lamindb 0.69.8__py3-none-any.whl → 0.69.9__py3-none-any.whl

lamindb/__init__.py

@@ -40,7 +40,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.69.8"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.69.9"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 

lamindb/_artifact.py

@@ -22,7 +22,6 @@ from lamindb_setup.core.upath import (
 from lnschema_core import Artifact, Run, Storage
 from lnschema_core.models import IsTree
 from lnschema_core.types import (
-    DataLike,
     VisibilityChoice,
 )
 
@@ -114,7 +113,7 @@ def process_pathlike(
 
 def process_data(
     provisional_uid: str,
-    data: UPathStr | DataLike,
+    data: UPathStr | pd.DataFrame | AnnData,
     format: str | None,
     key: str | None,
     default_storage: Storage,
@@ -138,7 +137,7 @@ def process_data(
         )
         suffix = extract_suffix_from_path(path)
         memory_rep = None
-    elif isinstance(data, (pd.DataFrame, AnnData)):  # DataLike, spelled out
+    elif isinstance(data, (pd.DataFrame, AnnData)):
         storage = default_storage
         memory_rep = data
         if key is not None:
@@ -427,7 +426,7 @@ def log_storage_hint(
     logger.hint(hint)
 
 
-def data_is_anndata(data: DataLike):
+def data_is_anndata(data: AnnData | UPathStr):
     if isinstance(data, AnnData):
         return True
     if isinstance(data, (str, Path, UPath)):
@@ -435,7 +434,7 @@ def data_is_anndata(data: DataLike):
     return False  # pragma: no cover
 
 
-def data_is_mudata(data: DataLike):  # pragma: no cover
+def data_is_mudata(data: Any | UPathStr):  # pragma: no cover
     try:
         from mudata import MuData
     except ModuleNotFoundError:
@@ -725,7 +724,7 @@ def from_dir(
 # docstring handled through attach_func_to_class_method
 def replace(
     self,
-    data: UPathStr | DataLike,
+    data: UPathStr,
     run: Run | None = None,
     format: str | None = None,
 ) -> None:
@@ -808,9 +807,7 @@ def backed(self, is_run_input: bool | None = None) -> AnnDataAccessor | BackedAc
 
 
 # docstring handled through attach_func_to_class_method
-def load(
-    self, is_run_input: bool | None = None, stream: bool = False, **kwargs
-) -> DataLike:
+def load(self, is_run_input: bool | None = None, stream: bool = False, **kwargs) -> Any:
     _track_run_input(self, is_run_input)
     if hasattr(self, "_memory_rep") and self._memory_rep is not None:
         return self._memory_rep

lamindb/_collection.py

@@ -16,7 +16,7 @@ from lamin_utils import logger
 from lamindb_setup.core._docs import doc_args
 from lamindb_setup.core.hashing import hash_set
 from lnschema_core.models import Collection, CollectionArtifact, FeatureSet
-from lnschema_core.types import DataLike, VisibilityChoice
+from lnschema_core.types import VisibilityChoice
 
 from lamindb._utils import attach_func_to_class_method
 from lamindb.core._data import _track_run_input
@@ -65,7 +65,7 @@ def __init__(
     data: Artifact | Iterable[Artifact] = (
         kwargs.pop("data") if len(args) == 0 else args[0]
     )
-    meta: str | None = kwargs.pop("meta") if "meta" in kwargs else None
+    meta: Artifact | None = kwargs.pop("meta") if "meta" in kwargs else None
     name: str | None = kwargs.pop("name") if "name" in kwargs else None
     description: str | None = (
         kwargs.pop("description") if "description" in kwargs else None
@@ -273,7 +273,7 @@ def load(
     join: Literal["inner", "outer"] = "outer",
     is_run_input: bool | None = None,
     **kwargs,
-) -> DataLike:
+) -> Any:
     # cannot call _track_run_input here, see comment further down
     all_artifacts = self.artifacts.all()
     suffixes = [artifact.suffix for artifact in all_artifacts]

lamindb/core/_feature_manager.py

@@ -23,7 +23,7 @@ from lamindb.core.storage import LocalPathClasses
 from ._settings import settings
 
 if TYPE_CHECKING:
-    from lnschema_core.types import AnnDataLike, FieldAttr
+    from lnschema_core.types import FieldAttr
 
     from lamindb._query_set import QuerySet
 
@@ -132,7 +132,7 @@ def print_features(self: Data) -> str:
 
 
 def parse_feature_sets_from_anndata(
-    adata: AnnDataLike,
+    adata: AnnData,
     var_field: FieldAttr,
     obs_field: FieldAttr = Feature.name,
     **kwargs,

lamindb/core/storage/file.py

@@ -136,6 +136,9 @@ def delete_storage_using_key(
 
 def delete_storage(storagepath: Path):
     """Delete arbitrary artifact."""
+    # TODO is_relative_to is not available in 3.8 and deprecated since 3.12
+    # replace with check_path_is_child_of_root but this needs to first be debugged
+    # if not check_path_is_child_of_root(storagepath, settings.storage):
     if not storagepath.is_relative_to(settings.storage):  # type: ignore
         logger.warning("couldn't delete files outside of default storage")
         return "did-not-delete"

lamindb/core/types.py

@@ -4,14 +4,12 @@
    :toctree: .
 
