Default zarr.open to open_group if shape is not provided#2158

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Merged
jhamman merged 11 commits into from
Sep 27, 2024
Merged

Default zarr.open to open_group if shape is not provided #2158

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a43ef03
Default zarr.open to open_group if shape is not provided
agoodm Sep 8, 2024
a4d8113
linting
agoodm Sep 8, 2024
8af66e7
Address failing tests
agoodm Sep 10, 2024
2f7fed1
Add check if store_path contains array to open()
agoodm Sep 13, 2024
82b1742
Allow AsyncArray constructor to accept dictionary metadata
agoodm Sep 14, 2024
2ebc465
Explicitly construct array from metadata in open()
agoodm Sep 14, 2024
186c1d9
Merge branch 'v3' of https://github.com/zarr-developers/zarr-python i…
agoodm Sep 14, 2024
eef5f60
Check if metadata input is dict rather than ArrayMetadata
agoodm Sep 14, 2024
3b7c554
Merge branch 'v3' into v3_open_group
jhamman Sep 17, 2024
307ab97
Merge branch 'v3' into v3_open_group
jhamman Sep 27, 2024
2ba10f2
fixup
jhamman Sep 27, 2024
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14 changes: 13 additions & 1 deletion src/zarr/api/asynchronous.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,7 @@
import numpy as np
import numpy.typing as npt

from zarr.core.array import Array, AsyncArray
from zarr.core.array import Array, AsyncArray, get_array_metadata
from zarr.core.common import JSON, AccessModeLiteral, ChunkCoords, MemoryOrder, ZarrFormat
from zarr.core.config import config
from zarr.core.group import AsyncGroup
Expand DownExpand Up@@ -230,6 +230,18 @@ async def open(
if path is not None:
store_path = store_path / path

if "shape" not in kwargs and mode in {"a", "w", "w-"}:
try:
metadata_dict = await get_array_metadata(store_path, zarr_format=zarr_format)
# for v2, the above would already have raised an exception if not an array
zarr_format = metadata_dict["zarr_format"]
is_v3_array = zarr_format == 3 and metadata_dict.get("node_type") == "array"
if is_v3_array or zarr_format == 2:
return AsyncArray(store_path=store_path, metadata=metadata_dict)
except (AssertionError, FileNotFoundError):
pass
return await open_group(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs)

try:
return await open_array(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs)
except KeyError:
Expand Down
103 changes: 57 additions & 46 deletions src/zarr/core/array.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -106,6 +106,53 @@ def create_codec_pipeline(metadata: ArrayV2Metadata | ArrayV3Metadata) -> CodecP
raise TypeError


async def get_array_metadata(
store_path: StorePath, zarr_format: ZarrFormat | None = 3
) -> dict[str, Any]:
if zarr_format == 2:
zarray_bytes, zattrs_bytes = await gather(
(store_path / ZARRAY_JSON).get(), (store_path / ZATTRS_JSON).get()
)
if zarray_bytes is None:
raise FileNotFoundError(store_path)
elif zarr_format == 3:
zarr_json_bytes = await (store_path / ZARR_JSON).get()
if zarr_json_bytes is None:
raise FileNotFoundError(store_path)
elif zarr_format is None:
zarr_json_bytes, zarray_bytes, zattrs_bytes = await gather(
(store_path / ZARR_JSON).get(),
(store_path / ZARRAY_JSON).get(),
(store_path / ZATTRS_JSON).get(),
)
if zarr_json_bytes is not None and zarray_bytes is not None:
# TODO: revisit this exception type
# alternatively, we could warn and favor v3
raise ValueError("Both zarr.json and .zarray objects exist")
if zarr_json_bytes is None and zarray_bytes is None:
raise FileNotFoundError(store_path)
# set zarr_format based on which keys were found
if zarr_json_bytes is not None:
zarr_format = 3
else:
zarr_format = 2
else:
raise ValueError(f"unexpected zarr_format: {zarr_format}")

metadata_dict: dict[str, Any]
if zarr_format == 2:
# V2 arrays are comprised of a .zarray and .zattrs objects
assert zarray_bytes is not None
metadata_dict = json.loads(zarray_bytes.to_bytes())
zattrs_dict = json.loads(zattrs_bytes.to_bytes()) if zattrs_bytes is not None else {}
metadata_dict["attributes"] = zattrs_dict
else:
# V3 arrays are comprised of a zarr.json object
assert zarr_json_bytes is not None
metadata_dict = json.loads(zarr_json_bytes.to_bytes())
return metadata_dict


@dataclass(frozen=True)
class AsyncArray:
metadata: ArrayMetadata
Expand All@@ -115,10 +162,17 @@ class AsyncArray:

def __init__(
self,
metadata: ArrayMetadata,
metadata: ArrayMetadata | dict[str, Any],
store_path: StorePath,
order: Literal["C", "F"] | None = None,
) -> None:
if isinstance(metadata, dict):
zarr_format = metadata["zarr_format"]
if zarr_format == 2:
metadata = ArrayV2Metadata.from_dict(metadata)
else:
metadata = ArrayV3Metadata.from_dict(metadata)

metadata_parsed = parse_array_metadata(metadata)
order_parsed = parse_indexing_order(order or config.get("array.order"))

Expand DownExpand Up@@ -341,51 +395,8 @@ async def open(
zarr_format: ZarrFormat | None = 3,
) -> AsyncArray:
store_path = await make_store_path(store)

if zarr_format == 2:
zarray_bytes, zattrs_bytes = await gather(
(store_path / ZARRAY_JSON).get(), (store_path / ZATTRS_JSON).get()
)
if zarray_bytes is None:
raise FileNotFoundError(store_path)
elif zarr_format == 3:
zarr_json_bytes = await (store_path / ZARR_JSON).get()
if zarr_json_bytes is None:
raise FileNotFoundError(store_path)
elif zarr_format is None:
zarr_json_bytes, zarray_bytes, zattrs_bytes = await gather(
(store_path / ZARR_JSON).get(),
(store_path / ZARRAY_JSON).get(),
(store_path / ZATTRS_JSON).get(),
)
if zarr_json_bytes is not None and zarray_bytes is not None:
# TODO: revisit this exception type
# alternatively, we could warn and favor v3
raise ValueError("Both zarr.json and .zarray objects exist")
if zarr_json_bytes is None and zarray_bytes is None:
raise FileNotFoundError(store_path)
# set zarr_format based on which keys were found
if zarr_json_bytes is not None:
zarr_format = 3
else:
zarr_format = 2
else:
raise ValueError(f"unexpected zarr_format: {zarr_format}")

if zarr_format == 2:
# V2 arrays are comprised of a .zarray and .zattrs objects
assert zarray_bytes is not None
zarray_dict = json.loads(zarray_bytes.to_bytes())
zattrs_dict = json.loads(zattrs_bytes.to_bytes()) if zattrs_bytes is not None else {}
zarray_dict["attributes"] = zattrs_dict
return cls(store_path=store_path, metadata=ArrayV2Metadata.from_dict(zarray_dict))
else:
# V3 arrays are comprised of a zarr.json object
assert zarr_json_bytes is not None
return cls(
store_path=store_path,
metadata=ArrayV3Metadata.from_dict(json.loads(zarr_json_bytes.to_bytes())),
)
metadata_dict = await get_array_metadata(store_path, zarr_format=zarr_format)
return cls(store_path=store_path, metadata=metadata_dict)

@property
def ndim(self) -> int:
Expand Down
7 changes: 6 additions & 1 deletion tests/v3/test_api.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -140,7 +140,12 @@ def test_open_with_mode_r_plus(tmp_path: pathlib.Path) -> None:
z2[:] = 3


def test_open_with_mode_a(tmp_path: pathlib.Path) -> None:
async def test_open_with_mode_a(tmp_path: pathlib.Path) -> None:
# Open without shape argument should default to group
g = zarr.open(store=tmp_path, mode="a")
assert isinstance(g, Group)
await g.store_path.delete()
Comment thread
agoodm marked this conversation as resolved.

