data: npt.DTypeLike) -> np.dtype[Any]:
 # todo: real validation
 return np.dtype(data)

Expand Down

41 changes: 22 additions & 19 deletions
src/zarr/metadata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -22,6 +22,7 @@

 from typing_extensions import Self

import numcodecs.abc

from zarr.common import (
 JSON,
Expand DownExpand Up@@ -168,15 +169,15 @@ class ArrayV3Metadata(ArrayMetadata):
 def __init__(
 self,
 *,
 shape,
 data_type,
 chunk_grid,
 chunk_key_encoding,
 fill_value,
 codecs,
 attributes,
 dimension_names,
 ):
 shape: Iterable[int],
 data_type: npt.DTypeLike,
 chunk_grid: dict[str, JSON] | ChunkGrid,
 chunk_key_encoding: dict[str, JSON] | ChunkKeyEncoding,
 fill_value: Any,
 codecs: Iterable[Codec | JSON],
 attributes: None | dict[str, JSON],
 dimension_names: None | Iterable[str],
 ) -> None:
 """
 Because the class is a frozen dataclass, we set attributes using object.__setattr__
 """
Expand DownExpand Up@@ -249,14 +250,14 @@ def encode_chunk_key(self, chunk_coords: ChunkCoords) -> str:
 return self.chunk_key_encoding.encode_chunk_key(chunk_coords)

 def to_buffer_dict(self) -> dict[str, Buffer]:
 def _json_convert(o):
 def _json_convert(o: np.dtype[Any] | Enum | Codec) -> str | dict[str, Any]:
 if isinstance(o, np.dtype):
 return str(o)
 if isinstance(o, Enum):
 return o.name
 # this serializes numcodecs compressors
 # todo: implement to_dict for codecs
 elif hasattr(o, "get_config"):
 elif isinstance(o, numcodecs.abc.Codec):
 return o.get_config()
 raise TypeError

Expand All@@ -271,9 +272,10 @@ def from_dict(cls, data: dict[str, JSON]) -> ArrayV3Metadata:
 # check that the node_type attribute is correct
 _ = parse_node_type_array(data.pop("node_type"))

 dimension_names = data.pop("dimension_names", None)
data["dimension_names"] = data.pop("dimension_names", None)

 return cls(**data, dimension_names=dimension_names)
 # TODO: Remove the ignores and use a TypedDict to type `data`
 return cls(**data) # type: ignore[arg-type]

 def to_dict(self) -> dict[str, Any]:
 out_dict = super().to_dict()
Expand DownExpand Up@@ -367,7 +369,9 @@ def codec_pipeline(self) -> CodecPipeline:
 )

 def to_buffer_dict(self) -> dict[str, Buffer]:
 def _json_convert(o):
 def _json_convert(
 o: np.dtype[Any],
 ) -> str | list[tuple[str, str] | tuple[str, str, tuple[int, ...]]]:
 if isinstance(o, np.dtype):
 if o.fields is None:
 return o.str
Expand DownExpand Up@@ -399,7 +403,7 @@ def to_dict(self) -> JSON:
 zarray_dict["chunks"] = self.chunk_grid.chunk_shape

 _ = zarray_dict.pop("data_type")
 zarray_dict["dtype"] = self.data_type
 zarray_dict["dtype"] = self.data_type.str

 return zarray_dict

Expand All@@ -422,7 +426,7 @@ def update_attributes(self, attributes: dict[str, JSON]) -> Self:
 return replace(self, attributes=attributes)


def parse_dimension_names(data: Any) -> tuple[str, ...] | None:
def parse_dimension_names(data: None | Iterable[str]) -> tuple[str, ...] | None:
 if data is None:
 return data
 if isinstance(data, Iterable) and all([isinstance(x, str) for x in data]):
Expand All@@ -432,12 +436,11 @@ def parse_dimension_names(data: Any) -> tuple[str, ...] | None:


# todo: real validation
def parse_attributes(data: Any) -> dict[str, JSON]:
def parse_attributes(data: None | dict[str, JSON]) -> dict[str, JSON]:
 if data is None:
 return {}

 data_json = cast(dict[str, JSON], data)
 return data_json
 return data


# todo: move to its own module and drop _v3 suffix
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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Finish typing zarr.metadata#1880

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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privacy statement. We’ll occasionally send you account related emails.