    UPathStr
-   DataLike
    StrField
    ListLike
    TransformType
 """
 from lamindb_setup.core.types import UPathStr
 from lnschema_core.types import (
-    DataLike,
     ListLike,
     StrField,
     TransformType,

lamindb/setup/core/__init__.py

@@ -1,15 +1,4 @@
-"""Core setup library.
+import lamindb_setup as _lamindb_setup
+from lamindb_setup.core import *  # noqa: F403
 
-.. autosummary::
-   :toctree:
-
-   UserSettings
-   InstanceSettings
-   StorageSettings
-
-"""
-from lamindb_setup.core import (  # pragma: no cover
-    InstanceSettings,
-    StorageSettings,
-    UserSettings,
-)
+__doc__ = _lamindb_setup.core.__doc__.replace("lamindb_setup", "lamindb.setup")

{lamindb-0.69.8.dist-info → lamindb-0.69.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.69.8
+Version: 0.69.9
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,10 +9,10 @@ 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==0.64.5
-Requires-Dist: lamindb_setup==0.68.5
+Requires-Dist: lnschema_core==0.64.6
+Requires-Dist: lamindb_setup==0.69.0
 Requires-Dist: lamin_utils==0.13.1
-Requires-Dist: lamin_cli==0.12.0
+Requires-Dist: lamin_cli==0.12.1
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0

