lamindb 0.69.6__py3-none-any.whl → 0.69.8__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (44) hide show
  1. lamindb/__init__.py +1 -1
  2. lamindb/_annotate.py +46 -42
  3. lamindb/_artifact.py +63 -64
  4. lamindb/_can_validate.py +29 -25
  5. lamindb/_collection.py +28 -32
  6. lamindb/_feature.py +10 -8
  7. lamindb/_feature_set.py +17 -15
  8. lamindb/_filter.py +2 -2
  9. lamindb/_finish.py +14 -8
  10. lamindb/_from_values.py +13 -9
  11. lamindb/_is_versioned.py +2 -2
  12. lamindb/_parents.py +16 -11
  13. lamindb/_query_manager.py +8 -4
  14. lamindb/_query_set.py +15 -15
  15. lamindb/_registry.py +36 -34
  16. lamindb/_run.py +3 -5
  17. lamindb/_save.py +13 -11
  18. lamindb/_transform.py +9 -11
  19. lamindb/_ulabel.py +11 -9
  20. lamindb/_view.py +3 -2
  21. lamindb/core/_data.py +21 -17
  22. lamindb/core/_feature_manager.py +17 -12
  23. lamindb/core/_label_manager.py +13 -9
  24. lamindb/core/_mapped_collection.py +32 -19
  25. lamindb/core/_run_context.py +21 -17
  26. lamindb/core/_settings.py +19 -16
  27. lamindb/core/_sync_git.py +4 -5
  28. lamindb/core/_track_environment.py +6 -1
  29. lamindb/core/_transform_settings.py +3 -3
  30. lamindb/core/_view_tree.py +2 -1
  31. lamindb/core/datasets/_core.py +3 -2
  32. lamindb/core/datasets/_fake.py +2 -2
  33. lamindb/core/storage/_anndata_sizes.py +2 -0
  34. lamindb/core/storage/_backed_access.py +17 -12
  35. lamindb/core/storage/_zarr.py +7 -3
  36. lamindb/core/storage/file.py +10 -6
  37. lamindb/core/storage/object.py +7 -3
  38. lamindb/core/versioning.py +12 -8
  39. lamindb/integrations/_vitessce.py +2 -0
  40. {lamindb-0.69.6.dist-info → lamindb-0.69.8.dist-info}/METADATA +6 -5
  41. lamindb-0.69.8.dist-info/RECORD +54 -0
  42. lamindb-0.69.6.dist-info/RECORD +0 -54
  43. {lamindb-0.69.6.dist-info → lamindb-0.69.8.dist-info}/LICENSE +0 -0
  44. {lamindb-0.69.6.dist-info → lamindb-0.69.8.dist-info}/WHEEL +0 -0
@@ -1,5 +1,6 @@
1
+ from __future__ import annotations
2
+
1
3
  from pathlib import Path
2
- from typing import Union
3
4
  from urllib.request import urlretrieve
4
5
 
5
6
  import anndata as ad
@@ -448,7 +449,7 @@ def df_iris_in_meter_study2() -> pd.DataFrame:
448
449
 
449
450
 
450
451
  def dir_scrnaseq_cellranger(
451
- sample_name: str, basedir: Union[str, Path] = "./", output_only: bool = True
452
+ sample_name: str, basedir: str | Path = "./", output_only: bool = True
452
453
  ): # pragma: no cover
453
454
  """Generate mock cell ranger outputs.
454
455
 
@@ -1,7 +1,7 @@
1
- from typing import List
1
+ from __future__ import annotations
2
2
 
3
3
 
4
- def fake_bio_notebook_titles(n=100) -> List[str]:
4
+ def fake_bio_notebook_titles(n=100) -> list[str]:
5
5
  """A fake collection of study titles."""
6
6
  from faker import Faker
7
7
 
@@ -1,3 +1,5 @@
1
+ from __future__ import annotations
2
+
1
3
  import warnings
2
4
 
3
5
  import scipy.sparse as sparse
@@ -1,9 +1,10 @@
1
+ from __future__ import annotations
2
+
1
3
  import inspect
2
4
  from dataclasses import dataclass
3
5
  from functools import cached_property
4
6
  from itertools import chain
5
- from pathlib import Path
6
- from typing import Callable, Dict, Mapping, Optional, Union
7
+ from typing import TYPE_CHECKING, Callable, Mapping, Union
7
8
 
