lamindb 1.2a2__py3-none-any.whl → 1.3.1__py3-none-any.whl

lamindb/models/run.py

@@ -23,11 +23,13 @@ from lamindb.errors import ValidationError
 
 from ..base.ids import base62_20
 from .can_curate import CanCurate
-from .record import BasicRecord, LinkORM, Record
+from .record import BasicRecord, LinkORM, Record, Registry
 
 if TYPE_CHECKING:
     from datetime import datetime
 
+    from lamindb.base.types import Dtype, FieldAttr
+
     from .artifact import Artifact
     from .collection import Collection
     from .project import Project
@@ -206,12 +208,8 @@ class Param(Record, CanCurate, TracksRun, TracksUpdates):
     _name_field: str = "name"
 
     name: str = CharField(max_length=100, db_index=True)
-    dtype: str | None = CharField(db_index=True, null=True)
-    """Data type ("num", "cat", "int", "float", "bool", "datetime").
-
-    For categorical types, can define from which registry values are
-    sampled, e.g., `cat[ULabel]` or `cat[bionty.CellType]`.
-    """
+    dtype: Dtype | None = CharField(db_index=True, null=True)
+    """Data type (:class:`~lamindb.base.types.Dtype`)."""
     type: Param | None = ForeignKey("self", PROTECT, null=True, related_name="records")
     """Type of param (e.g., 'Pipeline', 'ModelTraining', 'PostProcessing').
 
@@ -235,6 +233,21 @@ class Param(Record, CanCurate, TracksRun, TracksUpdates):
     values: ParamValue
     """Values for this parameter."""
 
+    @overload
+    def __init__(
+        self,
+        name: str,
+        dtype: Dtype | Registry | list[Registry] | FieldAttr,
+        type: Param | None = None,
+        is_type: bool = False,
+    ): ...
+
+    @overload
+    def __init__(
+        self,
+        *db_args,
+    ): ...
+
     def __init__(self, *args, **kwargs):
         from .feature import process_init_feature_param
 

lamindb/models/schema.py

@@ -28,8 +28,8 @@ from ._relations import (
 from .can_curate import CanCurate
 from .feature import (
     Feature,
-    convert_pandas_dtype_to_lamin_dtype,
-    get_dtype_str_from_dtype,
+    serialize_dtype,
+    serialize_pandas_dtype,
 )
 from .record import (
     BasicRecord,
@@ -352,7 +352,7 @@ class Schema(Record, CanCurate, TracksRun):
             if otype is None:
                 raise InvalidArgument("Please pass otype != None for composite schemas")
         if itype is not None and not isinstance(itype, str):
-            itype_str = get_dtype_str_from_dtype(itype, is_itype=True)
+            itype_str = serialize_dtype(itype, is_itype=True)
         else:
             itype_str = itype
         validated_kwargs = {
@@ -482,14 +482,14 @@ class Schema(Record, CanCurate, TracksRun):
         organism: Record | str | None = None,
         source: Record | None = None,
     ) -> Schema | None:
-        """Create feature set for validated features."""
+        """Create schema for valid columns."""
         registry = field.field.model
         validated = registry.validate(
             df.columns, field=field, mute=mute, organism=organism
         )
         if validated.sum() == 0:
-            if mute is True:
-                logger.warning("no validated features, skip creating feature set")
+            if not mute:
+                logger.warning("no validated features, skip creating schema")
             return None
         if registry == Feature:
             validated_features = Feature.from_values(  # type: ignore
@@ -502,7 +502,7 @@ class Schema(Record, CanCurate, TracksRun):
             dtypes = [col.dtype for (_, col) in df.loc[:, validated].items()]
             if len(set(dtypes)) != 1:
                 raise ValueError(f"data types are heterogeneous: {set(dtypes)}")
-            dtype = convert_pandas_dtype_to_lamin_dtype(dtypes[0])
+            dtype = serialize_pandas_dtype(dtypes[0])
             validated_features = registry.from_values(
                 df.columns[validated],
                 field=field,
@@ -585,14 +585,6 @@ class Schema(Record, CanCurate, TracksRun):
             self._aux["af"] = {}
         self._aux["af"]["0"] = value
 
-    @coerce_dtype.setter
-    def coerce_dtype(self, value: bool) -> None:
-        if self._aux is None:
-            self._aux = {}
-        if "af" not in self._aux:
-            self._aux["af"] = {}
-        self._aux["af"]["0"] = value
-
     # @property
     # def index_feature(self) -> None | Feature:
     #     # index_feature: `Record | None = None` A :class:`~lamindb.Feature` to validate the index of a `DataFrame`.

