lamindb 0.76.15__py3-none-any.whl → 0.77.0__py3-none-any.whl

lamindb/core/_label_manager.py

@@ -6,7 +6,7 @@ from typing import TYPE_CHECKING
 import numpy as np
 from django.db import connections
 from lamin_utils import colors, logger
-from lnschema_core.models import CanValidate, Feature
+from lnschema_core.models import CanCurate, Feature
 
 from lamindb._from_values import _print_values
 from lamindb._record import (
@@ -116,7 +116,7 @@ def validate_labels(labels: QuerySet | list | dict):
             label_uids = np.array(
                 [getattr(label, field) for label in labels if label is not None]
             )
-        if issubclass(registry, CanValidate):
+        if issubclass(registry, CanCurate):
             validated = registry.validate(label_uids, field=field, mute=True)
             validated_uids = label_uids[validated]
             validated_labels = registry.filter(
@@ -202,7 +202,7 @@ class LabelManager:
             transfer_logs = {"mapped": [], "transferred": [], "run": None}
         using_key = settings._using_key
         for related_name, (_, labels) in get_labels_as_dict(
-            data, instance=self._host._state.db
+            data, instance=data._state.db
         ).items():
             labels = labels.all()
             if not labels.exists():

lamindb/core/loaders.py

@@ -24,12 +24,13 @@ from typing import TYPE_CHECKING
 
 import anndata as ad
 import pandas as pd
+from lamin_utils import logger
 from lamindb_setup.core.upath import (
     create_path,
     infer_filesystem,
 )
 
-from lamindb.core._settings import settings
+from ._settings import settings
 
 if TYPE_CHECKING:
     import mudata as md
@@ -79,7 +80,7 @@ def load_h5mu(filepath: UPathStr, **kwargs):
     return md.read_h5mu(path_sanitized, **kwargs)
 
 
-def load_html(path: UPathStr):
+def load_html(path: UPathStr) -> None | UPathStr:
     """Display `.html` in ipython, otherwise return path."""
     if is_run_from_ipython:
         with open(path, encoding="utf-8") as f:
@@ -95,6 +96,7 @@ def load_html(path: UPathStr):
         from IPython.display import HTML, display
 
         display(HTML(data=body_content))
+        return None
     else:
         return path
 
@@ -108,17 +110,18 @@ def load_json(path: UPathStr) -> dict:
     return data
 
 
-def load_image(path: UPathStr):
+def load_image(path: UPathStr) -> None | UPathStr:
     """Display `.svg` in ipython, otherwise return path."""
     if is_run_from_ipython:
         from IPython.display import Image, display
 
         display(Image(filename=path))
+        return None
     else:
         return path
 
 
-def load_svg(path: UPathStr) -> None | Path:
+def load_svg(path: UPathStr) -> None | UPathStr:
     """Display `.svg` in ipython, otherwise return path."""
     if is_run_from_ipython:
         from IPython.display import SVG, display
@@ -129,6 +132,12 @@ def load_svg(path: UPathStr) -> None | Path:
         return path
 
 
+def load_rds(path: UPathStr) -> UPathStr:
+    """Just warn when trying to load `.rds`."""
+    logger.warning("Please use `laminr` to load `.rds` files")
+    return path
+
+
 FILE_LOADERS = {
     ".csv": pd.read_csv,
     ".tsv": load_tsv,
@@ -142,9 +151,10 @@ FILE_LOADERS = {
     ".jpg": load_image,
     ".png": load_image,
     ".svg": load_svg,
+    ".rds": load_rds,
 }
 
-SUPPORTED_SUFFIXES = list(FILE_LOADERS.keys())
+SUPPORTED_SUFFIXES = [sfx for sfx in FILE_LOADERS.keys() if sfx != ".rds"]
 """Suffixes with defined artifact loaders."""
 
