lamindb 0.69.7__py3-none-any.whl → 0.69.8__py3-none-any.whl

lamindb/core/storage/_backed_access.py

@@ -1,9 +1,10 @@
+from __future__ import annotations
+
 import inspect
 from dataclasses import dataclass
 from functools import cached_property
 from itertools import chain
-from pathlib import Path
-from typing import Callable, Dict, Mapping, Optional, Union
+from typing import TYPE_CHECKING, Callable, Mapping, Union
 
 import h5py
 import numpy as np
@@ -15,7 +16,6 @@ from anndata._core.views import _resolve_idx
 from anndata._io.h5ad import read_dataframe_legacy as read_dataframe_legacy_h5
 from anndata._io.specs.registry import get_spec, read_elem, read_elem_partial
 from anndata.compat import _read_attr
-from fsspec.core import OpenFile
 from fsspec.implementations.local import LocalFileSystem
 from lamin_utils import logger
 from lamindb_setup.core.upath import UPath, create_mapper, infer_filesystem
@@ -24,6 +24,11 @@ from packaging import version
 
 from lamindb.core.storage.file import filepath_from_artifact
 
+if TYPE_CHECKING:
+    from pathlib import Path
+
+    from fsspec.core import OpenFile
+
 anndata_version_parse = version.parse(anndata_version)
 
 if anndata_version_parse < version.parse("0.10.0"):
@@ -60,7 +65,7 @@ else:
 
 
 # zarr and CSRDataset have problems with full selection
-def _subset_sparse(sparse_ds: Union[CSRDataset, SparseDataset], indices):
+def _subset_sparse(sparse_ds: CSRDataset | SparseDataset, indices):
     has_arrays = isinstance(indices[0], np.ndarray) or isinstance(
         indices[1], np.ndarray
     )
@@ -140,7 +145,7 @@ registry = Registry()
 
 
 @registry.register_open("h5py")
-def open(filepath: Union[UPath, Path, str]):
+def open(filepath: UPath | Path | str):
     fs, file_path_str = infer_filesystem(filepath)
     if isinstance(fs, LocalFileSystem):
         return None, h5py.File(file_path_str, mode="r")
@@ -154,7 +159,7 @@ def open(filepath: Union[UPath, Path, str]):
 
 
 @registry.register("h5py")
-def read_dataframe(elem: Union[h5py.Dataset, h5py.Group]):
+def read_dataframe(elem: h5py.Dataset | h5py.Group):
     if isinstance(elem, h5py.Dataset):
         return read_dataframe_legacy_h5(elem)
     else:
@@ -164,7 +169,7 @@ def read_dataframe(elem: Union[h5py.Dataset, h5py.Group]):
 @registry.register("h5py")
 def safer_read_partial(elem, indices):
     is_dataset = isinstance(elem, h5py.Dataset)
-    indices_inverse: Optional[list] = None
+    indices_inverse: list | None = None
     encoding_type = get_spec(elem).encoding_type
     # h5py selection for datasets requires sorted indices
     if is_dataset or encoding_type == "dataframe":
@@ -226,7 +231,7 @@ def safer_read_partial(elem, indices):
 
 @registry.register("h5py")
 def keys(storage: h5py.File):
-    attrs_keys: Dict[str, list] = {}
+    attrs_keys: dict[str, list] = {}
     for attr in storage.keys():
         if attr == "X":
             continue
@@ -314,7 +319,7 @@ if ZARR_INSTALLED:
     def keys(storage: zarr.Group):  # noqa
         paths = storage._store.keys()
 
-        attrs_keys: Dict[str, list] = {}
+        attrs_keys: dict[str, list] = {}
         obs_var_arrays = []
 
         for path in paths:
@@ -648,7 +653,7 @@ class AnnDataAccessor(_AnnDataAttrsMixin):
 
     def __init__(
         self,
-        connection: Union[OpenFile, None],
+        connection: OpenFile | None,
         storage: StorageType,
         filename: str,
     ):
@@ -724,8 +729,8 @@ class BackedAccessor:
 
 
 def backed_access(
-    artifact_or_filepath: Union[Artifact, Path], using_key: Optional[str]
-) -> Union[AnnDataAccessor, BackedAccessor]:
+    artifact_or_filepath: Artifact | Path, using_key: str | None
+) -> AnnDataAccessor | BackedAccessor:
     if isinstance(artifact_or_filepath, Artifact):
         filepath = filepath_from_artifact(artifact_or_filepath, using_key=using_key)
     else:

lamindb/core/storage/_zarr.py

@@ -1,15 +1,19 @@
+from __future__ import annotations
+
 import warnings
-from typing import Optional
+from typing import TYPE_CHECKING
 
 import scipy.sparse as sparse
 import zarr
-from anndata import AnnData
 from anndata._io import read_zarr
 from anndata._io.specs import write_elem
 from lamindb_setup.core.upath import create_mapper, infer_filesystem
 
 from ._anndata_sizes import _size_elem, _size_raw, size_adata
 
+if TYPE_CHECKING:
+    from anndata import AnnData
+
 
 def read_adata_zarr(storepath) -> AnnData:
     fs, storepath = infer_filesystem(storepath)
@@ -38,7 +42,7 @@ def write_adata_zarr(
     adata_size = None
     cumulative_val = 0
 
