lamindb 0.76.13__py3-none-any.whl → 0.76.15__py3-none-any.whl

lamindb/core/storage/_pyarrow_dataset.py

@@ -0,0 +1,31 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+import pyarrow.dataset
+from lamindb_setup.core.upath import LocalPathClasses
+
+if TYPE_CHECKING:
+    from upath import UPath
+
+
+PYARROW_SUFFIXES = (".parquet", ".csv", ".json", ".orc", ".arrow", ".feather")
+
+
+def _is_pyarrow_dataset(path: UPath) -> bool:
+    # it is assumed here that path exists
+    if path.is_file():
+        return path.suffix in PYARROW_SUFFIXES
+    else:
+        objects = path.rglob("*")
+        suffixes = {object.suffix for object in objects if object.suffix != ""}
+        return len(suffixes) == 1 and suffixes.pop() in PYARROW_SUFFIXES
+
+
+def _open_pyarrow_dataset(path: UPath) -> pyarrow.dataset.Dataset:
+    if isinstance(path, LocalPathClasses):
+        path_str, filesystem = path.as_posix(), None
+    else:
+        path_str, filesystem = path.path, path.fs
+
+    return pyarrow.dataset.dataset(path_str, filesystem=filesystem)

lamindb/core/types.py

@@ -13,6 +13,7 @@
 from lamindb_setup.core.types import UPathStr
 from lnschema_core.types import (
     ArtifactType,
+    FieldAttr,
     ListLike,
     StrField,
     TransformType,

{lamindb-0.76.13.dist-info → lamindb-0.76.15.dist-info}/METADATA

@@ -1,29 +1,28 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.76.13
+Version: 0.76.15
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
-Requires-Python: >=3.9
+Requires-Python: >=3.9,<3.13
 Description-Content-Type: text/markdown
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Dist: lnschema_core==0.75.0
-Requires-Dist: lamin_utils==0.13.6
-Requires-Dist: lamin_cli==0.19.0
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: lnschema_core==0.76.1
+Requires-Dist: lamin_utils==0.13.7
+Requires-Dist: lamin_cli==0.20.1
 Requires-Dist: lamindb_setup
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
 Requires-Dist: python-dateutil
 Requires-Dist: anndata>=0.8.0,<=0.10.9
-Requires-Dist: scipy<1.13.0rc1
 Requires-Dist: fsspec
-Requires-Dist: pandas
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.51.2 ; extra == "bionty"
+Requires-Dist: bionty==0.52.0 ; extra == "bionty"
 Requires-Dist: line_profiler ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
@@ -35,9 +34,9 @@ Requires-Dist: mudata ; extra == "dev"
 Requires-Dist: nbproject_test>=0.5.1 ; extra == "dev"
 Requires-Dist: faker-biology ; extra == "dev"
 Requires-Dist: django-schema-graph ; extra == "erdiagram"
-Requires-Dist: readfcs>=1.1.8 ; extra == "fcs"
+Requires-Dist: readfcs>=1.1.9 ; extra == "fcs"
 Requires-Dist: lamindb_setup[gcp] ; extra == "gcp"
-Requires-Dist: nbproject==0.10.4 ; extra == "jupyter"
+Requires-Dist: nbproject==0.10.5 ; extra == "jupyter"
 Requires-Dist: jupytext ; extra == "jupyter"
 Requires-Dist: nbconvert ; extra == "jupyter"
 Requires-Dist: zarr>=2.16.0 ; extra == "zarr"