{lamindb-1.2a2.dist-info → lamindb-1.3.1.dist-info}/METADATA

@@ -1,16 +1,17 @@
 Metadata-Version: 2.3
 Name: lamindb
-Version: 1.2a2
+Version: 1.3.1
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
-Requires-Python: >=3.10,<3.13
+Requires-Python: >=3.10,<3.14
 Description-Content-Type: text/markdown
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Requires-Dist: lamin_utils==0.13.10
-Requires-Dist: lamin_cli==1.1.0
-Requires-Dist: lamindb_setup[aws]==1.3.0
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: lamin_utils==0.13.11
+Requires-Dist: lamin_cli==1.2.0
+Requires-Dist: lamindb_setup[aws]==1.4.0
 Requires-Dist: pyyaml
 Requires-Dist: pyarrow
 Requires-Dist: pandera
@@ -22,7 +23,7 @@ Requires-Dist: anndata>=0.8.0,<=0.11.3
 Requires-Dist: fsspec
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
-Requires-Dist: bionty ; extra == "bionty"
+Requires-Dist: bionty>=1.2a1 ; extra == "bionty"
 Requires-Dist: cellregistry ; extra == "cellregistry"
 Requires-Dist: clinicore ; extra == "clinicore"
 Requires-Dist: tomlkit ; extra == "dev"
@@ -39,7 +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==0.10.5 ; extra == "jupyter"
+Requires-Dist: nbproject==0.10.6 ; extra == "jupyter"
 Requires-Dist: jupytext ; extra == "jupyter"
 Requires-Dist: nbconvert>=7.2.1 ; extra == "jupyter"
 Requires-Dist: mistune!=3.1.0 ; extra == "jupyter"

