lamindb 1.4.0__py3-none-any.whl → 1.5.0__py3-none-any.whl

lamindb/models/transform.py

@@ -35,7 +35,7 @@ if TYPE_CHECKING:
 # does not inherit from TracksRun because the Transform
 # is needed to define a run
 class Transform(Record, IsVersioned):
-    """Data transformations.
+    """Data transformations such as scripts, notebooks, functions, or pipelines.
 
     A "transform" can refer to a Python function, a script, a notebook, or a
     pipeline. If you execute a transform, you generate a run
@@ -280,7 +280,7 @@ class Transform(Record, IsVersioned):
             update_attributes(self, {"description": description})
             return None
         if revises is not None and key is not None and revises.key != key:
-            logger.warning(f"renaming transform '{revises.key}' to {key}")
+            logger.important(f"renaming transform {revises.key} to {key}")
         new_uid, version, key, description, revises = process_revises(
             revises, version, key, description, Transform
         )

lamindb/models/ulabel.py

@@ -48,9 +48,8 @@ class ULabel(Record, HasParents, CanCurate, TracksRun, TracksUpdates):
     Often, a ulabel is measured *within* a dataset. For instance, an artifact
     might characterize 2 species of the Iris flower (`"setosa"` &
     `"versicolor"`) measured by a `"species"` feature. Use the
-    :class:`~lamindb.Curator` flow to automatically parse, validate, and
-    annotate with labels that are contained in `DataFrame` or `AnnData`
-    artifacts.
+    :class:`~lamindb.curators.DataFrameCurator` flow to automatically parse, validate, and
+    annotate with labels that are contained in `DataFrame` objects.
 
     .. note::
 
@@ -82,9 +81,9 @@ class ULabel(Record, HasParents, CanCurate, TracksRun, TracksUpdates):
 
         >>> artifact.ulabels.add(ulabel)
 
-        Query by `ULabel`:
+        Query an artifact by label:
 
-        >>> ln.Artifact.filter(ulabels=train_split)
+        >>> ln.Artifact.filter(ulabels=train_split).df()
     """
 
     class Meta(Record.Meta, TracksRun.Meta, TracksUpdates.Meta):
@@ -176,6 +175,8 @@ class ULabel(Record, HasParents, CanCurate, TracksRun, TracksUpdates):
         description: str | None = kwargs.pop("description", None)
         reference: str | None = kwargs.pop("reference", None)
         reference_type: str | None = kwargs.pop("reference_type", None)
+        _skip_validation = kwargs.pop("_skip_validation", False)
+        _aux = kwargs.pop("_aux", None)
         if len(kwargs) > 0:
             valid_keywords = ", ".join([val[0] for val in _get_record_kwargs(ULabel)])
             raise FieldValidationError(
@@ -188,6 +189,8 @@ class ULabel(Record, HasParents, CanCurate, TracksRun, TracksUpdates):
             description=description,
             reference=reference,
             reference_type=reference_type,
+            _skip_validation=_skip_validation,
+            _aux=_aux,
         )
 
 

{lamindb-1.4.0.dist-info → lamindb-1.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamindb
-Version: 1.4.0
+Version: 1.5.0
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10,<3.14
@@ -9,9 +9,9 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Dist: lamin_utils==0.13.11
-Requires-Dist: lamin_cli==1.3.0
-Requires-Dist: lamindb_setup[aws]==1.5.1
+Requires-Dist: lamin_utils==0.14.0
+Requires-Dist: lamin_cli==1.4.0
+Requires-Dist: lamindb_setup[aws]==1.5.2
 Requires-Dist: pyyaml
 Requires-Dist: pyarrow
 Requires-Dist: pandera
@@ -23,7 +23,7 @@ Requires-Dist: anndata>=0.8.0,<=0.11.4
 Requires-Dist: fsspec
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
-Requires-Dist: bionty>=1.3.0 ; extra == "bionty"
+Requires-Dist: bionty>=1.3.2 ; extra == "bionty"
 Requires-Dist: cellregistry ; extra == "cellregistry"
 Requires-Dist: clinicore ; extra == "clinicore"
 Requires-Dist: tomlkit ; extra == "dev"
@@ -40,7 +40,7 @@ Requires-Dist: faker-biology ; extra == "dev"
 Requires-Dist: django-schema-graph ; extra == "erdiagram"
 Requires-Dist: readfcs>=2.0.1 ; extra == "fcs"
 Requires-Dist: lamindb_setup[gcp] ; extra == "gcp"
-Requires-Dist: nbproject==0.10.6 ; extra == "jupyter"
+Requires-Dist: nbproject==0.11.1 ; extra == "jupyter"
 Requires-Dist: jupytext ; extra == "jupyter"
 Requires-Dist: nbconvert>=7.2.1 ; extra == "jupyter"
 Requires-Dist: mistune!=3.1.0 ; extra == "jupyter"