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to your account

 Merged

jhamman
merged 1 commit into

from

May 21, 2024
 Merged


Finish typing zarr.metadata
#1880
Show file tree
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1 change: 0 additions & 1 deletion
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -241,7 +241,6 @@ module = [
 "zarr.array",
 "zarr.common",
 "zarr.group",
 "zarr.metadata"
]
disallow_untyped_defs = false

Expand Down

2 changes: 2 additions & 0 deletions
src/zarr/array.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -199,6 +199,8 @@ async def _create_v3(

 if chunk_key_encoding is None:
 chunk_key_encoding = ("default", "/")
 assert chunk_key_encoding is not None

 if isinstance(chunk_key_encoding, tuple):
 chunk_key_encoding = (
 V2ChunkKeyEncoding(separator=chunk_key_encoding[1])
Expand Down

8 changes: 4 additions & 4 deletions
src/zarr/chunk_grids.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@
import itertools
from collections.abc import Iterator
from dataclasses import dataclass
from typing import TYPE_CHECKING, Any
from typing import TYPE_CHECKING

from zarr.abc.metadata import Metadata
from zarr.common import (
Expand All@@ -22,13 +22,13 @@
@dataclass(frozen=True)
class ChunkGrid(Metadata):
 @classmethod
 def from_dict(cls, data: dict[str, JSON]) -> ChunkGrid:
 def from_dict(cls, data: dict[str, JSON] | ChunkGrid) -> ChunkGrid:
@jhammanjhammanMay 21, 2024

Copy link


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Member
Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

your change is fine but I don't know why from_dict accepts a ChunkGrid object. 🤷
 if isinstance(data, ChunkGrid):
 return data

 name_parsed, _ = parse_named_configuration(data)
 if name_parsed == "regular":
 return RegularChunkGrid.from_dict(data)
 return RegularChunkGrid._from_dict(data)
 raise ValueError(f"Unknown chunk grid. Got {name_parsed}.")

 def all_chunk_coords(self, array_shape: ChunkCoords) -> Iterator[ChunkCoords]:
Expand All@@ -45,7 +45,7 @@ def __init__(self, *, chunk_shape: ChunkCoordsLike) -> None:
 object.__setattr__(self, "chunk_shape", chunk_shape_parsed)

 @classmethod
 def from_dict(cls, data: dict[str, Any]) -> Self:
 def _from_dict(cls, data: dict[str, JSON]) -> Self:
 _, configuration_parsed = parse_named_configuration(data, "regular")

 return cls(**configuration_parsed) # type: ignore[arg-type]
Expand Down

2 changes: 1 addition & 1 deletion
src/zarr/chunk_key_encodings.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -34,7 +34,7 @@ def __init__(self, *, separator: SeparatorLiteral) -> None:
 object.__setattr__(self, "separator", separator_parsed)

 @classmethod
 def from_dict(cls, data: dict[str, JSON]) -> ChunkKeyEncoding:
 def from_dict(cls, data: dict[str, JSON] | ChunkKeyEncoding) -> ChunkKeyEncoding:
 if isinstance(data, ChunkKeyEncoding):
 return data

Expand Down

5 changes: 3 additions & 2 deletions
src/zarr/common.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@
 from collections.abc import Awaitable, Callable, Iterator

import numpy as np
import numpy.typing as npt

ZARR_JSON = "zarr.json"
ZARRAY_JSON = ".zarray"
Expand DownExpand Up@@ -150,7 +151,7 @@ def parse_named_configuration(
 return name_parsed, configuration_parsed


def parse_shapelike(data: Any) -> tuple[int, ...]:
def parse_shapelike(data: Iterable[int]) -> tuple[int, ...]:
 if not isinstance(data, Iterable):
 raise TypeError(f"Expected an iterable. Got {data} instead.")
 data_tuple = tuple(data)
Expand All@@ -164,7 +165,7 @@ def parse_shapelike(data: Any) -> tuple[int, ...]:
 return data_tuple


def parse_dtype(data: Any) -> np.dtype[Any]:
def parse_dtype(data: npt.DTypeLike) -> np.dtype[Any]:
 # todo: real validation
 return np.dtype(data)