# 'a' means read/write (create if doesn't exist)
arr = zarr.open(store=tmp_path, mode="a", shape=(3, 3))
assert isinstance(arr, Array)
Comment thread
agoodm marked this conversation as resolved.
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
Default zarr.open to open_group if shape is not provided#2158

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 Merged

jhamman
merged 11 commits into

from

Sep 27, 2024
 Merged


Default zarr.open to open_group if shape is not provided
#2158
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a43ef03

Default zarr.open to open_group if shape is not provided


agoodm Sep 8, 2024
a4d8113

linting


agoodm Sep 8, 2024
8af66e7

Address failing tests


agoodm Sep 10, 2024
2f7fed1

Add check if store_path contains array to open()


agoodm Sep 13, 2024
82b1742

Allow AsyncArray constructor to accept dictionary metadata


agoodm Sep 14, 2024
2ebc465

Explicitly construct array from metadata in open()


agoodm Sep 14, 2024
186c1d9

Merge branch 'v3' of https://github.com/zarr-developers/zarr-python i…


agoodm Sep 14, 2024
eef5f60

Check if metadata input is dict rather than ArrayMetadata


agoodm Sep 14, 2024
3b7c554

Merge branch 'v3' into v3_open_group


jhamman Sep 17, 2024
307ab97

Merge branch 'v3' into v3_open_group


jhamman Sep 27, 2024
2ba10f2

fixup


jhamman Sep 27, 2024

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14 changes: 13 additions & 1 deletion
src/zarr/api/asynchronous.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,7 @@
import numpy as np
import numpy.typing as npt

from zarr.core.array import Array, AsyncArray
from zarr.core.array import Array, AsyncArray, get_array_metadata
from zarr.core.common import JSON, AccessModeLiteral, ChunkCoords, MemoryOrder, ZarrFormat
from zarr.core.config import config
from zarr.core.group import AsyncGroup
Expand DownExpand Up@@ -230,6 +230,18 @@ async def open(
 if path is not None:
 store_path = store_path / path

 if "shape" not in kwargs and mode in {"a", "w", "w-"}:
 try:
 metadata_dict = await get_array_metadata(store_path, zarr_format=zarr_format)
 # for v2, the above would already have raised an exception if not an array
 zarr_format = metadata_dict["zarr_format"]
 is_v3_array = zarr_format == 3 and metadata_dict.get("node_type") == "array"
 if is_v3_array or zarr_format == 2:
 return AsyncArray(store_path=store_path, metadata=metadata_dict)
 except (AssertionError, FileNotFoundError):
 pass
 return await open_group(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs)

 try:
 return await open_array(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs)
 except KeyError:
Expand Down

103 changes: 57 additions & 46 deletions
src/zarr/core/array.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -106,6 +106,53 @@ def create_codec_pipeline(metadata: ArrayV2Metadata | ArrayV3Metadata) -> CodecP
 raise TypeError


async def get_array_metadata(
 store_path: StorePath, zarr_format: ZarrFormat | None = 3
) -> dict[str, Any]:
 if zarr_format == 2:
 zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARRAY_JSON).get(), (store_path / ZATTRS_JSON).get()
 )
 if zarray_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format == 3:
 zarr_json_bytes = await (store_path / ZARR_JSON).get()
 if zarr_json_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format is None:
 zarr_json_bytes, zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARR_JSON).get(),
 (store_path / ZARRAY_JSON).get(),
 (store_path / ZATTRS_JSON).get(),
 )
 if zarr_json_bytes is not None and zarray_bytes is not None:
 # TODO: revisit this exception type
 # alternatively, we could warn and favor v3
 raise ValueError("Both zarr.json and .zarray objects exist")
 if zarr_json_bytes is None and zarray_bytes is None:
 raise FileNotFoundError(store_path)
 # set zarr_format based on which keys were found
 if zarr_json_bytes is not None:
 zarr_format = 3
 else:
 zarr_format = 2
 else:
 raise ValueError(f"unexpected zarr_format: {zarr_format}")

 metadata_dict: dict[str, Any]
 if zarr_format == 2:
 # V2 arrays are comprised of a .zarray and .zattrs objects
 assert zarray_bytes is not None
 metadata_dict = json.loads(zarray_bytes.to_bytes())
 zattrs_dict = json.loads(zattrs_bytes.to_bytes()) if zattrs_bytes is not None else {}
 metadata_dict["attributes"] = zattrs_dict
 else:
 # V3 arrays are comprised of a zarr.json object
 assert zarr_json_bytes is not None
 metadata_dict = json.loads(zarr_json_bytes.to_bytes())
 return metadata_dict


@dataclass(frozen=True)
class AsyncArray:
 metadata: ArrayMetadata
Expand All@@ -115,10 +162,17 @@ class AsyncArray:

 def __init__(
 self,
 metadata: ArrayMetadata,
 metadata: ArrayMetadata | dict[str, Any],
 store_path: StorePath,
 order: Literal["C", "F"] | None = None,
 ) -> None:
 if isinstance(metadata, dict):
 zarr_format = metadata["zarr_format"]
 if zarr_format == 2:
 metadata = ArrayV2Metadata.from_dict(metadata)
 else:
 metadata = ArrayV3Metadata.from_dict(metadata)

 metadata_parsed = parse_array_metadata(metadata)
 order_parsed = parse_indexing_order(order or config.get("array.order"))

Expand DownExpand Up@@ -341,51 +395,8 @@ async def open(
 zarr_format: ZarrFormat | None = 3,
 ) -> AsyncArray:
 store_path = await make_store_path(store)

 if zarr_format == 2:
 zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARRAY_JSON).get(), (store_path / ZATTRS_JSON).get()
 )
 if zarray_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format == 3:
 zarr_json_bytes = await (store_path / ZARR_JSON).get()
 if zarr_json_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format is None:
 zarr_json_bytes, zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARR_JSON).get(),
 (store_path / ZARRAY_JSON).get(),
 (store_path / ZATTRS_JSON).get(),
 )
 if zarr_json_bytes is not None and zarray_bytes is not None:
 # TODO: revisit this exception type
 # alternatively, we could warn and favor v3
 raise ValueError("Both zarr.json and .zarray objects exist")
 if zarr_json_bytes is None and zarray_bytes is None:
 raise FileNotFoundError(store_path)
 # set zarr_format based on which keys were found
 if zarr_json_bytes is not None:
 zarr_format = 3
 else:
 zarr_format = 2
 else:
 raise ValueError(f"unexpected zarr_format: {zarr_format}")

 if zarr_format == 2:
 # V2 arrays are comprised of a .zarray and .zattrs objects
 assert zarray_bytes is not None
 zarray_dict = json.loads(zarray_bytes.to_bytes())
 zattrs_dict = json.loads(zattrs_bytes.to_bytes()) if zattrs_bytes is not None else {}
 zarray_dict["attributes"] = zattrs_dict
 return cls(store_path=store_path, metadata=ArrayV2Metadata.from_dict(zarray_dict))
 else:
 # V3 arrays are comprised of a zarr.json object
 assert zarr_json_bytes is not None
 return cls(
 store_path=store_path,
 metadata=ArrayV3Metadata.from_dict(json.loads(zarr_json_bytes.to_bytes())),
 )
 metadata_dict = await get_array_metadata(store_path, zarr_format=zarr_format)
 return cls(store_path=store_path, metadata=metadata_dict)

 @property
 def ndim(self) -> int:
Expand Down

7 changes: 6 additions & 1 deletion
tests/v3/test_api.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -140,7 +140,12 @@ def test_open_with_mode_r_plus(tmp_path: pathlib.Path) -> None:
 z2[:] = 3


def test_open_with_mode_a(tmp_path: pathlib.Path) -> None:
async def test_open_with_mode_a(tmp_path: pathlib.Path) -> None:
 # Open without shape argument should default to group
 g = zarr.open(store=tmp_path, mode="a")
 assert isinstance(g, Group)
 await g.store_path.delete()
Comment thread
agoodm marked this conversation as resolved.


 # 'a' means read/write (create if doesn't exist)
 arr = zarr.open(store=tmp_path, mode="a", shape=(3, 3))
 assert isinstance(arr, Array)
Comment thread
agoodm marked this conversation as resolved.

