lamindb 0.48a2__py3-none-any.whl → 0.48.1__py3-none-any.whl

lamindb/dev/storage/file.py

@@ -6,7 +6,7 @@ from typing import Union
 import anndata as ad
 import fsspec
 import pandas as pd
-from lamin_logger import logger
+from lamin_utils import logger
 from lamindb_setup import settings
 from lamindb_setup.dev import StorageSettings
 from lamindb_setup.dev.upath import UPath, infer_filesystem
@@ -59,6 +59,8 @@ def attempt_accessing_path(file: File, storage_key: str):
 
 # add type annotations back asap when re-organizing the module
 def filepath_from_file(file: File):
+    if hasattr(file, "_local_filepath") and file._local_filepath is not None:
+        return file._local_filepath.resolve()
     storage_key = auto_storage_key_from_file(file)
     path = attempt_accessing_path(file, storage_key)
     return path

{lamindb-0.48a2.dist-info → lamindb-0.48.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.48a2
+Version: 0.48.1
 Summary: LaminDB: Manage R&D data & analyses.
 Author-email: Lamin Labs <laminlabs@gmail.com>
 Requires-Python: >=3.8
@@ -8,9 +8,9 @@ Description-Content-Type: text/markdown
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
-Requires-Dist: lnschema_core==0.39.0
-Requires-Dist: lamindb_setup==0.49.0
-Requires-Dist: lamin_logger==0.8.2
+Requires-Dist: lnschema_core==0.42.2
+Requires-Dist: lamindb_setup==0.49.1
+Requires-Dist: lamin_utils==0.9.3
 Requires-Dist: erdiagram>=0.1.2
 Requires-Dist: rapidfuzz
 Requires-Dist: pydantic[dotenv]
@@ -25,7 +25,7 @@ Requires-Dist: botocore==1.29.76 ; extra == "aws"
 Requires-Dist: urllib3<2 ; extra == "aws"
 Requires-Dist: boto3==1.26.76 ; extra == "aws"
 Requires-Dist: fsspec[s3]==2023.5.0 ; extra == "aws"
-Requires-Dist: lnschema_bionty==0.27.3 ; extra == "bionty"
+Requires-Dist: lnschema_bionty==0.28.2 ; extra == "bionty"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
 Requires-Dist: laminci>=0.3 ; extra == "dev"
@@ -73,7 +73,7 @@ Update 2023-06-14:
 
 ## Introduction
 
-LaminDB is a free & open-source Python library to:
+LaminDB is an open-source Python library to:
 
 - Manage files & datasets while tracking provenance across pipelines, notebooks & app uploads.
 - Manage biological registries, ontologies, features & schemas.
@@ -83,7 +83,7 @@ LaminDB is a free & open-source Python library to:
 
 LaminApp is a data management app built on LaminDB. If LaminDB ~ git, LaminApp ~ GitHub.
 
-LaminApp, support, code templates & auto-dispatched integration tests for a BioTech data & analytics platform are currently only available on an enterprise plan. LaminApp is available for your cloud or AWS infrastructure or hosted by us.
+LaminApp, support, code templates & auto-dispatched integration tests for a BioTech data & analytics platform are currently only available on an enterprise plan. LaminApp is available for your cloud infrastructure or hosted by us.
 
 ## Quickstart
 
@@ -257,7 +257,7 @@ pip install lamindb  # basic data management
 You can configure the installation using `extras`, e.g.,
 
 ```shell
-pip install lamindb[jupyter,bionty,fcs,aws]
+pip install 'lamindb[jupyter,bionty,fcs,aws]'
 ```
 
 Supported `extras` are:
@@ -313,6 +313,8 @@ LaminDB consists of the `lamindb` Python package (repository [here](https://gith
 - [lnschema-bionty](https://github.com/laminlabs/lnschema-bionty): Bionty schema, ORMs that are coupled to Bionty's entities.
 - [lnschema-lamin1](https://github.com/laminlabs/lnschema-lamin1): Exemplary configured schema to track samples, treatments, etc.
 - [nbproject](https://github.com/laminlabs/nbproject): Parse metadata from Jupyter notebooks.
+- [lamin-utils](https://github.com/laminlabs/lamin-utils): Utilities for LaminDB and Bionty.
+- [readfcs](https://github.com/laminlabs/readfcs): FCS file reader.
 