 

lamindb/core/storage/_anndata_accessor.py

@@ -54,13 +54,16 @@ if anndata_version_parse < version.parse("0.10.0"):
         return SparseDataset(group)
 
 else:
+    if anndata_version_parse >= version.parse("0.11.0"):
+        from anndata._core.sparse_dataset import (  # type: ignore
+            _CSRDataset as CSRDataset,
+        )
+    else:
+        from anndata._core.sparse_dataset import CSRDataset  # type: ignore
     from anndata._core.sparse_dataset import (
         BaseCompressedSparseDataset as SparseDataset,
     )
-    from anndata._core.sparse_dataset import (  # type: ignore
-        CSRDataset,
-        sparse_dataset,
-    )
+    from anndata._core.sparse_dataset import sparse_dataset  # type: ignore
 
     def _check_group_format(*args):
         pass

lamindb/core/storage/_zarr.py

@@ -5,14 +5,21 @@ from typing import TYPE_CHECKING
 
 import scipy.sparse as sparse
 import zarr
-from anndata._io import read_zarr
+from anndata import __version__ as anndata_version
 from anndata._io.specs import write_elem
 from anndata._io.specs.registry import get_spec
 from fsspec.implementations.local import LocalFileSystem
 from lamindb_setup.core.upath import create_mapper, infer_filesystem
+from packaging import version
 
 from ._anndata_sizes import _size_elem, _size_raw, size_adata
 
+if version.parse(anndata_version) < version.parse("0.11.0"):
+    from anndata._io import read_zarr
+else:
+    from anndata.io import read_zarr
+
+
 if TYPE_CHECKING:
     from anndata import AnnData
     from lamindb_setup.core.types import UPathStr

{lamindb-0.76.15.dist-info → lamindb-0.77.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.76.15
+Version: 0.77.0
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.9,<3.13
@@ -9,20 +9,22 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 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: lnschema_core==0.77.0
+Requires-Dist: lamin_utils==0.13.8
+Requires-Dist: lamin_cli==0.21.3
 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: anndata>=0.8.0,<=0.11.1
 Requires-Dist: fsspec
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.52.0 ; extra == "bionty"
+Requires-Dist: bionty==0.53.1 ; extra == "bionty"
+Requires-Dist: cellregistry ; extra == "cellregistry"
+Requires-Dist: clinicore ; extra == "clinicore"
 Requires-Dist: line_profiler ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
@@ -35,19 +37,29 @@ 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>=1.1.9 ; extra == "fcs"
+Requires-Dist: findrefs ; extra == "findrefs"
 Requires-Dist: lamindb_setup[gcp] ; extra == "gcp"
 Requires-Dist: nbproject==0.10.5 ; extra == "jupyter"
 Requires-Dist: jupytext ; extra == "jupyter"
 Requires-Dist: nbconvert ; extra == "jupyter"
+Requires-Dist: omop ; extra == "omop"
+Requires-Dist: ourprojects ; extra == "ourprojects"
+Requires-Dist: wetlab ; extra == "wetlab"
 Requires-Dist: zarr>=2.16.0 ; extra == "zarr"
 Project-URL: Home, https://github.com/laminlabs/lamindb
 Provides-Extra: aws
 Provides-Extra: bionty
+Provides-Extra: cellregistry
+Provides-Extra: clinicore
 Provides-Extra: dev
 Provides-Extra: erdiagram
 Provides-Extra: fcs
+Provides-Extra: findrefs
 Provides-Extra: gcp
 Provides-Extra: jupyter
+Provides-Extra: omop
+Provides-Extra: ourprojects
+Provides-Extra: wetlab
 Provides-Extra: zarr
 
 [![Stars](https://img.shields.io/github/stars/laminlabs/lamindb?logo=GitHub&color=yellow)](https://github.com/laminlabs/lamindb)