8
9
  import h5py
9
10
  import numpy as np
@@ -15,7 +16,6 @@ from anndata._core.views import _resolve_idx
15
16
  from anndata._io.h5ad import read_dataframe_legacy as read_dataframe_legacy_h5
16
17
  from anndata._io.specs.registry import get_spec, read_elem, read_elem_partial
17
18
  from anndata.compat import _read_attr
18
- from fsspec.core import OpenFile
19
19
  from fsspec.implementations.local import LocalFileSystem
20
20
  from lamin_utils import logger
21
21
  from lamindb_setup.core.upath import UPath, create_mapper, infer_filesystem
@@ -24,6 +24,11 @@ from packaging import version
24
24
 
25
25
  from lamindb.core.storage.file import filepath_from_artifact
26
26
 
27
+ if TYPE_CHECKING:
28
+ from pathlib import Path
29
+
30
+ from fsspec.core import OpenFile
31
+
27
32
  anndata_version_parse = version.parse(anndata_version)
28
33
 
29
34
  if anndata_version_parse < version.parse("0.10.0"):
@@ -60,7 +65,7 @@ else:
60
65
 
61
66
 
62
67
  # zarr and CSRDataset have problems with full selection
63
- def _subset_sparse(sparse_ds: Union[CSRDataset, SparseDataset], indices):
68
+ def _subset_sparse(sparse_ds: CSRDataset | SparseDataset, indices):
64
69
  has_arrays = isinstance(indices[0], np.ndarray) or isinstance(
65
70
  indices[1], np.ndarray
66
71
  )
@@ -140,7 +145,7 @@ registry = Registry()
140
145
 
141
146
 
142
147
  @registry.register_open("h5py")
143
- def open(filepath: Union[UPath, Path, str]):
148
+ def open(filepath: UPath | Path | str):
144
149
  fs, file_path_str = infer_filesystem(filepath)
145
150
  if isinstance(fs, LocalFileSystem):
146
151
  return None, h5py.File(file_path_str, mode="r")
@@ -154,7 +159,7 @@ def open(filepath: Union[UPath, Path, str]):
154
159
 
155
160
 
156
161
  @registry.register("h5py")
157
- def read_dataframe(elem: Union[h5py.Dataset, h5py.Group]):
162
+ def read_dataframe(elem: h5py.Dataset | h5py.Group):
158
163
  if isinstance(elem, h5py.Dataset):
159
164
  return read_dataframe_legacy_h5(elem)
160
165
  else:
@@ -164,7 +169,7 @@ def read_dataframe(elem: Union[h5py.Dataset, h5py.Group]):
164
169
  @registry.register("h5py")
165
170
  def safer_read_partial(elem, indices):
166
171
  is_dataset = isinstance(elem, h5py.Dataset)
167
- indices_inverse: Optional[list] = None
172
+ indices_inverse: list | None = None
168
173
  encoding_type = get_spec(elem).encoding_type
169
174
  # h5py selection for datasets requires sorted indices
170
175
  if is_dataset or encoding_type == "dataframe":
@@ -226,7 +231,7 @@ def safer_read_partial(elem, indices):
226
231
 
227
232
  @registry.register("h5py")
228
233
  def keys(storage: h5py.File):
229
- attrs_keys: Dict[str, list] = {}
234
+ attrs_keys: dict[str, list] = {}
230
235
  for attr in storage.keys():
231
236
  if attr == "X":
232
237
  continue
@@ -314,7 +319,7 @@ if ZARR_INSTALLED:
314
319
  def keys(storage: zarr.Group): # noqa
315
320
  paths = storage._store.keys()
316
321
 
317
- attrs_keys: Dict[str, list] = {}
322
+ attrs_keys: dict[str, list] = {}
318
323
  obs_var_arrays = []
319
324
 
320
325
  for path in paths:
@@ -648,7 +653,7 @@ class AnnDataAccessor(_AnnDataAttrsMixin):
648
653
 
649
654
  def __init__(
650
655
  self,
651
- connection: Union[OpenFile, None],
656
+ connection: OpenFile | None,
652
657
  storage: StorageType,
653
658
  filename: str,
654
659
  ):
@@ -724,8 +729,8 @@ class BackedAccessor:
724
729
 
725
730
 
726
731
  def backed_access(
727
- artifact_or_filepath: Union[Artifact, Path], using_key: Optional[str]
728
- ) -> Union[AnnDataAccessor, BackedAccessor]:
732
+ artifact_or_filepath: Artifact | Path, using_key: str | None
733
+ ) -> AnnDataAccessor | BackedAccessor:
729
734
  if isinstance(artifact_or_filepath, Artifact):
730
735
  filepath = filepath_from_artifact(artifact_or_filepath, using_key=using_key)
731
736
  else:
@@ -1,15 +1,19 @@
1
+ from __future__ import annotations
2
+
1
3
  import warnings
2
- from typing import Optional
4
+ from typing import TYPE_CHECKING
3
5
 