 LaminHub & LaminApp are not open-sourced, and neither are templates that model lab operations.
 

lamindb-0.48.1.dist-info/RECORD

@@ -0,0 +1,42 @@
+lamindb/__init__.py,sha256=2z4YI7b6UvGZHwooeAkDKiCVDpQ5TkxRK62EDLT9iMA,2647
+lamindb/_context.py,sha256=lRGju9hB_rqaSAtIFY28kIciPSxy9yG86frdIBI1bBc,17875
+lamindb/_dataset.py,sha256=nR1cGJZmNEoiATECFEBMKskk5ynP46ODejvSoOLH_hA,5546
+lamindb/_delete.py,sha256=Jzb0sTlpdNDMa90ORMFiPbX0d-GhZsjmobQFc1miuJ8,1877
+lamindb/_feature.py,sha256=CNSZpnMX25JX5C11ie6GPAvwPiKzd7EYhLZ9Uk1HEWk,4043
+lamindb/_feature_manager.py,sha256=EaIUaFa67VyIJZ1u6ncPfiCzJkGNKmt2RZ9P3b_tzUA,6713
+lamindb/_feature_set.py,sha256=zkhCuH33PgTc3-zsWT7XlJcxIf7fBv7OI4n8R8cS_8I,6747
+lamindb/_file.py,sha256=sKCkAg0IMm0M4f0FwZhBKmgRUZPVN97vvwakicAp6oM,32815
+lamindb/_from_values.py,sha256=bbahbzm18yLam3LC_rguX7wFaBX8KYG3So6BrPcvJzI,12106
+lamindb/_label.py,sha256=taBj95rOrj56xQhjKN04E4FA1qWtsKZbCzC5OGLcIPA,2771
+lamindb/_logger.py,sha256=Q9ugUnZE4EwH0N6qFMG2HlILmu-SArnEEy-nafTPjRg,47
+lamindb/_manager.py,sha256=x6-rRsFlPHL1VAN_mipfNKInY_E6E-M28Q8xn4fphUo,1895
+lamindb/_orm.py,sha256=AHia6AzRKLldg6n1emm02e9BOFGTbTv1qy-tdMJjWdY,23727
+lamindb/_queryset.py,sha256=hhToC5NcKS2PF59jxpdbsA16VBg1oVqVeMzWEFQXQRE,9713
+lamindb/_save.py,sha256=ZgV5qXBKLf84U0ssCS8z19bkIsh9SgjcJe38-laKlY8,9004
+lamindb/_select.py,sha256=w-a_vOLBm-HFIfDhtLJd9ieeU-V8vn16EQ2QlgU0jyA,325
+lamindb/_transform.py,sha256=K-Y37UqQPu06lsA3Jfnkyt5dssRpuMnpCDDHDbT40Z4,1251
+lamindb/_view.py,sha256=V5zatnXT40UmcRQx1ZBxyRJUnIqTv_iEelv4Tli3WyI,2074
+lamindb/types.py,sha256=svg5S_aynuGfbEOsbmqkR_gF9d9YMzfOkcvGN37Rzvg,232
+lamindb/dev/__init__.py,sha256=JYmmgCbPdYNGL6J4aXxWd988su__uFAScRppvLsOzLo,431
+lamindb/dev/_settings.py,sha256=2mV4K29PZaf1FVM5XbMZD85_1wSvHc3iF20VSBRsFKY,2842
+lamindb/dev/_view_parents.py,sha256=IgW2fSwgViSJPIZhloW76pWvvljJ07Ev7Y1xl3ixF1E,7844
+lamindb/dev/hashing.py,sha256=oYHDSEjINsmDYgCLasnhh_VHbB1dLag27ufVUwDgLyQ,1385
+lamindb/dev/utils.py,sha256=LGdiW4k3GClLz65vKAVRkL6Tw-Gkx9DWAdez1jyA5bE,428
+lamindb/dev/datasets/__init__.py,sha256=ZVnWS5LhUjzrIe_v81hlqoCzgi_gDiV-W9T_rnqTuXo,1215
+lamindb/dev/datasets/_core.py,sha256=NAjisahI6C7GaZfIvmaIl_MTgvin-1NJAjxSG-EZbUA,11767
+lamindb/dev/datasets/_fake.py,sha256=S8mNho-oSh1M9x9oOSsUBLLHmBAegsOLlFk6LnF81EA,942
+lamindb/dev/storage/__init__.py,sha256=zFr8mpH1c3fzaQMYMwoLU9-zIMQ7laiPn5YDHDdFL5Y,424
+lamindb/dev/storage/_anndata_sizes.py,sha256=0XVzA6AQeVGPaGPrhGusKyxFgFjeo3qSN29hxb8D5E8,993
+lamindb/dev/storage/_backed_access.py,sha256=V7fhzx2R41ps91T0zzTLVN3x7wUuMZOxxMF_0PoJjxI,18695
+lamindb/dev/storage/_zarr.py,sha256=7W1Jos1QOOF3f41uML_arQoDTNPZVpRyP2m3SLWaCAo,2766
+lamindb/dev/storage/file.py,sha256=hO3t8nUncrUhSHtOdgvtfOAGnUJ2C9IRqPeq1TvFG0o,5978
+lamindb/dev/storage/object.py,sha256=x8sy23WqkGir2sg2c3AngQPgv0RbErEA6cpvVN0Zc4I,945
+lamindb/schema/__init__.py,sha256=PznznlFvbeNSZKpn1RS6Gv0JMXFkLmU2_ej_1hVLSTs,796
+lamindb/schema/_core.py,sha256=nWR3X_rNd1AbWw3naMiBi8ppAEpqIDyEYqM54feRB_s,766
+lamindb/setup/__init__.py,sha256=8-0F2C4Glx23-b8-D_1CBGgRBM5PppVhazhoXZYOLsg,275
+lamindb/setup/dev/__init__.py,sha256=iD0f2lx_Hgp-udkiPGal7si5waJSOgvnG6Id-g1mMOY,213
+lamindb-0.48.1.dist-info/entry_points.txt,sha256=MioM8vSpKwXxY3geNBwjo1wnwy1l15WjJYlI3lpKuZI,53
+lamindb-0.48.1.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+lamindb-0.48.1.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+lamindb-0.48.1.dist-info/METADATA,sha256=hV5390-kWv89OW9gmlWPCNQ3-t2ynnezhp18bhh3klM,10843
+lamindb-0.48.1.dist-info/RECORD,,