{lamindb-0.76.13.dist-info → lamindb-0.76.15.dist-info}/RECORD

@@ -1,40 +1,40 @@
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-lamindb/_artifact.py,sha256=AHyKZ_D_qMGtywAklo42je8BZB-VBqQ-ZTaI9AB_Yxs,44905
-lamindb/_can_validate.py,sha256=1pUavLwZ_yPAtbVYKOGYUHaPxlJGZ246qZ0e-4ZUDSc,19552
-lamindb/_collection.py,sha256=ZQ45_9n0komz1y8l_vzZ-cRn-ghinE0Izl889Mk-TSA,14249
-lamindb/_curate.py,sha256=KpEP0-9nQUmiRn6z7fiGs6BmQdpqSg3QPlAgV-S9_wA,58839
-lamindb/_feature.py,sha256=nZhtrH0ssoNls-hV-dkwfK9sKypg2El59R9qfarxfUE,5340
-lamindb/_feature_set.py,sha256=JQSP-YLam1KW-rDzly5Dm4IYVL2A6ec7ufIf6iCc2W8,8169
+lamindb/__init__.py,sha256=ZoRboX4PQc0sbVajeZ1fd4GoLN3YDj5U74zVUpcSd9I,2278
+lamindb/_artifact.py,sha256=WNdKAJFu3sFgQ_Qe1JflDHiTP4EGhAIkzaHFwTthAjY,44903
+lamindb/_can_validate.py,sha256=TKfkHgkPl1bwuJrQCp6pHgQbi7m2pc_zjFhZfUAUU20,19573
+lamindb/_collection.py,sha256=MLOEoOgTu7rTlRD7zkm1k0YIk_gVhQDO17JbmZCptOs,14573
+lamindb/_curate.py,sha256=pLsdtnnTn0qQbsUB4hrU3yuoVnVNh-BQe10EpMNZ4Ns,64083
+lamindb/_feature.py,sha256=9cgrcHoyOa1jpON-9KiUfFSHcxiGECiefUAqAx4cVvU,5325
+lamindb/_feature_set.py,sha256=WdXw_YGlMXCs8l0WVHOrqvvrH2hsQLqCiho8LFDYwhI,8161
 lamindb/_filter.py,sha256=Pf9NHV4gm7NOC0Frtvx4W7nvwt2EowOP74DwppyXAZs,635
 lamindb/_finish.py,sha256=VMAmxCUFmTKIMSCx7LEh4QAnWDeue6MeUAAzkMVEYMU,9546
-lamindb/_from_values.py,sha256=iqcR8T8i9VZpnn09W441zW-djhWMh8EZj7XFJq9jP2k,14211
-lamindb/_is_versioned.py,sha256=5lAnhTboltFkZCKVRV1uxkm0OCjJz_HKi3yQq_vEuMs,1306
-lamindb/_parents.py,sha256=KMBUfCLNqjmFzOdZIXaUFqDPeEpWP28MCkHHPq887h8,16341
-lamindb/_query_manager.py,sha256=pmPhJQ85-7XeAU9TFv6LPGi9F7dBgztZgZcXz33HYJM,3710
-lamindb/_query_set.py,sha256=81y1c-Y-PGCmqc64WizlCiGTbsrApsajtX2xj7xrsMo,12730
-lamindb/_record.py,sha256=LkKtDxqlTq43UlAiJ96_nbpjj9eQbU4N3HpfBVfImJo,23395
+lamindb/_from_values.py,sha256=uRtZLaMWKoANMMXm1hrADHfckRCTiK8_d02Yp07nLkw,14119
+lamindb/_is_versioned.py,sha256=GWZk-usV6aB33Cl9AlrnEGE5nxUkZic7QJzOW_DrwQA,1298
+lamindb/_parents.py,sha256=INhbqh6IaUjuYVUOp-6rnOGN-8kGZirNqqW9XQ1qz_M,17119
+lamindb/_query_manager.py,sha256=noc05Ad-aADxckOVBVDAiErFB7gL8XTgckELvI4rGmM,3702
+lamindb/_query_set.py,sha256=6vHOvB_uXzKVVIw8AAVw7EYOIAGuw3TYcUzkpNlFLdE,12973
+lamindb/_record.py,sha256=isR9GMQFwUUwVSmPNABvEzcJS38TbjhD7Cc6kygPsTA,26819
 lamindb/_run.py,sha256=K_5drpLn3D7y3XtZ3vtAw35rG5RCSvB4bXQZx4ESSI0,1964