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
Default zarr.open to open_group if shape is not provided#2158

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

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Sign in
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 Merged

jhamman
merged 11 commits into

from

Sep 27, 2024
 Merged


Default zarr.open to open_group if shape is not provided
#2158
Show file tree
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Commits

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11 commits


Select commit
Hold shift + click to select a range
a43ef03

Default zarr.open to open_group if shape is not provided


agoodm Sep 8, 2024
a4d8113

linting


agoodm Sep 8, 2024
8af66e7

Address failing tests


agoodm Sep 10, 2024
2f7fed1

Add check if store_path contains array to open()


agoodm Sep 13, 2024
82b1742

Allow AsyncArray constructor to accept dictionary metadata


agoodm Sep 14, 2024
2ebc465

Explicitly construct array from metadata in open()


agoodm Sep 14, 2024
186c1d9

Merge branch 'v3' of https://github.com/zarr-developers/zarr-python i…


agoodm Sep 14, 2024
eef5f60

Check if metadata input is dict rather than ArrayMetadata


agoodm Sep 14, 2024
3b7c554

Merge branch 'v3' into v3_open_group


jhamman Sep 17, 2024
307ab97

Merge branch 'v3' into v3_open_group


jhamman Sep 27, 2024
2ba10f2

fixup


jhamman Sep 27, 2024

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14 changes: 13 additions & 1 deletion
src/zarr/api/asynchronous.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,7 @@
import numpy as np
import numpy.typing as npt

from zarr.core.array import Array, AsyncArray
from zarr.core.array import Array, AsyncArray, get_array_metadata
from zarr.core.common import JSON, AccessModeLiteral, ChunkCoords, MemoryOrder, ZarrFormat
from zarr.core.config import config
from zarr.core.group import AsyncGroup
Expand DownExpand Up@@ -230,6 +230,18 @@ async def open(
 if path is not None:
 store_path = store_path / path

 if "shape" not in kwargs and mode in {"a", "w", "w-"}:
 try:
 metadata_dict = await get_array_metadata(store_path, zarr_format=zarr_format)
 # for v2, the above would already have raised an exception if not an array
 zarr_format = metadata_dict["zarr_format"]
 is_v3_array = zarr_format == 3 and metadata_dict.get("node_type") == "array"
 if is_v3_array or zarr_format == 2:
 return AsyncArray(store_path=store_path, metadata=metadata_dict)
 except (AssertionError, FileNotFoundError):
 pass
 return await open_group(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs)

 try:
 return await open_array(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs)
 except KeyError:
Expand Down

103 changes: 57 additions & 46 deletions
src/zarr/core/array.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -106,6 +106,53 @@ def create_codec_pipeline(metadata: ArrayV2Metadata | ArrayV3Metadata) -> CodecP
 raise TypeError


async def get_array_metadata(
 store_path: StorePath, zarr_format: ZarrFormat | None = 3
) -> dict[str, Any]:
 if zarr_format == 2:
 zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARRAY_JSON).get(), (store_path / ZATTRS_JSON).get()
 )
 if zarray_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format == 3:
 zarr_json_bytes = await (store_path / ZARR_JSON).get()
 if zarr_json_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format is None:
 zarr_json_bytes, zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARR_JSON).get(),
 (store_path / ZARRAY_JSON).get(),
 (store_path / ZATTRS_JSON).get(),
 )
 if zarr_json_bytes is not None and zarray_bytes is not None:
 # TODO: revisit this exception type
 # alternatively, we could warn and favor v3
 raise ValueError("Both zarr.json and .zarray objects exist")
 if zarr_json_bytes is None and zarray_bytes is None:
 raise FileNotFoundError(store_path)
 # set zarr_format based on which keys were found
 if zarr_json_bytes is not None:
 zarr_format = 3
 else:
 zarr_format = 2
 else:
 raise ValueError(f"unexpected zarr_format: {zarr_format}")

 metadata_dict: dict[str, Any]
 if zarr_format == 2:
 # V2 arrays are comprised of a .zarray and .zattrs objects
 assert zarray_bytes is not None
 metadata_dict = json.loads(zarray_bytes.to_bytes())
 zattrs_dict = json.loads(zattrs_bytes.to_bytes()) if zattrs_bytes is not None else {}
 metadata_dict["attributes"] = zattrs_dict
 else:
 # V3 arrays are comprised of a zarr.json object
 assert zarr_json_bytes is not None
 metadata_dict = json.loads(zarr_json_bytes.to_bytes())
 return metadata_dict


@dataclass(frozen=True)
class AsyncArray:
 metadata: ArrayMetadata
Expand All@@ -115,10 +162,17 @@ class AsyncArray:

 def __init__(
 self,
 metadata: ArrayMetadata,
 metadata: ArrayMetadata | dict[str, Any],
 store_path: StorePath,
 order: Literal["C", "F"] | None = None,
 ) -> None:
 if isinstance(metadata, dict):
 zarr_format = metadata["zarr_format"]
 if zarr_format == 2:
 metadata = ArrayV2Metadata.from_dict(metadata)
 else:
 metadata = ArrayV3Metadata.from_dict(metadata)

 metadata_parsed = parse_array_metadata(metadata)
 order_parsed = parse_indexing_order(order or config.get("array.order"))

Expand DownExpand Up@@ -341,51 +395,8 @@ async def open(
 zarr_format: ZarrFormat | None = 3,
 ) -> AsyncArray:
 store_path = await make_store_path(store)

 if zarr_format == 2:
 zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARRAY_JSON).get(), (store_path / ZATTRS_JSON).get()
 )
 if zarray_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format == 3:
 zarr_json_bytes = await (store_path / ZARR_JSON).get()
 if zarr_json_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format is None:
 zarr_json_bytes, zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARR_JSON).get(),
 (store_path / ZARRAY_JSON).get(),
 (store_path / ZATTRS_JSON).get(),
 )
 if zarr_json_bytes is not None and zarray_bytes is not None:
 # TODO: revisit this exception type
 # alternatively, we could warn and favor v3
 raise ValueError("Both zarr.json and .zarray objects exist")
 if zarr_json_bytes is None and zarray_bytes is None:
 raise FileNotFoundError(store_path)
 # set zarr_format based on which keys were found
 if zarr_json_bytes is not None:
 zarr_format = 3
 else:
 zarr_format = 2
 else:
 raise ValueError(f"unexpected zarr_format: {zarr_format}")

 if zarr_format == 2:
 # V2 arrays are comprised of a .zarray and .zattrs objects
 assert zarray_bytes is not None
 zarray_dict = json.loads(zarray_bytes.to_bytes())
 zattrs_dict = json.loads(zattrs_bytes.to_bytes()) if zattrs_bytes is not None else {}
 zarray_dict["attributes"] = zattrs_dict
 return cls(store_path=store_path, metadata=ArrayV2Metadata.from_dict(zarray_dict))
 else:
 # V3 arrays are comprised of a zarr.json object
 assert zarr_json_bytes is not None
 return cls(
 store_path=store_path,
 metadata=ArrayV3Metadata.from_dict(json.loads(zarr_json_bytes.to_bytes())),
 )
 metadata_dict = await get_array_metadata(store_path, zarr_format=zarr_format)
 return cls(store_path=store_path, metadata=metadata_dict)

 @property
 def ndim(self) -> int:
Expand Down

7 changes: 6 additions & 1 deletion
tests/v3/test_api.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -140,7 +140,12 @@ def test_open_with_mode_r_plus(tmp_path: pathlib.Path) -> None:
 z2[:] = 3


def test_open_with_mode_a(tmp_path: pathlib.Path) -> None:
async def test_open_with_mode_a(tmp_path: pathlib.Path) -> None:
 # Open without shape argument should default to group
 g = zarr.open(store=tmp_path, mode="a")
 assert isinstance(g, Group)
 await g.store_path.delete()
Comment thread
agoodm marked this conversation as resolved.


 # 'a' means read/write (create if doesn't exist)
 arr = zarr.open(store=tmp_path, mode="a", shape=(3, 3))
 assert isinstance(arr, Array)
Comment thread
agoodm marked this conversation as resolved.