lamindb/_category.py

@@ -1,42 +0,0 @@
-from typing import List
-
-from lamindb_setup.dev._docs import doc_args
-from lnschema_core import Category, Feature
-from lnschema_core.types import ListLike
-
-from lamindb.dev.utils import attach_func_to_class_method
-
-from . import _TESTING
-from ._from_values import get_or_create_records, index_iterable
-
-
-@classmethod  # type:ignore
-@doc_args(Category.from_values.__doc__)
-def from_values(cls, values: ListLike, feature: Feature, **kwargs) -> List["Category"]:
-    """{}"""
-    iterable_idx = index_iterable(values)
-    records = get_or_create_records(
-        iterable=iterable_idx,
-        field=Category.name,
-        # here, feature_id is a kwarg, which is an additional condition
-        # in queries for potentially existing records
-        feature_id=feature.id,
-    )
-    return records
-
-
-METHOD_NAMES = [
-    "from_values",
-]
-
-if _TESTING:
-    from inspect import signature
-
-    SIGS = {
-        name: signature(getattr(Category, name))
-        for name in METHOD_NAMES
-        if name != "__init__"
-    }
-
-for name in METHOD_NAMES:
-    attach_func_to_class_method(name, Category, globals())

lamindb-0.48a2.dist-info/RECORD

@@ -1,41 +0,0 @@
-lamindb/__init__.py,sha256=lYI9U2XcQVYh27tMMGvGIge12n3p6iSU2UoUs6JSMV4,2768
-lamindb/_category.py,sha256=YfSFedvi6CoqwneXGwG1Xt1emnq_-Zr1FW2mCE7BZuQ,1100
-lamindb/_context.py,sha256=c07en-4ELXpAOIrQ8YO3Kd8amgorFZw1hnE36CZZQNk,17848
-lamindb/_dataset.py,sha256=J4kmPfS9cSPr9qJ5Rn7L0Zv2FnVA6FrUBvwEgGBMUDQ,5438
-lamindb/_delete.py,sha256=XwPqQ6AePgBLv6o0Uz-PHKaZQUgwwISPXDG03f6RCcs,1854
-lamindb/_feature.py,sha256=1C3pfOo76HJXEhy7fEUjlDoakweycLoxTuGURIW5MMw,2889
-lamindb/_feature_set.py,sha256=IJG5fiAyM1Z1xTJ1NffVdJQ_jD77r6ChSq4LH5qFghI,5511
-lamindb/_file.py,sha256=-TRRIZ0d9yb9myA7fY5wTIHzkFk8pZLKjDOk3hbY04o,31625
-lamindb/_from_values.py,sha256=Rxx8jmVP5ScA9iBz7ellzKKPP9adgYPdmRV4nH6ErQc,9583
-lamindb/_logger.py,sha256=d1jQdFL4gMKbzcc1dMOgKoEaUlWhyK-VsnxYLlG9caY,48
-lamindb/_manager.py,sha256=ZvBG9X8v1Vyvopd-_9zAGlxluFTN07Slq5kEv7Dq_0s,1651
-lamindb/_orm.py,sha256=CIk10FcHRLqMVhnmP8RQ9LjkOoM5q8r2W8IxmneagVI,19156
-lamindb/_queryset.py,sha256=RErd6jLi94qh14_3Ios9NPxMc2q4b4yEgezYqhmgaro,9693