-lamindb/_save.py,sha256=BCaSFnANYPxTqL5gw7Hrh_9kz7SDyOxrJV2KW6rXqts,11366
+lamindb/_save.py,sha256=OD052Qr_hiMyAonHTktKETe_Bhnp1RY810y0rwZqpBQ,11352
 lamindb/_storage.py,sha256=GBVChv-DHVMNEBJL5l_JT6B4RDhZ6NnwgzmUICphYKk,413
-lamindb/_transform.py,sha256=wZDkY8lp4d_OsO5a7rLs1RamkDzBXZSLaWJU34zRnmA,4728
-lamindb/_ulabel.py,sha256=XDSdZBXX_ki5s1vOths3MjF2x5DPggBR_PV_KF4SGyg,1611
+lamindb/_transform.py,sha256=HpqRCk0ZTmqxSV4nRbyvDq8fAQEE9wTj31d-CusiL6A,4720
+lamindb/_ulabel.py,sha256=DQQzAPkrOg8W9I77BJ5umajR8MQcFSvXYUy53YNN2HA,1604
 lamindb/_utils.py,sha256=LGdiW4k3GClLz65vKAVRkL6Tw-Gkx9DWAdez1jyA5bE,428
 lamindb/_view.py,sha256=4Ln2ItTb3857PAI-70O8eJYqoTJ_NNFc7E_wds6OGns,2412
-lamindb/core/__init__.py,sha256=57AXQ286eOX2_o5HUeqIFJrfqN-OZ_E7FVHd3Xm5oOk,1483
+lamindb/core/__init__.py,sha256=y87MCP1BEC2qHNVDIOwqVteIP_2hPCdIoa9JXr0EG8U,1524
 lamindb/core/_context.py,sha256=dI3z7fCMRPC3IMb7-EIaQYhacSZBA4HfLVFyoJtVL7I,22900
-lamindb/core/_data.py,sha256=P0vlbw_UQp9UDNMmUo9YFxqurcWtMaKPWCT12IRA2C0,19672
+lamindb/core/_data.py,sha256=BVZkxK8aloSecH25LivbwnjcG1fz7Gs2UDceO5pWd3I,20049
 lamindb/core/_django.py,sha256=yeMPp1n9WrFmEjVRdavfpVqAolPLd24RseTQlvsK67w,7157
-lamindb/core/_feature_manager.py,sha256=yH6HGF_c0NwIE6hxcMUZdZrokx75Kz-54d_3JhyCglQ,39020
-lamindb/core/_label_manager.py,sha256=bhD6krOrf0SWXfCzhFsEA-7h0ZLJ59YSPxWnlq7DZiE,9991
-lamindb/core/_mapped_collection.py,sha256=M50haewVAFONeF71QQbzD09L8lVZCL1hyf0W87jKE5U,24575
+lamindb/core/_feature_manager.py,sha256=q4WmzJvFLL_fAs-vNRgV2klanAoU6Wu8_g0O2dyIjVg,40027
+lamindb/core/_label_manager.py,sha256=yh-r4KbtOArMUKPJL75yOxJc8HUKqsik8pExBVKyDlA,10949
+lamindb/core/_mapped_collection.py,sha256=EDS0xzOdCc_iGE_Iqv5COTVHNm4jWue7Jtcd8DdXkJU,24591
 lamindb/core/_settings.py,sha256=6jNadlQdimxCsKR2ZyUD0YJYzOdubTnKktki-MqEWqQ,6137
 lamindb/core/_sync_git.py,sha256=lIgl6YfpH4rCFT1WILAp7zlemZfxog1d0zp3cX0KIZw,4531
 lamindb/core/_track_environment.py,sha256=Ywzg_sJ7guI1dcsN7h5orce9VdYl8VGVE3OLITlHBXQ,820
-lamindb/core/exceptions.py,sha256=0B36kOVo-Dik5KbSKvy5GPuMjUfhVb99dJwXl_J0ldo,1636
+lamindb/core/exceptions.py,sha256=Y1XQGbv9MgNLVvoClpcwN4NugrLW3Xgy1up15wZK740,1783
 lamindb/core/fields.py,sha256=47Jmh3efUr5ZscgimR_yckY-I3cNf8ScLutbwKCK3j4,162
 lamindb/core/loaders.py,sha256=KMTkDa73jkRVvI9uc5Fgr0t6mq22cAxBwhSlUZKUaBg,4016