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('^' + ".*" + '

Skip to content
Default zarr.open to open_group if shape is not provided#2158

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 Merged

jhamman
merged 11 commits into

from

Sep 27, 2024
 Merged


Default zarr.open to open_group if shape is not provided
#2158
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a43ef03

Default zarr.open to open_group if shape is not provided


agoodm Sep 8, 2024
a4d8113

linting


agoodm Sep 8, 2024
8af66e7

Address failing tests


agoodm Sep 10, 2024
2f7fed1

Add check if store_path contains array to open()


agoodm Sep 13, 2024
82b1742

Allow AsyncArray constructor to accept dictionary metadata


agoodm Sep 14, 2024
2ebc465

Explicitly construct array from metadata in open()


agoodm Sep 14, 2024
186c1d9

Merge branch 'v3' of https://github.com/zarr-developers/zarr-python i…


agoodm Sep 14, 2024
eef5f60

Check if metadata input is dict rather than ArrayMetadata


agoodm Sep 14, 2024
3b7c554

Merge branch 'v3' into v3_open_group


jhamman Sep 17, 2024
307ab97

Merge branch 'v3' into v3_open_group


jhamman Sep 27, 2024
2ba10f2

fixup


jhamman Sep 27, 2024

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14 changes: 13 additions & 1 deletion
src/zarr/api/asynchronous.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,7 @@
import numpy as np
import numpy.typing as npt

from zarr.core.array import Array, AsyncArray
from zarr.core.array import Array, AsyncArray, get_array_metadata
from zarr.core.common import JSON, AccessModeLiteral, ChunkCoords, MemoryOrder, ZarrFormat
from zarr.core.config import config
from zarr.core.group import AsyncGroup
Expand DownExpand Up@@ -230,6 +230,18 @@ async def open(
 if path is not None:
 store_path = store_path / path

 if "shape" not in kwargs and mode in {"a", "w", "w-"}:
 try:
 metadata_dict = await get_array_metadata(store_path, zarr_format=zarr_format)
 # for v2, the above would already have raised an exception if not an array
 zarr_format = metadata_dict["zarr_format"]
 is_v3_array = zarr_format == 3 and metadata_dict.get("node_type") == "array"
 if is_v3_array or zarr_format == 2:
 return AsyncArray(store_path=store_path, metadata=metadata_dict)
 except (AssertionError, FileNotFoundError):
 pass
 return await open_group(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs)

 try:
 return await open_array(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs)
 except KeyError:
Expand Down

103 changes: 57 additions & 46 deletions
src/zarr/core/array.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -106,6 +106,53 @@ def create_codec_pipeline(metadata: ArrayV2Metadata | ArrayV3Metadata) -> CodecP
 raise TypeError


async def get_array_metadata(
 store_path: StorePath, zarr_format: ZarrFormat | None = 3
) -> dict[str, Any]:
 if zarr_format == 2:
 zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARRAY_JSON).get(), (store_path / ZATTRS_JSON).get()
 )
 if zarray_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format == 3:
 zarr_json_bytes = await (store_path / ZARR_JSON).get()
 if zarr_json_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format is None:
 zarr_json_bytes, zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARR_JSON).get(),
 (store_path / ZARRAY_JSON).get(),
 (store_path / ZATTRS_JSON).get(),
 )
 if zarr_json_bytes is not None and zarray_bytes is not None:
 # TODO: revisit this exception type
 # alternatively, we could warn and favor v3
 raise ValueError("Both zarr.json and .zarray objects exist")
 if zarr_json_bytes is None and zarray_bytes is None:
 raise FileNotFoundError(store_path)
 # set zarr_format based on which keys were found
 if zarr_json_bytes is not None:
 zarr_format = 3
 else:
 zarr_format = 2
 else:
 raise ValueError(f"unexpected zarr_format: {zarr_format}")

 metadata_dict: dict[str, Any]
 if zarr_format == 2:
 # V2 arrays are comprised of a .zarray and .zattrs objects
 assert zarray_bytes is not None
 metadata_dict = json.loads(zarray_bytes.to_bytes())
 zattrs_dict = json.loads(zattrs_bytes.to_bytes()) if zattrs_bytes is not None else {}
 metadata_dict["attributes"] = zattrs_dict
 else:
 # V3 arrays are comprised of a zarr.json object
 assert zarr_json_bytes is not None
 metadata_dict = json.loads(zarr_json_bytes.to_bytes())
 return metadata_dict


@dataclass(frozen=True)
class AsyncArray:
 metadata: ArrayMetadata
Expand All@@ -115,10 +162,17 @@ class AsyncArray:

 def __init__(
 self,
 metadata: ArrayMetadata,
 metadata: ArrayMetadata | dict[str, Any],
 store_path: StorePath,
 order: Literal["C", "F"] | None = None,
 ) -> None:
 if isinstance(metadata, dict):
 zarr_format = metadata["zarr_format"]
 if zarr_format == 2:
 metadata = ArrayV2Metadata.from_dict(metadata)
 else:
 metadata = ArrayV3Metadata.from_dict(metadata)

 metadata_parsed = parse_array_metadata(metadata)
 order_parsed = parse_indexing_order(order or config.get("array.order"))

Expand DownExpand Up@@ -341,51 +395,8 @@ async def open(
 zarr_format: ZarrFormat | None = 3,
 ) -> AsyncArray:
 store_path = await make_store_path(store)

 if zarr_format == 2:
 zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARRAY_JSON).get(), (store_path / ZATTRS_JSON).get()
 )
 if zarray_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format == 3:
 zarr_json_bytes = await (store_path / ZARR_JSON).get()
 if zarr_json_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format is None:
 zarr_json_bytes, zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARR_JSON).get(),
 (store_path / ZARRAY_JSON).get(),
 (store_path / ZATTRS_JSON).get(),
 )
 if zarr_json_bytes is not None and zarray_bytes is not None:
 # TODO: revisit this exception type
 # alternatively, we could warn and favor v3
 raise ValueError("Both zarr.json and .zarray objects exist")
 if zarr_json_bytes is None and zarray_bytes is None:
 raise FileNotFoundError(store_path)
 # set zarr_format based on which keys were found
 if zarr_json_bytes is not None:
 zarr_format = 3
 else:
 zarr_format = 2
 else:
 raise ValueError(f"unexpected zarr_format: {zarr_format}")

 if zarr_format == 2:
 # V2 arrays are comprised of a .zarray and .zattrs objects
 assert zarray_bytes is not None
 zarray_dict = json.loads(zarray_bytes.to_bytes())
 zattrs_dict = json.loads(zattrs_bytes.to_bytes()) if zattrs_bytes is not None else {}
 zarray_dict["attributes"] = zattrs_dict
 return cls(store_path=store_path, metadata=ArrayV2Metadata.from_dict(zarray_dict))
 else:
 # V3 arrays are comprised of a zarr.json object
 assert zarr_json_bytes is not None
 return cls(
 store_path=store_path,
 metadata=ArrayV3Metadata.from_dict(json.loads(zarr_json_bytes.to_bytes())),
 )
 metadata_dict = await get_array_metadata(store_path, zarr_format=zarr_format)
 return cls(store_path=store_path, metadata=metadata_dict)

 @property
 def ndim(self) -> int:
Expand Down

7 changes: 6 additions & 1 deletion
tests/v3/test_api.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -140,7 +140,12 @@ def test_open_with_mode_r_plus(tmp_path: pathlib.Path) -> None:
 z2[:] = 3


def test_open_with_mode_a(tmp_path: pathlib.Path) -> None:
async def test_open_with_mode_a(tmp_path: pathlib.Path) -> None:
 # Open without shape argument should default to group
 g = zarr.open(store=tmp_path, mode="a")
 assert isinstance(g, Group)
 await g.store_path.delete()
Comment thread
agoodm marked this conversation as resolved.


 # 'a' means read/write (create if doesn't exist)
 arr = zarr.open(store=tmp_path, mode="a", shape=(3, 3))
 assert isinstance(arr, Array)
Comment thread
agoodm marked this conversation as resolved.