{lamindb-1.2a2.dist-info → lamindb-1.3.1.dist-info}/RECORD

@@ -1,41 +1,42 @@
-lamindb/__init__.py,sha256=VtRDWO-21Ce2MyV55Bt7YCnY2vg7X19wnUBBsZ7q43w,2426
+lamindb/__init__.py,sha256=oZOWUS3k5h0WraaCC0_gGCmoTTp64_BSia24_UVNwOQ,2468
 lamindb/_finish.py,sha256=UK9XW1qZCd32Nqz0cdKYmpX9ilFU0nGyNb6Urwfx_Nw,19612
 lamindb/_tracked.py,sha256=JKzYEpqVojklTms0VpP-tU34AHVZG8a13dSl3CfIzwQ,4472
-lamindb/_view.py,sha256=O9qvwLmgKKsuFMoJ9YjV12cdOUjG6Ez1cQyLGCywm8Y,4964
+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=JfZk0xmhLsWusU0s4SNjhRnQ52mn-cSiG5Gf4SsACBs,1227
+lamindb/base/types.py,sha256=w_dQ2t9Htk8030OA_blksY9FG4NNcx3p7qJumFkBWkg,2714
 lamindb/base/users.py,sha256=8MSmAvCKoUF15YsDE6BGLBXsFWpfoEEg8iDTKZ7kD48,848
 lamindb/core/__init__.py,sha256=aaBq0UVjNolMynbT1V5hB6UrJm1tK0M6WHu_r6em9_4,604
-lamindb/core/_context.py,sha256=kkvc8NMGPi44YrBa4VCieG2-HTDnMeT4OtHSbLoks_k,30131
+lamindb/core/_compat.py,sha256=NLnKk1qk4xdgMV-QwFDnBnbio02ujjlF86icvhpdv4c,2029
+lamindb/core/_context.py,sha256=0JqPGrMsri8XhFwg7ugV-7xBJMF5czR2S610bCpLdZM,30411
 lamindb/core/_mapped_collection.py,sha256=dxyZ1ZHFn5SBl1xILqN9N6TTUJP0PptVBV-2O0EdZww,25751
 lamindb/core/_settings.py,sha256=WLjFn9XunEZ9zMy2Qvmc3aJqWMXw2hcG0EBNX9wjkfU,5706
 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=dGolbYz4naKGG76Xyq8xYEe7xkqbb0Ekpwd5CAHZvjI,5145
-lamindb/core/types.py,sha256=DS4uXaCswAW9tqz4MZ_sYc1_QZ6il--Z4x8HeHNQgRw,162
-lamindb/core/datasets/__init__.py,sha256=PPraqD4nMr-DvI1_6aDQde2p9MkgJY-ukV0Qb34xnyg,1722
-lamindb/core/datasets/_core.py,sha256=9-By-vT7KUbdD8jFQK7KaRcvODj0hiwQMeM2d9mgmss,19661
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+lamindb/core/datasets/_core.py,sha256=_PrZSr_rRpfScdzU216YMUR6TxihqA2hffRXmjD5Azw,20344
 lamindb/core/datasets/_fake.py,sha256=BZF9R_1iF0HDnvtZNqL2FtsjSMuqDIfuFxnw_LJYIh4,953
-lamindb/core/datasets/_small.py,sha256=bjjEGXHGLsHNRS9n7xKouyWWVyhdztSqy1R5hjjDUGg,5005
+lamindb/core/datasets/_small.py,sha256=NuovAoA1oMpknQUASErdZgRz4byRQvT4ZgfQRX3GaHY,5597
 lamindb/core/storage/__init__.py,sha256=JOIMu_7unbyhndtH1j0Q-9AvY8knSuc1IJO9sQnyBAQ,498
 lamindb/core/storage/_anndata_accessor.py,sha256=oq2e4vlBnGhIeGR5a_8traOV3tKklZJUqcgKt0pEO8c,26187
 lamindb/core/storage/_anndata_sizes.py,sha256=aXO3OB--tF5MChenSsigW6Q-RuE8YJJOUTVukkLrv9A,1029
 lamindb/core/storage/_backed_access.py,sha256=98KdO0Qw6ZrYHAnHG-zUzjxr8Jb-ujIWtGWjg_Wdk9c,3854
 lamindb/core/storage/_pyarrow_dataset.py,sha256=Kvrwuw1-44WpyI7iuKWV5XU3u-wI9-hz0FiXPzxErmI,1892
-lamindb/core/storage/_tiledbsoma.py,sha256=CenVY5Bg2gEvDEpqKhKkbk3rn0jqlKOd5lTglzQD2_U,10299
+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=39hd1E6ruHupkxgQ7qY3p9c6I_UcrZPfJiuF3fv3tIo,4639
-lamindb/core/storage/objects.py,sha256=jCBYSZldqf3kToz9aHRX0Vj4f3iyOrh24lTSlmKH5jE,2878