Expand Down

41 changes: 22 additions & 19 deletions
src/zarr/metadata.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -22,6 +22,7 @@

 from typing_extensions import Self

import numcodecs.abc

from zarr.common import (
 JSON,
Expand DownExpand Up@@ -168,15 +169,15 @@ class ArrayV3Metadata(ArrayMetadata):
 def __init__(
 self,
 *,
 shape,
 data_type,
 chunk_grid,
 chunk_key_encoding,
 fill_value,
 codecs,
 attributes,
 dimension_names,
 ):
 shape: Iterable[int],
 data_type: npt.DTypeLike,
 chunk_grid: dict[str, JSON] | ChunkGrid,
 chunk_key_encoding: dict[str, JSON] | ChunkKeyEncoding,
 fill_value: Any,
 codecs: Iterable[Codec | JSON],
 attributes: None | dict[str, JSON],
 dimension_names: None | Iterable[str],
 ) -> None:
 """
 Because the class is a frozen dataclass, we set attributes using object.__setattr__
 """
Expand DownExpand Up@@ -249,14 +250,14 @@ def encode_chunk_key(self, chunk_coords: ChunkCoords) -> str:
 return self.chunk_key_encoding.encode_chunk_key(chunk_coords)

 def to_buffer_dict(self) -> dict[str, Buffer]:
 def _json_convert(o):
 def _json_convert(o: np.dtype[Any] | Enum | Codec) -> str | dict[str, Any]:
 if isinstance(o, np.dtype):
 return str(o)
 if isinstance(o, Enum):
 return o.name
 # this serializes numcodecs compressors
 # todo: implement to_dict for codecs
 elif hasattr(o, "get_config"):
 elif isinstance(o, numcodecs.abc.Codec):
 return o.get_config()
 raise TypeError

Expand All@@ -271,9 +272,10 @@ def from_dict(cls, data: dict[str, JSON]) -> ArrayV3Metadata:
 # check that the node_type attribute is correct
 _ = parse_node_type_array(data.pop("node_type"))

 dimension_names = data.pop("dimension_names", None)
data["dimension_names"] = data.pop("dimension_names", None)

 return cls(**data, dimension_names=dimension_names)
 # TODO: Remove the ignores and use a TypedDict to type `data`
 return cls(**data) # type: ignore[arg-type]

 def to_dict(self) -> dict[str, Any]:
 out_dict = super().to_dict()
Expand DownExpand Up@@ -367,7 +369,9 @@ def codec_pipeline(self) -> CodecPipeline:
 )

 def to_buffer_dict(self) -> dict[str, Buffer]:
 def _json_convert(o):
 def _json_convert(
 o: np.dtype[Any],
 ) -> str | list[tuple[str, str] | tuple[str, str, tuple[int, ...]]]:
 if isinstance(o, np.dtype):
 if o.fields is None:
 return o.str
Expand DownExpand Up@@ -399,7 +403,7 @@ def to_dict(self) -> JSON:
 zarray_dict["chunks"] = self.chunk_grid.chunk_shape

 _ = zarray_dict.pop("data_type")
 zarray_dict["dtype"] = self.data_type
 zarray_dict["dtype"] = self.data_type.str

 return zarray_dict

Expand All@@ -422,7 +426,7 @@ def update_attributes(self, attributes: dict[str, JSON]) -> Self:
 return replace(self, attributes=attributes)


def parse_dimension_names(data: Any) -> tuple[str, ...] | None:
def parse_dimension_names(data: None | Iterable[str]) -> tuple[str, ...] | None:
 if data is None:
 return data
 if isinstance(data, Iterable) and all([isinstance(x, str) for x in data]):
Expand All@@ -432,12 +436,11 @@ def parse_dimension_names(data: Any) -> tuple[str, ...] | None:


# todo: real validation
def parse_attributes(data: Any) -> dict[str, JSON]:
def parse_attributes(data: None | dict[str, JSON]) -> dict[str, JSON]:
 if data is None:
 return {}

 data_json = cast(dict[str, JSON], data)
 return data_json
 return data


# todo: move to its own module and drop _v3 suffix
Expand Down