{lamindb-0.76.15.dist-info → lamindb-0.77.0.dist-info}/RECORD

@@ -1,18 +1,17 @@
-lamindb/__init__.py,sha256=ZoRboX4PQc0sbVajeZ1fd4GoLN3YDj5U74zVUpcSd9I,2278
-lamindb/_artifact.py,sha256=WNdKAJFu3sFgQ_Qe1JflDHiTP4EGhAIkzaHFwTthAjY,44903
-lamindb/_can_validate.py,sha256=TKfkHgkPl1bwuJrQCp6pHgQbi7m2pc_zjFhZfUAUU20,19573
+lamindb/__init__.py,sha256=6E6iDqtEpPJwkp-5H-1Om9KnyDYDyFUBKEF3_mXFDhM,2275
+lamindb/_artifact.py,sha256=4sHLnJQdWAjplB-dk0JXzhrHaaDn2ri5SeyvA7yzajQ,45166
+lamindb/_can_curate.py,sha256=LhF78TqMUMsOXxy8ODZX9FLlH1-zszR9sKh3l6iVQ4o,19942
 lamindb/_collection.py,sha256=MLOEoOgTu7rTlRD7zkm1k0YIk_gVhQDO17JbmZCptOs,14573
-lamindb/_curate.py,sha256=pLsdtnnTn0qQbsUB4hrU3yuoVnVNh-BQe10EpMNZ4Ns,64083
+lamindb/_curate.py,sha256=BoZgaBBPK8aUggHmZMqbRjRCBL9CDHQCiWw4Kzg-_ww,64491
 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/_finish.py,sha256=r8q6rhml2vHiDlojCnfSpS8pbfnq7u6MwIcBIwuVq2o,9745
 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/_parents.py,sha256=GTbDL4P9LnaoNXMe6uOrp4g_Q4ZUAEaW0tHULrBt8tU,17203
 lamindb/_query_manager.py,sha256=noc05Ad-aADxckOVBVDAiErFB7gL8XTgckELvI4rGmM,3702
-lamindb/_query_set.py,sha256=6vHOvB_uXzKVVIw8AAVw7EYOIAGuw3TYcUzkpNlFLdE,12973
-lamindb/_record.py,sha256=isR9GMQFwUUwVSmPNABvEzcJS38TbjhD7Cc6kygPsTA,26819
+lamindb/_query_set.py,sha256=dGEJuQsYrzc-mPdHSRjMPHWrri8Fg78I10AsT18jomI,14666
+lamindb/_record.py,sha256=5zpRt5mCSzlYxHlrMqDnduoRCx5ZiTUJyoJjFMmuVHY,31522
 lamindb/_run.py,sha256=K_5drpLn3D7y3XtZ3vtAw35rG5RCSvB4bXQZx4ESSI0,1964
 lamindb/_save.py,sha256=OD052Qr_hiMyAonHTktKETe_Bhnp1RY810y0rwZqpBQ,11352
 lamindb/_storage.py,sha256=GBVChv-DHVMNEBJL5l_JT6B4RDhZ6NnwgzmUICphYKk,413
@@ -20,19 +19,19 @@ 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=y87MCP1BEC2qHNVDIOwqVteIP_2hPCdIoa9JXr0EG8U,1524
-lamindb/core/_context.py,sha256=dI3z7fCMRPC3IMb7-EIaQYhacSZBA4HfLVFyoJtVL7I,22900
+lamindb/core/__init__.py,sha256=GX6MdHsEdrHbm19oDcWVap4k3b0bHj5ekG_J2snsFjs,1558
+lamindb/core/_context.py,sha256=xqvht5dlqFER6EPwCS6nA0I5_iFlmhPVVeFzB85G5B4,24164
 lamindb/core/_data.py,sha256=BVZkxK8aloSecH25LivbwnjcG1fz7Gs2UDceO5pWd3I,20049
-lamindb/core/_django.py,sha256=yeMPp1n9WrFmEjVRdavfpVqAolPLd24RseTQlvsK67w,7157
+lamindb/core/_django.py,sha256=cEalbKHCAHp7ElXFtFmUAvzGsk_xCyr4puZ0HElxVAw,7153
 lamindb/core/_feature_manager.py,sha256=q4WmzJvFLL_fAs-vNRgV2klanAoU6Wu8_g0O2dyIjVg,40027
-lamindb/core/_label_manager.py,sha256=yh-r4KbtOArMUKPJL75yOxJc8HUKqsik8pExBVKyDlA,10949
+lamindb/core/_label_manager.py,sha256=eOiHMyRW4p0TUo8d_ihnW9cO0CvGRR2AfDfs5KObbmk,10939
 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=Y1XQGbv9MgNLVvoClpcwN4NugrLW3Xgy1up15wZK740,1783