{lamindb-1.4.0.dist-info → lamindb-1.5.0.dist-info}/RECORD

@@ -1,44 +1,54 @@
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-lamindb/_finish.py,sha256=UK9XW1qZCd32Nqz0cdKYmpX9ilFU0nGyNb6Urwfx_Nw,19612
-lamindb/_tracked.py,sha256=JKzYEpqVojklTms0VpP-tU34AHVZG8a13dSl3CfIzwQ,4472
+lamindb/__init__.py,sha256=PvttGVLvK5zlO9ZI651ZzH36fKKUpaj2fAyOCKRnAoE,2676
+lamindb/_finish.py,sha256=Wqb846pCErsx5ZPulAfdF5PJbWzgAdfbuYuf4FndfhY,20124
+lamindb/_tracked.py,sha256=fse_H0ehc9WvU_l1572g7qya0sRdWCh22LZkq0XU4ic,4445
 lamindb/_view.py,sha256=kSmG8X4ULQZEKxY7ESnthQqsUf1DEzoYGeTLYRU1I7s,4938
-lamindb/errors.py,sha256=F6einUIStsTgWcBfSlG8eGf2Q6yWUaqMlSULqmkV8GA,1734
-lamindb/base/__init__.py,sha256=qS7BM1YVHWridJp2CsiH5Rb38z6kkuDYCjerNHvI2qQ,263
-lamindb/base/fields.py,sha256=RdwYHQmB7B-jopD_K2QNL5vjhOelu7DWGgqQItXr3pg,8024
-lamindb/base/ids.py,sha256=OOgD5vxry6s2vSslb8-E9zEykDMpyhnungfT844DhSU,1547
-lamindb/base/types.py,sha256=w_dQ2t9Htk8030OA_blksY9FG4NNcx3p7qJumFkBWkg,2714
+lamindb/errors.py,sha256=gVt7E5LRjc4OezrkIiRRTXUDIw_unQaKf2300OPxBxg,2003
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 lamindb/base/users.py,sha256=8MSmAvCKoUF15YsDE6BGLBXsFWpfoEEg8iDTKZ7kD48,848
 lamindb/core/__init__.py,sha256=aaBq0UVjNolMynbT1V5hB6UrJm1tK0M6WHu_r6em9_4,604
 lamindb/core/_compat.py,sha256=NLnKk1qk4xdgMV-QwFDnBnbio02ujjlF86icvhpdv4c,2029
-lamindb/core/_context.py,sha256=wHC-DRU6oNkv5SQXxZ2J88RS4E1A5cKo2FCOLsOnlsc,30197
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 lamindb/core/_mapped_collection.py,sha256=dxyZ1ZHFn5SBl1xILqN9N6TTUJP0PptVBV-2O0EdZww,25751
-lamindb/core/_settings.py,sha256=WLjFn9XunEZ9zMy2Qvmc3aJqWMXw2hcG0EBNX9wjkfU,5706
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 lamindb/core/_sync_git.py,sha256=Z7keuyS5X7CAj285sEbZIFExZF9mtjGH8DzKwz3xhHw,5881
 lamindb/core/_track_environment.py,sha256=gKmXiL2meqJT65X-66p_GlonoxzBZXNwNm-G9gk0fS4,847
 lamindb/core/exceptions.py,sha256=FMEoSvT3FvtLkxQAt2oDXPeaPem8V5x5UBbTsPFYU5w,53
-lamindb/core/loaders.py,sha256=1JHLr4e-gbh8QXiy5duOPsiKo7TKjo74vmvolqhkhgs,5458
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 lamindb/core/types.py,sha256=yHr2Vn_p1Hepz_mBooXmsKudqu8Tco7lXZmVS_ORQIw,383
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-lamindb/core/datasets/_core.py,sha256=_PrZSr_rRpfScdzU216YMUR6TxihqA2hffRXmjD5Azw,20344
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 lamindb/core/datasets/_fake.py,sha256=BZF9R_1iF0HDnvtZNqL2FtsjSMuqDIfuFxnw_LJYIh4,953
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 lamindb/core/storage/_tiledbsoma.py,sha256=gOcfgMHToI142KqyOYWJMOzmFMLos660k6ZFaAooYPc,10308
 lamindb/core/storage/_valid_suffixes.py,sha256=vUSeQ4s01rdhD_vSd6wKmFBsgMJAKkBMnL_T9Y1znMg,501