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" + '

Skip to content
Default zarr.open to open_group if shape is not provided#2158

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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.

Already on GitHub?
Sign in
to your account

 Merged

jhamman
merged 11 commits into

from

Sep 27, 2024
 Merged


Default zarr.open to open_group if shape is not provided
#2158
Show file tree
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a43ef03

Default zarr.open to open_group if shape is not provided


agoodm Sep 8, 2024
a4d8113

linting


agoodm Sep 8, 2024
8af66e7

Address failing tests


agoodm Sep 10, 2024
2f7fed1

Add check if store_path contains array to open()


agoodm Sep 13, 2024
82b1742

Allow AsyncArray constructor to accept dictionary metadata


agoodm Sep 14, 2024
2ebc465

Explicitly construct array from metadata in open()


agoodm Sep 14, 2024
186c1d9

Merge branch 'v3' of https://github.com/zarr-developers/zarr-python i…


agoodm Sep 14, 2024
eef5f60

Check if metadata input is dict rather than ArrayMetadata


agoodm Sep 14, 2024
3b7c554

Merge branch 'v3' into v3_open_group


jhamman Sep 17, 2024
307ab97

Merge branch 'v3' into v3_open_group


jhamman Sep 27, 2024
2ba10f2

fixup


jhamman Sep 27, 2024

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14 changes: 13 additions & 1 deletion
src/zarr/api/asynchronous.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,7 @@
import numpy as np
import numpy.typing as npt

from zarr.core.array import Array, AsyncArray
from zarr.core.array import Array, AsyncArray, get_array_metadata
from zarr.core.common import JSON, AccessModeLiteral, ChunkCoords, MemoryOrder, ZarrFormat
from zarr.core.config import config
from zarr.core.group import AsyncGroup
Expand DownExpand Up@@ -230,6 +230,18 @@ async def open(
 if path is not None:
 store_path = store_path / path

 if "shape" not in kwargs and mode in {"a", "w", "w-"}:
 try:
 metadata_dict = await get_array_metadata(store_path, zarr_format=zarr_format)
 # for v2, the above would already have raised an exception if not an array
 zarr_format = metadata_dict["zarr_format"]
 is_v3_array = zarr_format == 3 and metadata_dict.get("node_type") == "array"
 if is_v3_array or zarr_format == 2:
 return AsyncArray(store_path=store_path, metadata=metadata_dict)
 except (AssertionError, FileNotFoundError):
 pass
 return await open_group(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs)

 try:
 return await open_array(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs)
 except KeyError:
Expand Down

103 changes: 57 additions & 46 deletions
src/zarr/core/array.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -106,6 +106,53 @@ def create_codec_pipeline(metadata: ArrayV2Metadata | ArrayV3Metadata) -> CodecP
 raise TypeError


async def get_array_metadata(
 store_path: StorePath, zarr_format: ZarrFormat | None = 3
) -> dict[str, Any]:
 if zarr_format == 2:
 zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARRAY_JSON).get(), (store_path / ZATTRS_JSON).get()
 )
 if zarray_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format == 3:
 zarr_json_bytes = await (store_path / ZARR_JSON).get()
 if zarr_json_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format is None:
 zarr_json_bytes, zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARR_JSON).get(),
 (store_path / ZARRAY_JSON).get(),
 (store_path / ZATTRS_JSON).get(),
 )
 if zarr_json_bytes is not None and zarray_bytes is not None:
 # TODO: revisit this exception type
 # alternatively, we could warn and favor v3
 raise ValueError("Both zarr.json and .zarray objects exist")
 if zarr_json_bytes is None and zarray_bytes is None:
 raise FileNotFoundError(store_path)
 # set zarr_format based on which keys were found
 if zarr_json_bytes is not None:
 zarr_format = 3
 else:
 zarr_format = 2
 else:
 raise ValueError(f"unexpected zarr_format: {zarr_format}")

 metadata_dict: dict[str, Any]
 if zarr_format == 2:
 # V2 arrays are comprised of a .zarray and .zattrs objects
 assert zarray_bytes is not None
 metadata_dict = json.loads(zarray_bytes.to_bytes())
 zattrs_dict = json.loads(zattrs_bytes.to_bytes()) if zattrs_bytes is not None else {}
 metadata_dict["attributes"] = zattrs_dict
 else:
 # V3 arrays are comprised of a zarr.json object
 assert zarr_json_bytes is not None
 metadata_dict = json.loads(zarr_json_bytes.to_bytes())
 return metadata_dict


@dataclass(frozen=True)
class AsyncArray:
 metadata: ArrayMetadata
Expand All@@ -115,10 +162,17 @@ class AsyncArray:

 def __init__(
 self,
 metadata: ArrayMetadata,
 metadata: ArrayMetadata | dict[str, Any],
 store_path: StorePath,
 order: Literal["C", "F"] | None = None,
 ) -> None:
 if isinstance(metadata, dict):
 zarr_format = metadata["zarr_format"]
 if zarr_format == 2:
 metadata = ArrayV2Metadata.from_dict(metadata)
 else:
 metadata = ArrayV3Metadata.from_dict(metadata)

 metadata_parsed = parse_array_metadata(metadata)
 order_parsed = parse_indexing_order(order or config.get("array.order"))

Expand DownExpand Up@@ -341,51 +395,8 @@ async def open(
 zarr_format: ZarrFormat | None = 3,
 ) -> AsyncArray:
 store_path = await make_store_path(store)

 if zarr_format == 2:
 zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARRAY_JSON).get(), (store_path / ZATTRS_JSON).get()
 )
 if zarray_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format == 3:
 zarr_json_bytes = await (store_path / ZARR_JSON).get()
 if zarr_json_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format is None:
 zarr_json_bytes, zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARR_JSON).get(),
 (store_path / ZARRAY_JSON).get(),
 (store_path / ZATTRS_JSON).get(),
 )
 if zarr_json_bytes is not None and zarray_bytes is not None:
 # TODO: revisit this exception type
 # alternatively, we could warn and favor v3
 raise ValueError("Both zarr.json and .zarray objects exist")
 if zarr_json_bytes is None and zarray_bytes is None:
 raise FileNotFoundError(store_path)
 # set zarr_format based on which keys were found
 if zarr_json_bytes is not None:
 zarr_format = 3
 else:
 zarr_format = 2
 else:
 raise ValueError(f"unexpected zarr_format: {zarr_format}")

 if zarr_format == 2:
 # V2 arrays are comprised of a .zarray and .zattrs objects
 assert zarray_bytes is not None
 zarray_dict = json.loads(zarray_bytes.to_bytes())
 zattrs_dict = json.loads(zattrs_bytes.to_bytes()) if zattrs_bytes is not None else {}
 zarray_dict["attributes"] = zattrs_dict
 return cls(store_path=store_path, metadata=ArrayV2Metadata.from_dict(zarray_dict))
 else:
 # V3 arrays are comprised of a zarr.json object
 assert zarr_json_bytes is not None
 return cls(
 store_path=store_path,
 metadata=ArrayV3Metadata.from_dict(json.loads(zarr_json_bytes.to_bytes())),
 )
 metadata_dict = await get_array_metadata(store_path, zarr_format=zarr_format)
 return cls(store_path=store_path, metadata=metadata_dict)

 @property
 def ndim(self) -> int:
Expand Down

7 changes: 6 additions & 1 deletion
tests/v3/test_api.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -140,7 +140,12 @@ def test_open_with_mode_r_plus(tmp_path: pathlib.Path) -> None:
 z2[:] = 3


def test_open_with_mode_a(tmp_path: pathlib.Path) -> None:
async def test_open_with_mode_a(tmp_path: pathlib.Path) -> None:
 # Open without shape argument should default to group
 g = zarr.open(store=tmp_path, mode="a")
 assert isinstance(g, Group)
 await g.store_path.delete()
Comment thread
agoodm marked this conversation as resolved.


 # 'a' means read/write (create if doesn't exist)
 arr = zarr.open(store=tmp_path, mode="a", shape=(3, 3))
 assert isinstance(arr, Array)
Comment thread
agoodm marked this conversation as resolved.