-lamindb/_save.py,sha256=ZauBc5Fr6vMmCd-O66ap6cvS-5ZWvGA2DGInRSE1Rm4,8546
-lamindb/_select.py,sha256=w-a_vOLBm-HFIfDhtLJd9ieeU-V8vn16EQ2QlgU0jyA,325
-lamindb/_transform.py,sha256=EG87wlUffGI_-N92Qu-qklNRs4hTEeHpEtspYIVGKtc,911
-lamindb/_view.py,sha256=dgsIsCbPqtIiaBgvjm5z0ouzC0kjpAI5PXBuYZZAHFE,2075
-lamindb/types.py,sha256=svg5S_aynuGfbEOsbmqkR_gF9d9YMzfOkcvGN37Rzvg,232
-lamindb/dev/__init__.py,sha256=Dw-JxVxRW6UzZTf5ENiaGmeB5VPXqmu0x44R5v8BOLE,311
-lamindb/dev/_settings.py,sha256=lppVzaIQouqUC2RX8kocR1kdkauIC-gKeykQYjZcLmg,2843
-lamindb/dev/_view_parents.py,sha256=lSRhOdAdDQAVps5tI6hcVk7hI38cNOLe1FWSpni5pCs,6823
-lamindb/dev/hashing.py,sha256=oYHDSEjINsmDYgCLasnhh_VHbB1dLag27ufVUwDgLyQ,1385
-lamindb/dev/utils.py,sha256=LGdiW4k3GClLz65vKAVRkL6Tw-Gkx9DWAdez1jyA5bE,428
-lamindb/dev/datasets/__init__.py,sha256=4HzUArEtxe_QXMCiqmSFXhurCU09iKRWfUL0wLXbWpQ,905
-lamindb/dev/datasets/_core.py,sha256=peXltcOhWlzgbgs_y_Hd7Vgz0LPjlg0IOAtpBVyWRTg,10043
-lamindb/dev/datasets/_fake.py,sha256=S8mNho-oSh1M9x9oOSsUBLLHmBAegsOLlFk6LnF81EA,942
-lamindb/dev/storage/__init__.py,sha256=ux4W0cpr5jRn5bLjawMqVK4GIwTgp7eKSf_lgdo3lBk,463
-lamindb/dev/storage/_anndata_sizes.py,sha256=0XVzA6AQeVGPaGPrhGusKyxFgFjeo3qSN29hxb8D5E8,993
-lamindb/dev/storage/_backed_access.py,sha256=X03LRnFir3JdtKlriRExoPLscO7cX9qF01dfHstbHh4,16435
-lamindb/dev/storage/_zarr.py,sha256=7W1Jos1QOOF3f41uML_arQoDTNPZVpRyP2m3SLWaCAo,2766
-lamindb/dev/storage/file.py,sha256=IrkVNAZq0YhIKvR2p5x0USZ3rg3A6VvgtxxNyA0Z8Rs,5855
-lamindb/dev/storage/object.py,sha256=x8sy23WqkGir2sg2c3AngQPgv0RbErEA6cpvVN0Zc4I,945
-lamindb/schema/__init__.py,sha256=PznznlFvbeNSZKpn1RS6Gv0JMXFkLmU2_ej_1hVLSTs,796
-lamindb/schema/_core.py,sha256=nWR3X_rNd1AbWw3naMiBi8ppAEpqIDyEYqM54feRB_s,766
-lamindb/setup/__init__.py,sha256=8-0F2C4Glx23-b8-D_1CBGgRBM5PppVhazhoXZYOLsg,275
-lamindb/setup/dev/__init__.py,sha256=iD0f2lx_Hgp-udkiPGal7si5waJSOgvnG6Id-g1mMOY,213
-lamindb-0.48a2.dist-info/entry_points.txt,sha256=MioM8vSpKwXxY3geNBwjo1wnwy1l15WjJYlI3lpKuZI,53
-lamindb-0.48a2.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-lamindb-0.48a2.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
-lamindb-0.48a2.dist-info/METADATA,sha256=tpzX1nV9ihv4HfZZ1TIjit0GNv6cxhYazTnygRvGmYg,10694
-lamindb-0.48a2.dist-info/RECORD,,