4
6
  import scipy.sparse as sparse
5
7
  import zarr
6
- from anndata import AnnData
7
8
  from anndata._io import read_zarr
8
9
  from anndata._io.specs import write_elem
9
10
  from lamindb_setup.core.upath import create_mapper, infer_filesystem
10
11
 
11
12
  from ._anndata_sizes import _size_elem, _size_raw, size_adata
12
13
 
14
+ if TYPE_CHECKING:
15
+ from anndata import AnnData
16
+
13
17
 
14
18
  def read_adata_zarr(storepath) -> AnnData:
15
19
  fs, storepath = infer_filesystem(storepath)
@@ -38,7 +42,7 @@ def write_adata_zarr(
38
42
  adata_size = None
39
43
  cumulative_val = 0
40
44
 
41
- def _cb(key_write: Optional[str] = None):
45
+ def _cb(key_write: str | None = None):
42
46
  nonlocal adata_size
43
47
  nonlocal cumulative_val
44
48
 
@@ -1,15 +1,16 @@
1
+ from __future__ import annotations
2
+
1
3
  import builtins
2
4
  import re
3
5
  import shutil
4
6
  from pathlib import Path
5
- from typing import Optional, Union
7
+ from typing import TYPE_CHECKING
6
8
 
7
9
  import anndata as ad
8
10
  import pandas as pd
9
11
  from lamin_utils import logger
10
12
  from lamindb_setup import settings as setup_settings
11
13
  from lamindb_setup.core import StorageSettings
12
- from lamindb_setup.core.types import UPathStr
13
14
  from lamindb_setup.core.upath import (
14
15
  LocalPathClasses,
15
16
  UPath,
@@ -20,6 +21,9 @@ from lnschema_core.models import Artifact, Storage
20
21
 
21
22
  from lamindb.core._settings import settings
22
23
 
24
+ if TYPE_CHECKING:
25
+ from lamindb_setup.core.types import UPathStr
26
+
23
27
  try:
24
28
  from ._zarr import read_adata_zarr
25
29
  except ImportError:
@@ -54,8 +58,8 @@ def auto_storage_key_from_artifact_uid(uid: str, suffix: str, is_dir: bool) -> s
54
58
  def attempt_accessing_path(
55
59
  artifact: Artifact,
56
60
  storage_key: str,
57
- using_key: Optional[str] = None,
58
- access_token: Optional[str] = None,
61
+ using_key: str | None = None,
62
+ access_token: str | None = None,
59
63
  ):
60
64
  # check whether the file is in the default db and whether storage
61
65
  # matches default storage
@@ -88,7 +92,7 @@ def attempt_accessing_path(
88
92
 
89
93
 
90
94
  # add type annotations back asap when re-organizing the module
91
- def filepath_from_artifact(artifact: Artifact, using_key: Optional[str] = None):
95
+ def filepath_from_artifact(artifact: Artifact, using_key: str | None = None):
92
96
  if hasattr(artifact, "_local_filepath") and artifact._local_filepath is not None:
93
97
  return artifact._local_filepath.resolve()
94
98
  storage_key = auto_storage_key_from_artifact(artifact)
@@ -124,7 +128,7 @@ def store_artifact(localpath: UPathStr, storagepath: UPath) -> None:
124
128
 
125
129
 
126
130
  def delete_storage_using_key(
127
- artifact: Artifact, storage_key: str, using_key: Optional[str]
131
+ artifact: Artifact, storage_key: str, using_key: str | None
128
132
  ):
129
133
  filepath = attempt_accessing_path(artifact, storage_key, using_key=using_key)
130
134
  delete_storage(filepath)
@@ -1,11 +1,15 @@
1
- from typing import Optional
1
+ from __future__ import annotations
2
+
3
+ from typing import TYPE_CHECKING
2
4
 
3
5
  from anndata import AnnData
4
- from lamindb_setup.core.types import UPathStr
5
6
  from pandas import DataFrame
6
7
 
8
+ if TYPE_CHECKING:
9
+ from lamindb_setup.core.types import UPathStr
10
+
7
11
 