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
Default zarr.open to open_group if shape is not provided#2158

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 Merged

jhamman
merged 11 commits into

from

Sep 27, 2024
 Merged


Default zarr.open to open_group if shape is not provided
#2158
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a43ef03

Default zarr.open to open_group if shape is not provided


agoodm Sep 8, 2024
a4d8113

linting


agoodm Sep 8, 2024
8af66e7

Address failing tests


agoodm Sep 10, 2024
2f7fed1

Add check if store_path contains array to open()


agoodm Sep 13, 2024
82b1742

Allow AsyncArray constructor to accept dictionary metadata


agoodm Sep 14, 2024
2ebc465

Explicitly construct array from metadata in open()


agoodm Sep 14, 2024
186c1d9

Merge branch 'v3' of https://github.com/zarr-developers/zarr-python i…


agoodm Sep 14, 2024
eef5f60

Check if metadata input is dict rather than ArrayMetadata


agoodm Sep 14, 2024
3b7c554

Merge branch 'v3' into v3_open_group


jhamman Sep 17, 2024
307ab97

Merge branch 'v3' into v3_open_group


jhamman Sep 27, 2024
2ba10f2

fixup


jhamman Sep 27, 2024

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14 changes: 13 additions & 1 deletion
src/zarr/api/asynchronous.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,7 @@
import numpy as np
import numpy.typing as npt

from zarr.core.array import Array, AsyncArray
from zarr.core.array import Array, AsyncArray, get_array_metadata
from zarr.core.common import JSON, AccessModeLiteral, ChunkCoords, MemoryOrder, ZarrFormat
from zarr.core.config import config
from zarr.core.group import AsyncGroup
Expand DownExpand Up@@ -230,6 +230,18 @@ async def open(
 if path is not None:
 store_path = store_path / path

 if "shape" not in kwargs and mode in {"a", "w", "w-"}:
 try:
 metadata_dict = await get_array_metadata(store_path, zarr_format=zarr_format)
 # for v2, the above would already have raised an exception if not an array
 zarr_format = metadata_dict["zarr_format"]
 is_v3_array = zarr_format == 3 and metadata_dict.get("node_type") == "array"
 if is_v3_array or zarr_format == 2:
 return AsyncArray(store_path=store_path, metadata=metadata_dict)
 except (AssertionError, FileNotFoundError):
 pass
 return await open_group(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs)

 try:
 return await open_array(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs)
 except KeyError:
Expand Down

103 changes: 57 additions & 46 deletions
src/zarr/core/array.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -106,6 +106,53 @@ def create_codec_pipeline(metadata: ArrayV2Metadata | ArrayV3Metadata) -> CodecP
 raise TypeError


async def get_array_metadata(
 store_path: StorePath, zarr_format: ZarrFormat | None = 3
) -> dict[str, Any]:
 if zarr_format == 2:
 zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARRAY_JSON).get(), (store_path / ZATTRS_JSON).get()
 )
 if zarray_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format == 3:
 zarr_json_bytes = await (store_path / ZARR_JSON).get()
 if zarr_json_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format is None:
 zarr_json_bytes, zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARR_JSON).get(),
 (store_path / ZARRAY_JSON).get(),
 (store_path / ZATTRS_JSON).get(),
 )
 if zarr_json_bytes is not None and zarray_bytes is not None:
 # TODO: revisit this exception type
 # alternatively, we could warn and favor v3
 raise ValueError("Both zarr.json and .zarray objects exist")
 if zarr_json_bytes is None and zarray_bytes is None:
 raise FileNotFoundError(store_path)
 # set zarr_format based on which keys were found
 if zarr_json_bytes is not None:
 zarr_format = 3
 else:
 zarr_format = 2
 else:
 raise ValueError(f"unexpected zarr_format: {zarr_format}")

 metadata_dict: dict[str, Any]
 if zarr_format == 2:
 # V2 arrays are comprised of a .zarray and .zattrs objects
 assert zarray_bytes is not None
 metadata_dict = json.loads(zarray_bytes.to_bytes())
 zattrs_dict = json.loads(zattrs_bytes.to_bytes()) if zattrs_bytes is not None else {}
 metadata_dict["attributes"] = zattrs_dict
 else:
 # V3 arrays are comprised of a zarr.json object
 assert zarr_json_bytes is not None
 metadata_dict = json.loads(zarr_json_bytes.to_bytes())
 return metadata_dict


@dataclass(frozen=True)
class AsyncArray:
 metadata: ArrayMetadata
Expand All@@ -115,10 +162,17 @@ class AsyncArray:

 def __init__(
 self,
 metadata: ArrayMetadata,
 metadata: ArrayMetadata | dict[str, Any],
 store_path: StorePath,
 order: Literal["C", "F"] | None = None,
 ) -> None:
 if isinstance(metadata, dict):
 zarr_format = metadata["zarr_format"]
 if zarr_format == 2:
 metadata = ArrayV2Metadata.from_dict(metadata)
 else:
 metadata = ArrayV3Metadata.from_dict(metadata)

 metadata_parsed = parse_array_metadata(metadata)
 order_parsed = parse_indexing_order(order or config.get("array.order"))

Expand DownExpand Up@@ -341,51 +395,8 @@ async def open(
 zarr_format: ZarrFormat | None = 3,
 ) -> AsyncArray:
 store_path = await make_store_path(store)

 if zarr_format == 2:
 zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARRAY_JSON).get(), (store_path / ZATTRS_JSON).get()
 )
 if zarray_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format == 3:
 zarr_json_bytes = await (store_path / ZARR_JSON).get()
 if zarr_json_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format is None:
 zarr_json_bytes, zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARR_JSON).get(),
 (store_path / ZARRAY_JSON).get(),
 (store_path / ZATTRS_JSON).get(),
 )
 if zarr_json_bytes is not None and zarray_bytes is not None:
 # TODO: revisit this exception type
 # alternatively, we could warn and favor v3
 raise ValueError("Both zarr.json and .zarray objects exist")
 if zarr_json_bytes is None and zarray_bytes is None:
 raise FileNotFoundError(store_path)
 # set zarr_format based on which keys were found
 if zarr_json_bytes is not None:
 zarr_format = 3
 else:
 zarr_format = 2
 else:
 raise ValueError(f"unexpected zarr_format: {zarr_format}")

 if zarr_format == 2:
 # V2 arrays are comprised of a .zarray and .zattrs objects
 assert zarray_bytes is not None
 zarray_dict = json.loads(zarray_bytes.to_bytes())
 zattrs_dict = json.loads(zattrs_bytes.to_bytes()) if zattrs_bytes is not None else {}
 zarray_dict["attributes"] = zattrs_dict
 return cls(store_path=store_path, metadata=ArrayV2Metadata.from_dict(zarray_dict))
 else:
 # V3 arrays are comprised of a zarr.json object
 assert zarr_json_bytes is not None
 return cls(
 store_path=store_path,
 metadata=ArrayV3Metadata.from_dict(json.loads(zarr_json_bytes.to_bytes())),
 )
 metadata_dict = await get_array_metadata(store_path, zarr_format=zarr_format)
 return cls(store_path=store_path, metadata=metadata_dict)

 @property
 def ndim(self) -> int:
Expand Down

7 changes: 6 additions & 1 deletion
tests/v3/test_api.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -140,7 +140,12 @@ def test_open_with_mode_r_plus(tmp_path: pathlib.Path) -> None:
 z2[:] = 3


def test_open_with_mode_a(tmp_path: pathlib.Path) -> None:
async def test_open_with_mode_a(tmp_path: pathlib.Path) -> None:
 # Open without shape argument should default to group
 g = zarr.open(store=tmp_path, mode="a")
 assert isinstance(g, Group)
 await g.store_path.delete()
Comment thread
agoodm marked this conversation as resolved.


 # 'a' means read/write (create if doesn't exist)
 arr = zarr.open(store=tmp_path, mode="a", shape=(3, 3))
 assert isinstance(arr, Array)
Comment thread
agoodm marked this conversation as resolved.