-    def _cb(key_write: Optional[str] = None):
+    def _cb(key_write: str | None = None):
         nonlocal adata_size
         nonlocal cumulative_val
 

lamindb/core/storage/file.py

@@ -1,15 +1,16 @@
+from __future__ import annotations
+
 import builtins
 import re
 import shutil
 from pathlib import Path
-from typing import Optional, Union
+from typing import TYPE_CHECKING
 
 import anndata as ad
 import pandas as pd
 from lamin_utils import logger
 from lamindb_setup import settings as setup_settings
 from lamindb_setup.core import StorageSettings
-from lamindb_setup.core.types import UPathStr
 from lamindb_setup.core.upath import (
     LocalPathClasses,
     UPath,
@@ -20,6 +21,9 @@ from lnschema_core.models import Artifact, Storage
 
 from lamindb.core._settings import settings
 
+if TYPE_CHECKING:
+    from lamindb_setup.core.types import UPathStr
+
 try:
     from ._zarr import read_adata_zarr
 except ImportError:
@@ -54,8 +58,8 @@ def auto_storage_key_from_artifact_uid(uid: str, suffix: str, is_dir: bool) -> s
 def attempt_accessing_path(
     artifact: Artifact,
     storage_key: str,
-    using_key: Optional[str] = None,
-    access_token: Optional[str] = None,
+    using_key: str | None = None,
+    access_token: str | None = None,
 ):
     # check whether the file is in the default db and whether storage
     # matches default storage
@@ -88,7 +92,7 @@ def attempt_accessing_path(
 
 
 # add type annotations back asap when re-organizing the module
-def filepath_from_artifact(artifact: Artifact, using_key: Optional[str] = None):
+def filepath_from_artifact(artifact: Artifact, using_key: str | None = None):
     if hasattr(artifact, "_local_filepath") and artifact._local_filepath is not None:
         return artifact._local_filepath.resolve()
     storage_key = auto_storage_key_from_artifact(artifact)
@@ -124,7 +128,7 @@ def store_artifact(localpath: UPathStr, storagepath: UPath) -> None:
 
 
 def delete_storage_using_key(
-    artifact: Artifact, storage_key: str, using_key: Optional[str]
+    artifact: Artifact, storage_key: str, using_key: str | None
 ):
     filepath = attempt_accessing_path(artifact, storage_key, using_key=using_key)
     delete_storage(filepath)

lamindb/core/storage/object.py

@@ -1,11 +1,15 @@
-from typing import Optional
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
 
 from anndata import AnnData
-from lamindb_setup.core.types import UPathStr
 from pandas import DataFrame
 
+if TYPE_CHECKING:
+    from lamindb_setup.core.types import UPathStr
+
 
-def infer_suffix(dmem, adata_format: Optional[str] = None):
+def infer_suffix(dmem, adata_format: str | None = None):
     """Infer LaminDB storage file suffix from a data object."""
     if isinstance(dmem, AnnData):
         if adata_format is not None:

lamindb/core/versioning.py

@@ -1,11 +1,15 @@
-from typing import Optional, Tuple
+from __future__ import annotations
+
+from typing import TYPE_CHECKING, Optional, Tuple
 
 from lamindb_setup.core.upath import LocalPathClasses, UPath
 from lnschema_core import ids
-from lnschema_core.models import IsVersioned
+
+if TYPE_CHECKING:
+    from lnschema_core.models import IsVersioned
 
 
-def set_version(version: Optional[str] = None, previous_version: Optional[str] = None):
+def set_version(version: str | None = None, previous_version: str | None = None):
     """(Auto-) set version.
 
     If `version` is `None`, returns the stored version.
@@ -31,9 +35,9 @@ def set_version(version: Optional[str] = None, previous_version: Optional[str] =
 # uses `initial_version_id` to extract a stem_id that's part of id
 def init_uid(
     *,
-    version: Optional[str] = None,
+    version: str | None = None,
     n_full_id: int = 20,
-    is_new_version_of: Optional[IsVersioned] = None,
+    is_new_version_of: IsVersioned | None = None,
 ) -> str:
     if is_new_version_of is not None:
         stem_uid = is_new_version_of.stem_uid
@@ -53,9 +57,9 @@ def init_uid(
 
 def get_uid_from_old_version(
     is_new_version_of: IsVersioned,
-    version: Optional[str] = None,
-    using_key: Optional[str] = None,
-) -> Tuple[str, str]:
+    version: str | None = None,
+    using_key: str | None = None,
+) -> tuple[str, str]:
     """{}."""
     msg = ""
     if is_new_version_of.version is None:

lamindb/integrations/_vitessce.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import json
 from datetime import datetime, timezone
 

{lamindb-0.69.7.dist-info → lamindb-0.69.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.69.7
+Version: 0.69.8
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,8 +9,8 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Dist: lnschema_core==0.64.4
-Requires-Dist: lamindb_setup==0.68.4
+Requires-Dist: lnschema_core==0.64.5
+Requires-Dist: lamindb_setup==0.68.5
 Requires-Dist: lamin_utils==0.13.1
 Requires-Dist: lamin_cli==0.12.0
 Requires-Dist: rapidfuzz
@@ -27,7 +27,7 @@ Requires-Dist: urllib3<2 ; extra == "aws"
 Requires-Dist: aiobotocore[boto3]>=2.5.4,<3.0.0 ; extra == "aws"
 Requires-Dist: s3fs==2023.12.2 ; extra == "aws"
 Requires-Dist: fsspec[s3]==2023.12.2 ; extra == "aws"
-Requires-Dist: bionty==0.42.4 ; extra == "bionty"
+Requires-Dist: bionty==0.42.5 ; extra == "bionty"
 Requires-Dist: pandas<2 ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"

lamindb-0.69.8.dist-info/RECORD

@@ -0,0 +1,54 @@
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lamindb-0.69.7.dist-info/RECORD

@@ -1,54 +0,0 @@
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