 lamindb/core/storage/_zarr.py,sha256=cisYXU4_QXMF_ZY2pV52Incus6365mMxRphLaHO76W0,6801
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 lamindb/core/storage/paths.py,sha256=wJTD7qza87Xx7ZMo9HFHKgZWaVnst6qc4F2SzqvBMrE,7118
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 lamindb/core/subsettings/_creation_settings.py,sha256=NGHWKqCFSzVNBxAr2VnmdYguiFdW29XUK7T9wRsVshg,906
-lamindb/curators/__init__.py,sha256=3W3mM2SxWOcxhfWRIl24oRYiqks9KQ3enISZoWTPv-c,124727
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 lamindb/curators/_cellxgene_schemas/__init__.py,sha256=zqlFzMNMDGEBe6DV0gBsBMpfc9UHvNv1EpBsz_ktMoA,7502
 lamindb/curators/_cellxgene_schemas/schema_versions.csv,sha256=X9rmO88TW1Fht1f5mJs0JdW-VPvyKSajpf8lHNeECj4,1680
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+lamindb/examples/schemas/_simple.py,sha256=JdavLLrJnxDLTKBKRk2Tb534AInlzX0jyEvU9LcH-NQ,568
 lamindb/integrations/__init__.py,sha256=RWGMYYIzr8zvmNPyVB4m-p4gMDhxdRbjES2Ed23OItw,215
-lamindb/integrations/_vitessce.py,sha256=VgO9zAlTSIKDo1wEef_Q4BudTAVtRSZmuzRdCGwBvJk,4016
+lamindb/integrations/_vitessce.py,sha256=OvtnBAxlR_PvfeGjpySjzi2uRYsBwDwb3tMyhBzNVFk,4110
 lamindb/migrations/0069_squashed.py,sha256=gMWv65ErtjJZyWWo1b4uFHXWa6MSuBcmqz4ElZ6GPf4,62639
 lamindb/migrations/0070_lamindbv1_migrate_data.py,sha256=tyq_xi6U8TXi9C2Raf6v_UTtfyfqQOUIFJzYj4oCgAE,2429
 lamindb/migrations/0071_lamindbv1_migrate_schema.py,sha256=r3PPpq4RK7rhrLWjhVACd5i-tSUTBF0X6Luc5v-g0Lg,25125
@@ -62,34 +72,37 @@ lamindb/migrations/0088_schema_components.py,sha256=9EeoEXX2mf8RtGv_eqOH9zpI2Dg7
 lamindb/migrations/0089_subsequent_runs.py,sha256=ETXBqn-MwhFi3GIUbUqwM2j9un2o-0CI2Ux8b8FXuuw,5859
 lamindb/migrations/0090_runproject_project_runs.py,sha256=Ab9wyGxc6xjBfj-36cqdTlRLj2vgQM3QC9o-mvF0MD8,2449
 lamindb/migrations/0090_squashed.py,sha256=kx_A_25BYantikxCbGhJughFpv_lqyHH86pMh5YevEE,160823
+lamindb/migrations/0091_alter_featurevalue_options_alter_space_options_and_more.py,sha256=Df4EYAQlLKZ4BpFcsRRF52pGN3hDSo94laiO-V90Kn4,607
+lamindb/migrations/0092_alter_artifactfeaturevalue_artifact_and_more.py,sha256=x-2Pvi0GJugkLrR--Fw9PBzV-HxqXjl0NktxRtRFJno,2459
 lamindb/migrations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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 lamindb/models/_django.py,sha256=2LFaTvIPtxIV8_T6Kx0cvquTetj7C3OcnKukUyC9msY,7705
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 lamindb/models/_is_versioned.py,sha256=Th2_cBf9UWh27E6ANxg6LGmjBOumXFy7AjH0GG4FoXA,7601
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 lamindb/models/_relations.py,sha256=ONjHPiWIa_Ur7zMNTa_9Uw7K-366GORyPvGoVjf4EQs,3681
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