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
Default zarr.open to open_group if shape is not provided#2158

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

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 Merged

jhamman
merged 11 commits into

from

Sep 27, 2024
 Merged


Default zarr.open to open_group if shape is not provided
#2158
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a43ef03

Default zarr.open to open_group if shape is not provided


agoodm Sep 8, 2024
a4d8113

linting


agoodm Sep 8, 2024
8af66e7

Address failing tests


agoodm Sep 10, 2024
2f7fed1

Add check if store_path contains array to open()


agoodm Sep 13, 2024
82b1742

Allow AsyncArray constructor to accept dictionary metadata


agoodm Sep 14, 2024
2ebc465

Explicitly construct array from metadata in open()


agoodm Sep 14, 2024
186c1d9

Merge branch 'v3' of https://github.com/zarr-developers/zarr-python i…


agoodm Sep 14, 2024
eef5f60

Check if metadata input is dict rather than ArrayMetadata


agoodm Sep 14, 2024
3b7c554

Merge branch 'v3' into v3_open_group


jhamman Sep 17, 2024
307ab97

Merge branch 'v3' into v3_open_group


jhamman Sep 27, 2024
2ba10f2

fixup


jhamman Sep 27, 2024

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14 changes: 13 additions & 1 deletion
src/zarr/api/asynchronous.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,7 @@
import numpy as np
import numpy.typing as npt

from zarr.core.array import Array, AsyncArray
from zarr.core.array import Array, AsyncArray, get_array_metadata
from zarr.core.common import JSON, AccessModeLiteral, ChunkCoords, MemoryOrder, ZarrFormat
from zarr.core.config import config
from zarr.core.group import AsyncGroup
Expand DownExpand Up@@ -230,6 +230,18 @@ async def open(
 if path is not None:
 store_path = store_path / path

 if "shape" not in kwargs and mode in {"a", "w", "w-"}:
 try:
 metadata_dict = await get_array_metadata(store_path, zarr_format=zarr_format)
 # for v2, the above would already have raised an exception if not an array
 zarr_format = metadata_dict["zarr_format"]
 is_v3_array = zarr_format == 3 and metadata_dict.get("node_type") == "array"
 if is_v3_array or zarr_format == 2:
 return AsyncArray(store_path=store_path, metadata=metadata_dict)
 except (AssertionError, FileNotFoundError):
 pass
 return await open_group(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs)

 try:
 return await open_array(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs)
 except KeyError:
Expand Down

103 changes: 57 additions & 46 deletions
src/zarr/core/array.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -106,6 +106,53 @@ def create_codec_pipeline(metadata: ArrayV2Metadata | ArrayV3Metadata) -> CodecP
 raise TypeError


async def get_array_metadata(
 store_path: StorePath, zarr_format: ZarrFormat | None = 3
) -> dict[str, Any]:
 if zarr_format == 2:
 zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARRAY_JSON).get(), (store_path / ZATTRS_JSON).get()
 )
 if zarray_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format == 3:
 zarr_json_bytes = await (store_path / ZARR_JSON).get()
 if zarr_json_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format is None:
 zarr_json_bytes, zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARR_JSON).get(),
 (store_path / ZARRAY_JSON).get(),
 (store_path / ZATTRS_JSON).get(),
 )
 if zarr_json_bytes is not None and zarray_bytes is not None:
 # TODO: revisit this exception type
 # alternatively, we could warn and favor v3
 raise ValueError("Both zarr.json and .zarray objects exist")
 if zarr_json_bytes is None and zarray_bytes is None:
 raise FileNotFoundError(store_path)
 # set zarr_format based on which keys were found
 if zarr_json_bytes is not None:
 zarr_format = 3
 else:
 zarr_format = 2
 else:
 raise ValueError(f"unexpected zarr_format: {zarr_format}")

 metadata_dict: dict[str, Any]
 if zarr_format == 2:
 # V2 arrays are comprised of a .zarray and .zattrs objects
 assert zarray_bytes is not None
 metadata_dict = json.loads(zarray_bytes.to_bytes())
 zattrs_dict = json.loads(zattrs_bytes.to_bytes()) if zattrs_bytes is not None else {}
 metadata_dict["attributes"] = zattrs_dict
 else:
 # V3 arrays are comprised of a zarr.json object
 assert zarr_json_bytes is not None
 metadata_dict = json.loads(zarr_json_bytes.to_bytes())
 return metadata_dict


@dataclass(frozen=True)
class AsyncArray:
 metadata: ArrayMetadata
Expand All@@ -115,10 +162,17 @@ class AsyncArray:

 def __init__(
 self,
 metadata: ArrayMetadata,
 metadata: ArrayMetadata | dict[str, Any],
 store_path: StorePath,
 order: Literal["C", "F"] | None = None,
 ) -> None:
 if isinstance(metadata, dict):
 zarr_format = metadata["zarr_format"]
 if zarr_format == 2:
 metadata = ArrayV2Metadata.from_dict(metadata)
 else:
 metadata = ArrayV3Metadata.from_dict(metadata)

 metadata_parsed = parse_array_metadata(metadata)
 order_parsed = parse_indexing_order(order or config.get("array.order"))

Expand DownExpand Up@@ -341,51 +395,8 @@ async def open(
 zarr_format: ZarrFormat | None = 3,
 ) -> AsyncArray:
 store_path = await make_store_path(store)

 if zarr_format == 2:
 zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARRAY_JSON).get(), (store_path / ZATTRS_JSON).get()
 )
 if zarray_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format == 3:
 zarr_json_bytes = await (store_path / ZARR_JSON).get()
 if zarr_json_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format is None:
 zarr_json_bytes, zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARR_JSON).get(),
 (store_path / ZARRAY_JSON).get(),
 (store_path / ZATTRS_JSON).get(),
 )
 if zarr_json_bytes is not None and zarray_bytes is not None:
 # TODO: revisit this exception type
 # alternatively, we could warn and favor v3
 raise ValueError("Both zarr.json and .zarray objects exist")
 if zarr_json_bytes is None and zarray_bytes is None:
 raise FileNotFoundError(store_path)
 # set zarr_format based on which keys were found
 if zarr_json_bytes is not None:
 zarr_format = 3
 else:
 zarr_format = 2
 else:
 raise ValueError(f"unexpected zarr_format: {zarr_format}")

 if zarr_format == 2:
 # V2 arrays are comprised of a .zarray and .zattrs objects
 assert zarray_bytes is not None
 zarray_dict = json.loads(zarray_bytes.to_bytes())
 zattrs_dict = json.loads(zattrs_bytes.to_bytes()) if zattrs_bytes is not None else {}
 zarray_dict["attributes"] = zattrs_dict
 return cls(store_path=store_path, metadata=ArrayV2Metadata.from_dict(zarray_dict))
 else:
 # V3 arrays are comprised of a zarr.json object
 assert zarr_json_bytes is not None
 return cls(
 store_path=store_path,
 metadata=ArrayV3Metadata.from_dict(json.loads(zarr_json_bytes.to_bytes())),
 )
 metadata_dict = await get_array_metadata(store_path, zarr_format=zarr_format)
 return cls(store_path=store_path, metadata=metadata_dict)

 @property
 def ndim(self) -> int:
Expand Down

7 changes: 6 additions & 1 deletion
tests/v3/test_api.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -140,7 +140,12 @@ def test_open_with_mode_r_plus(tmp_path: pathlib.Path) -> None:
 z2[:] = 3


def test_open_with_mode_a(tmp_path: pathlib.Path) -> None:
async def test_open_with_mode_a(tmp_path: pathlib.Path) -> None:
 # Open without shape argument should default to group
 g = zarr.open(store=tmp_path, mode="a")
 assert isinstance(g, Group)
 await g.store_path.delete()
Comment thread
agoodm marked this conversation as resolved.


 # 'a' means read/write (create if doesn't exist)
 arr = zarr.open(store=tmp_path, mode="a", shape=(3, 3))
 assert isinstance(arr, Array)
Comment thread
agoodm marked this conversation as resolved.