+lamindb/core/storage/_zarr.py,sha256=cisYXU4_QXMF_ZY2pV52Incus6365mMxRphLaHO76W0,6801
+lamindb/core/storage/objects.py,sha256=l2JTHI7oLMH7JJqxwpyIgMXZJ3gaGv7xl_Jr21wWFAs,2809
 lamindb/core/storage/paths.py,sha256=wJTD7qza87Xx7ZMo9HFHKgZWaVnst6qc4F2SzqvBMrE,7118
 lamindb/core/subsettings/__init__.py,sha256=j6G9WAJLK-x9FzPSFw-HJUmOseZKGTbK-oLTKI_X_zs,126
 lamindb/core/subsettings/_creation_settings.py,sha256=NGHWKqCFSzVNBxAr2VnmdYguiFdW29XUK7T9wRsVshg,906
-lamindb/curators/__init__.py,sha256=F4InJZvAkPqTZ53rZz8v2WupJVJ4B-To7jEQCLn6_s8,142810
-lamindb/curators/_cellxgene_schemas/__init__.py,sha256=z-GL_JtFiZhEHUHxQuJBN6SgBCKAMHw9hheDbCje-zk,819
-lamindb/curators/_cellxgene_schemas/schema_versions.yml,sha256=nipsuquq-H9n0KNOxctYV6EVshh55FB5AjujLbxsabI,1942
+lamindb/curators/__init__.py,sha256=0yZXh_VNkkU_A6jkhzrYiKa1TUmPqfmFn6wUIv82B_Y,131303
+lamindb/curators/_cellxgene_schemas/__init__.py,sha256=zqlFzMNMDGEBe6DV0gBsBMpfc9UHvNv1EpBsz_ktMoA,7502
+lamindb/curators/_cellxgene_schemas/schema_versions.csv,sha256=X9rmO88TW1Fht1f5mJs0JdW-VPvyKSajpf8lHNeECj4,1680
 lamindb/integrations/__init__.py,sha256=RWGMYYIzr8zvmNPyVB4m-p4gMDhxdRbjES2Ed23OItw,215
 lamindb/integrations/_vitessce.py,sha256=VgO9zAlTSIKDo1wEef_Q4BudTAVtRSZmuzRdCGwBvJk,4016
 lamindb/migrations/0069_squashed.py,sha256=gMWv65ErtjJZyWWo1b4uFHXWa6MSuBcmqz4ElZ6GPf4,62639
@@ -65,30 +66,30 @@ lamindb/migrations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuF
 lamindb/models/__init__.py,sha256=NlnrPiBSv93PttHDrAYnF3RTfiIhgC7QOE_mP0M9Ddc,1934
 lamindb/models/_describe.py,sha256=B-lmzc8AYaeuKwwRRsF0q8qT6P1i93sEjYkfl0NuyWQ,4926
 lamindb/models/_django.py,sha256=2LFaTvIPtxIV8_T6Kx0cvquTetj7C3OcnKukUyC9msY,7705
-lamindb/models/_feature_manager.py,sha256=rmqCm0GExiBhnamrzwq9aPps-sPMkI-E9sssWC5Mtuw,48538
-lamindb/models/_from_values.py,sha256=-yNuFtG6zEvmTjEeCjcGW4mY2gesl6w-1PWYJrnn2us,13625
+lamindb/models/_feature_manager.py,sha256=f81DJElY1XXX-ps9tfnk3ddJJBzDO-QPzIP-Dn4rxe8,50058
+lamindb/models/_from_values.py,sha256=3IkJTA3KTJHyuVZ1Hki1MFa4PKbHrK6mhPsshYygku8,13327
 lamindb/models/_is_versioned.py,sha256=ivtC0t96YI6eaMFqg0ctWY3ert96I_2R-DI5O0Zx7kU,8011
-lamindb/models/_label_manager.py,sha256=iDmCO6SNJAaskM43wfOoyVweCDuXXXIVhD9fnFdv2Vk,11650
+lamindb/models/_label_manager.py,sha256=rdTAjN0PNxIuHv289_JPoxvdPVVOTgBWhjWqBpKEnm4,11935
 lamindb/models/_relations.py,sha256=ONjHPiWIa_Ur7zMNTa_9Uw7K-366GORyPvGoVjf4EQs,3681
-lamindb/models/artifact.py,sha256=R7Vxdy_cLWn6YwHZ_uyFqJoOcLy1_4t_TMcvGdqZSN8,101962
-lamindb/models/can_curate.py,sha256=PCns1oyH-3ZVBRTUmmX6gUftHLm5gSysdwkczgsNloo,30390
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 lamindb/models/collection.py,sha256=P1E4olaqaPsVYdcQe8AgH_yUUdeQBa6QcyD1Y6Gedjo,26311
 lamindb/models/core.py,sha256=cjQGk5r0Rzf3zTeC0gn_GB29UfKq34l4hThsNNVhi3o,3965