 lamindb/core/schema.py,sha256=Y1tGn93B236PtnYZkpgTNFgTXBcVujPM1qh1kNG6Nbs,3441
-lamindb/core/types.py,sha256=uVBqSVLoQaTkqP9nqsJhwU6yYnx8H5e6-ZxrB6vpOOw,265
+lamindb/core/types.py,sha256=cL4cmJFA1xfxAIFOQqoa_fvVzdUM3A5blHStVwRNtk4,280
 lamindb/core/versioning.py,sha256=KUpd94F5QpbDxx9eKgZwrpPyQpm9YeHVedrTEO2a_mI,4839
 lamindb/core/datasets/__init__.py,sha256=zRP98oqUAaXhqWyKMiH0s_ImVIuNeziQQ2kQ_t0f-DI,1353
 lamindb/core/datasets/_core.py,sha256=JGP_q-OQibDCEaI54jZ2F6fSbSW9Yg6oYOqgOCXM0v4,20414
@@ -42,7 +42,8 @@ lamindb/core/datasets/_fake.py,sha256=BZF9R_1iF0HDnvtZNqL2FtsjSMuqDIfuFxnw_LJYIh
 lamindb/core/storage/__init__.py,sha256=JOIMu_7unbyhndtH1j0Q-9AvY8knSuc1IJO9sQnyBAQ,498
 lamindb/core/storage/_anndata_accessor.py,sha256=2p1HjoatmZjQ1u94tjgmXgiv8MKowrQH5xInDmiLCw4,24191
 lamindb/core/storage/_anndata_sizes.py,sha256=aXO3OB--tF5MChenSsigW6Q-RuE8YJJOUTVukkLrv9A,1029
-lamindb/core/storage/_backed_access.py,sha256=O0zazsDlW0PKa52WHV5HooHGGI81FxLT6VEvNONdiEc,3234
+lamindb/core/storage/_backed_access.py,sha256=t9iS9mlZQBy1FfIS-Twt-96npYiShbPwEo2y9_3b6jY,3517
+lamindb/core/storage/_pyarrow_dataset.py,sha256=wuLsEvdblqMdUdDfMtis8AWrE3igzvFWTSTbxuD1Oc8,926
 lamindb/core/storage/_tiledbsoma.py,sha256=0NPLS5m1icEhzWPfXAv4U2SNiLGqGQd7FM6xCm5wYEc,7269
 lamindb/core/storage/_valid_suffixes.py,sha256=vUSeQ4s01rdhD_vSd6wKmFBsgMJAKkBMnL_T9Y1znMg,501
 lamindb/core/storage/_zarr.py,sha256=TODQD3p1eykoPwP-c-YRP_UDmsbMeBGMGvkBxxOMeYc,3663
@@ -55,7 +56,7 @@ lamindb/integrations/__init__.py,sha256=RWGMYYIzr8zvmNPyVB4m-p4gMDhxdRbjES2Ed23O
 lamindb/integrations/_vitessce.py,sha256=uPl45_w4Uu9_BhpBDDVonC1nDOuAnB7DAnzi5w5bZAE,4032
 lamindb/setup/__init__.py,sha256=OwZpZzPDv5lPPGXZP7-zK6UdO4FHvvuBh439yZvIp3A,410
 lamindb/setup/core/__init__.py,sha256=SevlVrc2AZWL3uALbE5sopxBnIZPWZ1IB0NBDudiAL8,167
-lamindb-0.76.13.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-lamindb-0.76.13.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
-lamindb-0.76.13.dist-info/METADATA,sha256=Vo8AcZfSEBwW3NJsFndztG1b2fAVSquWw2OENmncc8M,2361
-lamindb-0.76.13.dist-info/RECORD,,
+lamindb-0.76.15.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+lamindb-0.76.15.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+lamindb-0.76.15.dist-info/METADATA,sha256=31K0SoWfAxBpWR3x_7PLFfwpu-mnsQ8IHFqsvjdg_cw,2365
+lamindb-0.76.15.dist-info/RECORD,,