{lamindb-0.69.8.dist-info → lamindb-0.69.9.dist-info}/RECORD

@@ -1,8 +1,8 @@
-lamindb/__init__.py,sha256=sZVLIGCk1KRIVzcEW76yuJ3Hcdhaz-ZbKi2OIEELTeE,2163
+lamindb/__init__.py,sha256=rt70wiLn5OUFrtCA3UOodGkQp8M-1gdp4oB506MZ8ac,2163
 lamindb/_annotate.py,sha256=9YU0mC2ll8MDrgytFHy6xVBbHQSLRsYB9BlAu-3YA94,29918
-lamindb/_artifact.py,sha256=mB8QyQKozzQsUxC8fOslwZyDegendQCR4BDIUJmAZ8M,35569
+lamindb/_artifact.py,sha256=Y5FN6kFhOYn47ls14mOw1dToojg0akqlPcQ6XYsNv5w,35538
 lamindb/_can_validate.py,sha256=rvoL5py40L5MldqYMm_vB-0x9pj1MDNhcSUDLumw-nc,14498
-lamindb/_collection.py,sha256=w33zyFP5w4P5VoD8axwcZ_KPCqP2hjmWhIfOTtCjNN4,14418
+lamindb/_collection.py,sha256=P9B1jQul3umfNJ84bHKHbsjmze36Eh6jDQT9EqpvDFc,14408
 lamindb/_feature.py,sha256=srAKchY7gqD-h-cWlEiAWuHlpFKFwv0PWIA-JX0Go8c,6758
 lamindb/_feature_set.py,sha256=x9e6VWKq4iM_jDy-Al_YXL3LYveG8NN22KVbfr1yYuA,8710
 lamindb/_filter.py,sha256=xnjJzjF3Zj4dK_Kfymvhgczk27MhhXz5ZYc7XINbgHY,1331
@@ -22,7 +22,7 @@ lamindb/_utils.py,sha256=LGdiW4k3GClLz65vKAVRkL6Tw-Gkx9DWAdez1jyA5bE,428
 lamindb/_view.py,sha256=GV1FrqIMmdooEkA-5zvcTWgV1nqx1sehi6WdWEaFpxM,2171
 lamindb/core/__init__.py,sha256=Mw4sI-xgnMXNsu84oYFQBZOF8mxxxhp6-e3BjTQqjlA,1131
 lamindb/core/_data.py,sha256=A8NUs2Ii2R4FC_31zFGsi3Dae4Rzs66JtAK9MYn6M0k,17262
-lamindb/core/_feature_manager.py,sha256=pGRWUZ0hhGZcexD3LsSfGzfQUCit7FoIEwzt6HANowo,13914
+lamindb/core/_feature_manager.py,sha256=B65Rc1wlsc7QFQUH6H9bhiwy5bf6X_Y38LJKaqsGRoY,13897
 lamindb/core/_label_manager.py,sha256=duThEEgQxdNQBeTE1ssXX0XujUQa_M14B9e1TQKPwsQ,9078
 lamindb/core/_mapped_collection.py,sha256=nnXVqHAbSPe34lN79VthoAOkJVxSD6ZbzZqXgv9H6Y8,17244
 lamindb/core/_run_context.py,sha256=GS593lxHsbQyhbrp6ppzZ0r-fVe6W099NDXM6xyg8-U,17509
@@ -33,7 +33,7 @@ lamindb/core/_transform_settings.py,sha256=eV96QKX9jOojjzF-a0oo0wXQsMXN2F6QV7orE
 lamindb/core/_view_tree.py,sha256=PTwmKZSQL2UhKuSdV5Wp7o1JDjv1qwgsVCj3ThkbKb8,3447
 lamindb/core/exceptions.py,sha256=PHk5lyBdJPrrEQcid3ItfdNzz3fgiQsUmsEDdz063F0,197
 lamindb/core/fields.py,sha256=Jgi_XI-iTe6cT7oD8FV_JqEpjN1Q9rZWwL8VLtj4jkA,164
-lamindb/core/types.py,sha256=2CJdqGXxbYv4oOB_t6p2PJdg_5j9qDUSJJYEV-lcnqA,256
+lamindb/core/types.py,sha256=xeQF2x40p2pR9eIVQrXT74RrS810z2fbjmTRTSQUqPM,230
 lamindb/core/versioning.py,sha256=DsEHpCueNwhRiIaRH5-O8H_1fJVNtWslCRx30YiIS5o,3080
 lamindb/core/datasets/__init__.py,sha256=zRP98oqUAaXhqWyKMiH0s_ImVIuNeziQQ2kQ_t0f-DI,1353
 lamindb/core/datasets/_core.py,sha256=o1c8vGhO-Hss-osBGdxldDFYh_hwsksh8H1bm6rYIi0,18861
@@ -42,13 +42,13 @@ lamindb/core/storage/__init__.py,sha256=9alBNtyH59VnoWJS-IdjLwFKlK-kgeCGl6jXk0_w
 lamindb/core/storage/_anndata_sizes.py,sha256=aXO3OB--tF5MChenSsigW6Q-RuE8YJJOUTVukkLrv9A,1029
 lamindb/core/storage/_backed_access.py,sha256=6grFzub43w_k-Zxa4iqSY6GAoCewE1FZTx52wfGKZIg,24383
 lamindb/core/storage/_zarr.py,sha256=0i9-cJPjieIsp5UpK-IyRPkHAF-iKkWgpkWviSni2MM,2900
-lamindb/core/storage/file.py,sha256=N_t_EiWP29XwMDsbVz1Kw2ksVBmXnHYkPtWEXemknOM,7287
+lamindb/core/storage/file.py,sha256=qxIdPTXqtedXc1Zc4WunBorRLSo4bkYXbTAgQkWc-dE,7519
 lamindb/core/storage/object.py,sha256=5f_E4xLUjy4rG_klSmVjZWuVMxdzme-bQxCKfbY9nhM,1158
 lamindb/integrations/__init__.py,sha256=aH2PmO2m4-vwIifMYTB0Fyyr_gZWtVnV71jT0tVWSw0,123
 lamindb/integrations/_vitessce.py,sha256=xLlFr_GzoY5RjyouPFEO-W7crBlTVQdHR2ns1IcCZFc,1673
 lamindb/setup/__init__.py,sha256=OwZpZzPDv5lPPGXZP7-zK6UdO4FHvvuBh439yZvIp3A,410
-lamindb/setup/core/__init__.py,sha256=LqIIvJNcONxkqjbnP6CUaP4d45Lbd6TSMAcXFp4C7_8,231
-lamindb-0.69.8.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-lamindb-0.69.8.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
-lamindb-0.69.8.dist-info/METADATA,sha256=YmH_AI9gO24-zfttptrppfCdnp7c62ucvnN5xbW_ccw,2887
-lamindb-0.69.8.dist-info/RECORD,,
+lamindb/setup/core/__init__.py,sha256=SevlVrc2AZWL3uALbE5sopxBnIZPWZ1IB0NBDudiAL8,167
+lamindb-0.69.9.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+lamindb-0.69.9.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+lamindb-0.69.9.dist-info/METADATA,sha256=TviWVIwvJbMOdMe6PeCFHeQNmuujUSETcBfUJO6a_C0,2887
+lamindb-0.69.9.dist-info/RECORD,,