ngio 0.1.6__py3-none-any.whl → 0.2.0a2__py3-none-any.whl

ngio/io/_zarr.py

@@ -1,88 +0,0 @@
-from importlib.metadata import version
-from pathlib import Path
-from typing import Literal
-
-import zarr
-from packaging.version import Version
-
-from ngio.utils import NgioFileExistsError, NgioFileNotFoundError
-
-zarr_version = version("zarr")
-ZARR_PYTHON_V = 2 if Version(zarr_version) < Version("3.0.0a") else 3
-
-if ZARR_PYTHON_V == 2:
-    from zarr.errors import ContainsGroupError, GroupNotFoundError
-
-# Zarr v3 Imports
-# import zarr.store
-# from zarr.core.common import AccessModeLiteral, ZarrFormat
-# from zarr.store.common import StoreLike
-
-AccessModeLiteral = Literal["r", "r+", "w", "w-", "a"]
-ZarrFormat = Literal[2, 3]
-StoreLike = str | Path  # This type alias more narrrow than necessary
-StoreOrGroup = StoreLike | zarr.Group
-
-
-class ZarrV3Error(Exception):
-    pass
-
-
-def _pass_through_group(
-    group: zarr.Group, mode: AccessModeLiteral, zarr_format: ZarrFormat = 2
-) -> zarr.Group:
-    if ZARR_PYTHON_V == 2:
-        if zarr_format == 3:
-            raise ZarrV3Error("Zarr v3 is not supported in when using zarr-python v2.")
-        else:
-            return group
-
-    else:
-        if group.metadata.zarr_format != zarr_format:
-            raise ValueError(
-                f"Zarr format mismatch. Expected {zarr_format}, "
-                "got {store.metadata.zarr_format}."
-            )
-        else:
-            return group
-
-    raise ValueError("This should never be reached.")
-
-
-def _open_group_v2_v3(
-    store: StoreOrGroup, mode: AccessModeLiteral, zarr_format: ZarrFormat = 2
-) -> zarr.Group:
-    """Wrapper around zarr.open_group with some additional checks.
-
-    Args:
-        store (StoreOrGroup): The store (can also be a Path/str) or group to open.
-        mode (ReadOrEdirLiteral): The mode to open the group in.
-        zarr_format (ZarrFormat): The Zarr format to use.
-
-    Returns:
-        zarr.Group: The opened Zarr group.
-    """
-    if ZARR_PYTHON_V == 3:
-        return zarr.open_group(store=store, mode=mode, zarr_format=zarr_format)
-    else:
-        try:
-            group = zarr.open_group(store=store, mode=mode)
-
-        except ContainsGroupError as e:
-            raise NgioFileExistsError(
-                f"A Zarr group already exists at {store}, "
-                "consider setting overwrite=True."
-            ) from e
-
-        except GroupNotFoundError as e:
-            raise NgioFileNotFoundError(f"No Zarr group found at {store}") from e
-
-        return group
-
-
-def _is_group_readonly(group: zarr.Group) -> bool:
-    if ZARR_PYTHON_V == 3:
-        return group.store_path.store.mode.readonly
-
-    else:
-        return not group.store.is_writeable()

ngio/io/_zarr_group_utils.py

@@ -1,60 +0,0 @@
-from pathlib import Path
-
-import fsspec
-import zarr
-
-from ngio.io._zarr import (
-    AccessModeLiteral,
-    StoreLike,
-    StoreOrGroup,
-    ZarrFormat,
-    _open_group_v2_v3,
-    _pass_through_group,
-)
-from ngio.utils import ngio_logger
-
-# Zarr v3 Imports
-# import zarr.store
-# from zarr.core.common import AccessModeLiteral, ZarrFormat
-# from zarr.store.common import StoreLike
-
-
-def _check_store(store: StoreLike) -> StoreLike:
-    if isinstance(store, str) or isinstance(store, Path):
-        return store
-
-    if isinstance(store, fsspec.mapping.FSMap) or isinstance(
-        store, zarr.storage.FSStore
-    ):
-        return store
-
-    raise NotImplementedError(
-        f"Store type {type(store)} is not supported. supported types are: "
-        "str, Path, fsspec.mapping.FSMap, zarr.storage.FSStore"
-    )
-
-
-def open_group_wrapper(
-    store: StoreOrGroup, mode: AccessModeLiteral, zarr_format: ZarrFormat = 2
-) -> zarr.Group:
-    """Wrapper around zarr.open_group with some additional checks.
-
-    Args:
-        store (StoreOrGroup): The store (can also be a Path/str) or group to open.
-        mode (ReadOrEdirLiteral): The mode to open the group in.
-        zarr_format (ZarrFormat): The Zarr format to use.
-
-    Returns:
-        zarr.Group: The opened Zarr group.
-    """
-    if isinstance(store, zarr.Group):
-        _group = _pass_through_group(store, mode=mode, zarr_format=zarr_format)
-        ngio_logger.debug(
-            f"Passing through group: {_group}, located in store: {_group.store.path}"
-        )
-        return _group
-
-    store = _check_store(store)
-    _group = _open_group_v2_v3(store=store, mode=mode, zarr_format=zarr_format)
-    ngio_logger.debug(f"Opened located in store: {store}")
-    return _group

ngio/iterators/__init__.py

@@ -1 +0,0 @@
-"""Ngio iterators module."""

ngio/ngff_meta/__init__.py

@@ -1,27 +0,0 @@
-"""IO and validation of NGFF metadata."""
-
-from ngio.ngff_meta.fractal_image_meta import (
-    Dataset,
-    ImageLabelMeta,
-    ImageMeta,
-    LabelMeta,
-    PixelSize,
-    SpaceUnits,
-)
-from ngio.ngff_meta.meta_handler import get_ngff_image_meta_handler
-from ngio.ngff_meta.utils import (
-    create_image_metadata,
-    create_label_metadata,
-)
-
-__all__ = [
-    "Dataset",
-    "ImageMeta",
-    "LabelMeta",
-    "ImageLabelMeta",
-    "PixelSize",
-    "SpaceUnits",
-    "get_ngff_image_meta_handler",
-    "create_image_metadata",
-    "create_label_metadata",
-]