8
- def infer_suffix(dmem, adata_format: Optional[str] = None):
12
+ def infer_suffix(dmem, adata_format: str | None = None):
9
13
  """Infer LaminDB storage file suffix from a data object."""
10
14
  if isinstance(dmem, AnnData):
11
15
  if adata_format is not None:
@@ -1,11 +1,15 @@
1
- from typing import Optional, Tuple
1
+ from __future__ import annotations
2
+
3
+ from typing import TYPE_CHECKING, Optional, Tuple
2
4
 
3
5
  from lamindb_setup.core.upath import LocalPathClasses, UPath
4
6
  from lnschema_core import ids
5
- from lnschema_core.models import IsVersioned
7
+
8
+ if TYPE_CHECKING:
9
+ from lnschema_core.models import IsVersioned
6
10
 
7
11
 
8
- def set_version(version: Optional[str] = None, previous_version: Optional[str] = None):
12
+ def set_version(version: str | None = None, previous_version: str | None = None):
9
13
  """(Auto-) set version.
10
14
 
11
15
  If `version` is `None`, returns the stored version.
@@ -31,9 +35,9 @@ def set_version(version: Optional[str] = None, previous_version: Optional[str] =
31
35
  # uses `initial_version_id` to extract a stem_id that's part of id
32
36
  def init_uid(
33
37
  *,
34
- version: Optional[str] = None,
38
+ version: str | None = None,
35
39
  n_full_id: int = 20,
36
- is_new_version_of: Optional[IsVersioned] = None,
40
+ is_new_version_of: IsVersioned | None = None,
37
41
  ) -> str:
38
42
  if is_new_version_of is not None:
39
43
  stem_uid = is_new_version_of.stem_uid
@@ -53,9 +57,9 @@ def init_uid(
53
57
 
54
58
  def get_uid_from_old_version(
55
59
  is_new_version_of: IsVersioned,
56
- version: Optional[str] = None,
57
- using_key: Optional[str] = None,
58
- ) -> Tuple[str, str]:
60
+ version: str | None = None,
61
+ using_key: str | None = None,
62
+ ) -> tuple[str, str]:
59
63
  """{}."""
60
64
  msg = ""
61
65
  if is_new_version_of.version is None:
@@ -1,3 +1,5 @@
1
+ from __future__ import annotations
2
+
1
3
  import json
2
4
  from datetime import datetime, timezone
3
5
 