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); }
})();
})();

Skip to content
Default zarr.open to open_group if shape is not provided#2158

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?
Sign in
to your account

 Merged

jhamman
merged 11 commits into

from

Sep 27, 2024
 Merged


Default zarr.open to open_group if shape is not provided
#2158
Show file tree
Hide file tree
 Changes from all commits
Commits

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11 commits


Select commit
Hold shift + click to select a range
a43ef03

Default zarr.open to open_group if shape is not provided


agoodm Sep 8, 2024
a4d8113

linting


agoodm Sep 8, 2024
8af66e7

Address failing tests


agoodm Sep 10, 2024
2f7fed1

Add check if store_path contains array to open()


agoodm Sep 13, 2024
82b1742

Allow AsyncArray constructor to accept dictionary metadata


agoodm Sep 14, 2024
2ebc465

Explicitly construct array from metadata in open()


agoodm Sep 14, 2024
186c1d9

Merge branch 'v3' of https://github.com/zarr-developers/zarr-python i…


agoodm Sep 14, 2024
eef5f60

Check if metadata input is dict rather than ArrayMetadata


agoodm Sep 14, 2024
3b7c554

Merge branch 'v3' into v3_open_group


jhamman Sep 17, 2024
307ab97

Merge branch 'v3' into v3_open_group


jhamman Sep 27, 2024
2ba10f2

fixup


jhamman Sep 27, 2024

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14 changes: 13 additions & 1 deletion
src/zarr/api/asynchronous.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -7,7 +7,7 @@
import numpy as np
import numpy.typing as npt

from zarr.core.array import Array, AsyncArray
from zarr.core.array import Array, AsyncArray, get_array_metadata
from zarr.core.common import JSON, AccessModeLiteral, ChunkCoords, MemoryOrder, ZarrFormat
from zarr.core.config import config
from zarr.core.group import AsyncGroup
Expand DownExpand Up@@ -230,6 +230,18 @@ async def open(
 if path is not None:
 store_path = store_path / path

 if "shape" not in kwargs and mode in {"a", "w", "w-"}:
 try:
 metadata_dict = await get_array_metadata(store_path, zarr_format=zarr_format)
 # for v2, the above would already have raised an exception if not an array
 zarr_format = metadata_dict["zarr_format"]
 is_v3_array = zarr_format == 3 and metadata_dict.get("node_type") == "array"
 if is_v3_array or zarr_format == 2:
 return AsyncArray(store_path=store_path, metadata=metadata_dict)
 except (AssertionError, FileNotFoundError):
 pass
 return await open_group(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs)

 try:
 return await open_array(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs)
 except KeyError:
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103 changes: 57 additions & 46 deletions
src/zarr/core/array.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -106,6 +106,53 @@ def create_codec_pipeline(metadata: ArrayV2Metadata | ArrayV3Metadata) -> CodecP
 raise TypeError


async def get_array_metadata(
 store_path: StorePath, zarr_format: ZarrFormat | None = 3
) -> dict[str, Any]:
 if zarr_format == 2:
 zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARRAY_JSON).get(), (store_path / ZATTRS_JSON).get()
 )
 if zarray_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format == 3:
 zarr_json_bytes = await (store_path / ZARR_JSON).get()
 if zarr_json_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format is None:
 zarr_json_bytes, zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARR_JSON).get(),
 (store_path / ZARRAY_JSON).get(),
 (store_path / ZATTRS_JSON).get(),
 )
 if zarr_json_bytes is not None and zarray_bytes is not None:
 # TODO: revisit this exception type
 # alternatively, we could warn and favor v3
 raise ValueError("Both zarr.json and .zarray objects exist")
 if zarr_json_bytes is None and zarray_bytes is None:
 raise FileNotFoundError(store_path)
 # set zarr_format based on which keys were found
 if zarr_json_bytes is not None:
 zarr_format = 3
 else:
 zarr_format = 2
 else:
 raise ValueError(f"unexpected zarr_format: {zarr_format}")

 metadata_dict: dict[str, Any]
 if zarr_format == 2:
 # V2 arrays are comprised of a .zarray and .zattrs objects
 assert zarray_bytes is not None
 metadata_dict = json.loads(zarray_bytes.to_bytes())
 zattrs_dict = json.loads(zattrs_bytes.to_bytes()) if zattrs_bytes is not None else {}
 metadata_dict["attributes"] = zattrs_dict
 else:
 # V3 arrays are comprised of a zarr.json object
 assert zarr_json_bytes is not None
 metadata_dict = json.loads(zarr_json_bytes.to_bytes())
 return metadata_dict


@dataclass(frozen=True)
class AsyncArray:
 metadata: ArrayMetadata
Expand All@@ -115,10 +162,17 @@ class AsyncArray:

 def __init__(
 self,
 metadata: ArrayMetadata,
 metadata: ArrayMetadata | dict[str, Any],
 store_path: StorePath,
 order: Literal["C", "F"] | None = None,
 ) -> None:
 if isinstance(metadata, dict):
 zarr_format = metadata["zarr_format"]
 if zarr_format == 2:
 metadata = ArrayV2Metadata.from_dict(metadata)
 else:
 metadata = ArrayV3Metadata.from_dict(metadata)

 metadata_parsed = parse_array_metadata(metadata)
 order_parsed = parse_indexing_order(order or config.get("array.order"))

Expand DownExpand Up@@ -341,51 +395,8 @@ async def open(
 zarr_format: ZarrFormat | None = 3,
 ) -> AsyncArray:
 store_path = await make_store_path(store)

 if zarr_format == 2:
 zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARRAY_JSON).get(), (store_path / ZATTRS_JSON).get()
 )
 if zarray_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format == 3:
 zarr_json_bytes = await (store_path / ZARR_JSON).get()
 if zarr_json_bytes is None:
 raise FileNotFoundError(store_path)
 elif zarr_format is None:
 zarr_json_bytes, zarray_bytes, zattrs_bytes = await gather(
 (store_path / ZARR_JSON).get(),
 (store_path / ZARRAY_JSON).get(),
 (store_path / ZATTRS_JSON).get(),
 )
 if zarr_json_bytes is not None and zarray_bytes is not None:
 # TODO: revisit this exception type
 # alternatively, we could warn and favor v3
 raise ValueError("Both zarr.json and .zarray objects exist")
 if zarr_json_bytes is None and zarray_bytes is None:
 raise FileNotFoundError(store_path)
 # set zarr_format based on which keys were found
 if zarr_json_bytes is not None:
 zarr_format = 3
 else:
 zarr_format = 2
 else:
 raise ValueError(f"unexpected zarr_format: {zarr_format}")

 if zarr_format == 2:
 # V2 arrays are comprised of a .zarray and .zattrs objects
 assert zarray_bytes is not None
 zarray_dict = json.loads(zarray_bytes.to_bytes())
 zattrs_dict = json.loads(zattrs_bytes.to_bytes()) if zattrs_bytes is not None else {}
 zarray_dict["attributes"] = zattrs_dict
 return cls(store_path=store_path, metadata=ArrayV2Metadata.from_dict(zarray_dict))
 else:
 # V3 arrays are comprised of a zarr.json object
 assert zarr_json_bytes is not None
 return cls(
 store_path=store_path,
 metadata=ArrayV3Metadata.from_dict(json.loads(zarr_json_bytes.to_bytes())),
 )
 metadata_dict = await get_array_metadata(store_path, zarr_format=zarr_format)
 return cls(store_path=store_path, metadata=metadata_dict)

 @property
 def ndim(self) -> int:
Expand Down

7 changes: 6 additions & 1 deletion
tests/v3/test_api.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -140,7 +140,12 @@ def test_open_with_mode_r_plus(tmp_path: pathlib.Path) -> None:
 z2[:] = 3


def test_open_with_mode_a(tmp_path: pathlib.Path) -> None:
async def test_open_with_mode_a(tmp_path: pathlib.Path) -> None:
 # Open without shape argument should default to group
 g = zarr.open(store=tmp_path, mode="a")
 assert isinstance(g, Group)
 await g.store_path.delete()
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 # 'a' means read/write (create if doesn't exist)
 arr = zarr.open(store=tmp_path, mode="a", shape=(3, 3))
 assert isinstance(arr, Array)
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Expand Down