 lamindb/core/fields.py,sha256=47Jmh3efUr5ZscgimR_yckY-I3cNf8ScLutbwKCK3j4,162
-lamindb/core/loaders.py,sha256=KMTkDa73jkRVvI9uc5Fgr0t6mq22cAxBwhSlUZKUaBg,4016
+lamindb/core/loaders.py,sha256=CGgWWtdOCpfdC0hxRQuuGZEgnyRuIvReCYhauw598IA,4338
 lamindb/core/schema.py,sha256=Y1tGn93B236PtnYZkpgTNFgTXBcVujPM1qh1kNG6Nbs,3441
 lamindb/core/types.py,sha256=cL4cmJFA1xfxAIFOQqoa_fvVzdUM3A5blHStVwRNtk4,280
 lamindb/core/versioning.py,sha256=KUpd94F5QpbDxx9eKgZwrpPyQpm9YeHVedrTEO2a_mI,4839
@@ -40,13 +39,13 @@ lamindb/core/datasets/__init__.py,sha256=zRP98oqUAaXhqWyKMiH0s_ImVIuNeziQQ2kQ_t0
 lamindb/core/datasets/_core.py,sha256=JGP_q-OQibDCEaI54jZ2F6fSbSW9Yg6oYOqgOCXM0v4,20414
 lamindb/core/datasets/_fake.py,sha256=BZF9R_1iF0HDnvtZNqL2FtsjSMuqDIfuFxnw_LJYIh4,953
 lamindb/core/storage/__init__.py,sha256=JOIMu_7unbyhndtH1j0Q-9AvY8knSuc1IJO9sQnyBAQ,498
-lamindb/core/storage/_anndata_accessor.py,sha256=2p1HjoatmZjQ1u94tjgmXgiv8MKowrQH5xInDmiLCw4,24191
+lamindb/core/storage/_anndata_accessor.py,sha256=C321qng00vMmugukxv5dX8z3oJeRxq869DgAGaEd5rg,24413
 lamindb/core/storage/_anndata_sizes.py,sha256=aXO3OB--tF5MChenSsigW6Q-RuE8YJJOUTVukkLrv9A,1029
 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
+lamindb/core/storage/_zarr.py,sha256=sVd9jVt2q91maeL6GAqMhT6sqtD04vQRfxY3mvIUQlc,3854
 lamindb/core/storage/objects.py,sha256=OzvBCS-Urz5mr-O95qYt6RGBDDX5HmjfRRKWPPDn1ZE,1797
 lamindb/core/storage/paths.py,sha256=bQwRbGTOCx3DSFOQ404uT-3YBXrm8yfKuttNCdWwJpA,5892
 lamindb/core/subsettings/__init__.py,sha256=KFHPzIE7f7Bj4RgMjGQF4CjTdHVG_VNFBrCndo49ixo,198
@@ -56,7 +55,7 @@ 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-0.76.15.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,,
+lamindb-0.77.0.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+lamindb-0.77.0.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+lamindb-0.77.0.dist-info/METADATA,sha256=sRvsh2HFemzhSLonVj48xLEsFfSwQZZ_LvE2fbJn-js,2796
+lamindb-0.77.0.dist-info/RECORD,,

lamindb/_filter.py

@@ -1,21 +0,0 @@
-from __future__ import annotations
-
-from typing import TYPE_CHECKING
-
-from ._query_set import QuerySet, process_expressions
-
-if TYPE_CHECKING:
-    from lnschema_core import Record
-
-
-def filter(registry: type[Record], *queries, **expressions) -> QuerySet:
-    """See :meth:`~lamindb.core.Record.filter`."""
-    _using_key = None
-    if "_using_key" in expressions:
-        _using_key = expressions.pop("_using_key")
-    expressions = process_expressions(registry, expressions)
-    qs = QuerySet(model=registry, using=_using_key)
-    if len(expressions) > 0:
-        return qs.filter(*queries, **expressions)
-    else:
-        return qs