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: lamindb
3
- Version: 0.69.6
3
+ Version: 0.69.8
4
4
  Summary: A data framework for biology.
5
5
  Author-email: Lamin Labs <open-source@lamin.ai>
6
6
  Requires-Python: >=3.8
@@ -9,15 +9,16 @@ Classifier: Programming Language :: Python :: 3.8
9
9
  Classifier: Programming Language :: Python :: 3.9
10
10
  Classifier: Programming Language :: Python :: 3.10
11
11
  Classifier: Programming Language :: Python :: 3.11
12
- Requires-Dist: lnschema_core==0.64.4
13
- Requires-Dist: lamindb_setup==0.68.4
12
+ Requires-Dist: lnschema_core==0.64.5
13
+ Requires-Dist: lamindb_setup==0.68.5
14
14
  Requires-Dist: lamin_utils==0.13.1
15
- Requires-Dist: lamin_cli==0.11.0
15
+ Requires-Dist: lamin_cli==0.12.0
16
16
  Requires-Dist: rapidfuzz
17
17
  Requires-Dist: pyarrow
18
18
  Requires-Dist: typing_extensions!=4.6.0
19
19
  Requires-Dist: python-dateutil
20
20
  Requires-Dist: anndata>=0.8.0,<0.10.6
21
+ Requires-Dist: scipy<1.13.0rc1
21
22
  Requires-Dist: fsspec
22
23
  Requires-Dist: pandas
23
24
  Requires-Dist: graphviz
@@ -26,7 +27,7 @@ Requires-Dist: urllib3<2 ; extra == "aws"
26
27
  Requires-Dist: aiobotocore[boto3]>=2.5.4,<3.0.0 ; extra == "aws"
27
28
  Requires-Dist: s3fs==2023.12.2 ; extra == "aws"
28
29
  Requires-Dist: fsspec[s3]==2023.12.2 ; extra == "aws"
29
- Requires-Dist: bionty==0.42.4 ; extra == "bionty"
30
+ Requires-Dist: bionty==0.42.5 ; extra == "bionty"
30
31
  Requires-Dist: pandas<2 ; extra == "dev"
31
32
  Requires-Dist: pre-commit ; extra == "dev"
32
33
  Requires-Dist: nox ; extra == "dev"
@@ -0,0 +1,54 @@
1
+ lamindb/__init__.py,sha256=sZVLIGCk1KRIVzcEW76yuJ3Hcdhaz-ZbKi2OIEELTeE,2163
2
+ lamindb/_annotate.py,sha256=9YU0mC2ll8MDrgytFHy6xVBbHQSLRsYB9BlAu-3YA94,29918
3
+ lamindb/_artifact.py,sha256=mB8QyQKozzQsUxC8fOslwZyDegendQCR4BDIUJmAZ8M,35569
4
+ lamindb/_can_validate.py,sha256=rvoL5py40L5MldqYMm_vB-0x9pj1MDNhcSUDLumw-nc,14498
5
+ lamindb/_collection.py,sha256=w33zyFP5w4P5VoD8axwcZ_KPCqP2hjmWhIfOTtCjNN4,14418
6
+ lamindb/_feature.py,sha256=srAKchY7gqD-h-cWlEiAWuHlpFKFwv0PWIA-JX0Go8c,6758
7
+ lamindb/_feature_set.py,sha256=x9e6VWKq4iM_jDy-Al_YXL3LYveG8NN22KVbfr1yYuA,8710
8
+ lamindb/_filter.py,sha256=xnjJzjF3Zj4dK_Kfymvhgczk27MhhXz5ZYc7XINbgHY,1331
9
+ lamindb/_finish.py,sha256=4mCoDw24gXeOS_EALuUYIA57OqmcZWIi0Fk5fEDwmCg,8798
10
+ lamindb/_from_values.py,sha256=RaRMSTFM5j4Fn1rh-ezHdc5-F5AzMo85fVPqdZekMyo,11928
11
+ lamindb/_is_versioned.py,sha256=0PgRCmxEmYDcAjllLSOYZm132B1lW6QgmBBERhRyFt0,1341
12
+ lamindb/_parents.py,sha256=N9T8jbd3eaoHDLE9TD1y1QgGcO81E6Brapy8LILzRCQ,14790
13
+ lamindb/_query_manager.py,sha256=3zokXqxgj9vTJBnN2sbYKS-q69fyDDPF_aGq_rFHzXU,4066
14
+ lamindb/_query_set.py,sha256=fy6xMK9MPGbD8D_i5iNzR8XA009W05ud4tbgrzd5-Vg,11287
15
+ lamindb/_registry.py,sha256=Lc_0kBi984RuQM_rnwiDQbvRryEZZrQliFEkazOjVd0,19161
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+ lamindb/_run.py,sha256=b7A52M1On3QzFgIYyfQoz5Kk7V3wcu9p_Prq5bzd8v8,1838
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+ lamindb/_save.py,sha256=aqvE0ryZs4-sDk6DZPn-Ki724gHeLyA9w-1oN5m_XMU,11425
18
+ lamindb/_storage.py,sha256=VW8xq3VRv58-ciholvOdlcgvp_OIlLxx5GxLt-e2Irs,614
19
+ lamindb/_transform.py,sha256=rxojJ91qQSkeYDHYbwqjFAYxBMgJd3cq_K7Z0n5g8Aw,3482
20
+ lamindb/_ulabel.py,sha256=e5dw9h1tR0_u-DMn7Gzx0WhUhV5w7j4v3QbnLWQV7eI,1941
21
+ lamindb/_utils.py,sha256=LGdiW4k3GClLz65vKAVRkL6Tw-Gkx9DWAdez1jyA5bE,428
22
+ lamindb/_view.py,sha256=GV1FrqIMmdooEkA-5zvcTWgV1nqx1sehi6WdWEaFpxM,2171
23
+ lamindb/core/__init__.py,sha256=Mw4sI-xgnMXNsu84oYFQBZOF8mxxxhp6-e3BjTQqjlA,1131
24
+ lamindb/core/_data.py,sha256=A8NUs2Ii2R4FC_31zFGsi3Dae4Rzs66JtAK9MYn6M0k,17262
25
+ lamindb/core/_feature_manager.py,sha256=pGRWUZ0hhGZcexD3LsSfGzfQUCit7FoIEwzt6HANowo,13914
26
+ lamindb/core/_label_manager.py,sha256=duThEEgQxdNQBeTE1ssXX0XujUQa_M14B9e1TQKPwsQ,9078
27
+ lamindb/core/_mapped_collection.py,sha256=nnXVqHAbSPe34lN79VthoAOkJVxSD6ZbzZqXgv9H6Y8,17244
28
+ lamindb/core/_run_context.py,sha256=GS593lxHsbQyhbrp6ppzZ0r-fVe6W099NDXM6xyg8-U,17509
29
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