-lamindb/models/feature.py,sha256=vnyGBBh_omOn-7Oj8GeNzMKkrTkw6T8_1aibuQCgfj0,24921
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 lamindb/models/flextable.py,sha256=ET9j0fTFYQIdXOZfwCnosXOag7nYD1DUV6_wZNqhvOs,5400
 lamindb/models/has_parents.py,sha256=PEGDiNTK7ikHBHAGsiHK4e6TA9jqUFRom1HSQuyReyE,17942
-lamindb/models/project.py,sha256=MZey8OqhW8LfcuOA9lw7Hx5ypBjgsHWKMAj-WJvUZJc,13853
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 lamindb/models/query_manager.py,sha256=RqF842cqloAv5z4zLDlWAZfVkLQbhCPry6WQW3CaznI,3713
-lamindb/models/query_set.py,sha256=zh2nA2Vgv_BsXoUG_hDtDPqQusrV94efDVv9zalLzI0,26514
-lamindb/models/record.py,sha256=BOrqlwVL9MKt_LkKODqyo-6W7vpskC5jb_PZeOKZdV8,64470
-lamindb/models/run.py,sha256=fbIjUT9O1zTRod3354twLJFOzeHp0fzvSmrerKosNQo,18519
+lamindb/models/query_set.py,sha256=buJ-zuua5MTqeEE8WD3lOBZXs19k_r4DuRWPB8Bai5Y,27060
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 lamindb/models/save.py,sha256=VEq4kmDyDiw9zTQY6meA9c5yT_YU5ldFzRDgKqCX59M,13031
-lamindb/models/schema.py,sha256=ZK9Ys_k3aNuXkd7PT9L2oTg_PbgyhesdGRB3GsSOfCE,28971
+lamindb/models/schema.py,sha256=zbzzQ8UOLqhJh-PC0CoRu-sN5-NnIFXoDtj1KSPhj_s,28672
 lamindb/models/transform.py,sha256=PbtjakPWmw0iuCG0HPEbysISVX_CoIE2KAPF7L18Vak,13064
 lamindb/models/ulabel.py,sha256=A8zJcRiGNmq24njLJv7_FuVZJmdtSkN-MSKw5c1QJMo,8605
 lamindb/setup/__init__.py,sha256=OwZpZzPDv5lPPGXZP7-zK6UdO4FHvvuBh439yZvIp3A,410
 lamindb/setup/core/__init__.py,sha256=SevlVrc2AZWL3uALbE5sopxBnIZPWZ1IB0NBDudiAL8,167
-lamindb-1.2a2.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-lamindb-1.2a2.dist-info/WHEEL,sha256=CpUCUxeHQbRN5UGRQHYRJorO5Af-Qy_fHMctcQ8DSGI,82
-lamindb-1.2a2.dist-info/METADATA,sha256=aDHlZHBG07QDCc6y9I4-bLtMSjxKqpVh81Iw6zXNtKM,2675
-lamindb-1.2a2.dist-info/RECORD,,
+lamindb-1.3.1.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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+lamindb-1.3.1.dist-info/RECORD,,

lamindb/curators/_cellxgene_schemas/schema_versions.yml

@@ -1,104 +0,0 @@
-schema-version:
-  4.0.0:
-    CellType:
-      cl:
-        all: "2023-08-24"
-    ExperimentalFactor:
-      efo:
-        all: "3.57.0"
-    Ethnicity:
-      hancestro:
-        human: "3.0"
-    DevelopmentalStage:
-      hsapdv:
-        human: "2020-03-10"
-      mmusdv:
-        mouse: "2020-03-10"
-    Disease:
-      mondo:
-        all: "2023-08-02"
-    Organism:
-      ncbitaxon:
-        all: "2023-06-20"
-    Phenotype:
-      pato:
-        all: "2023-05-18"
-    Tissue:
-      uberon:
-        all: "2023-09-05"
-    Gene:
-      genecode:
-        human: "v38"
-        mouse: "vM27"
-  5.0.0:
-    CellType:
-      cl:
-        all: "2024-01-04"
-    ExperimentalFactor:
-      efo:
-        all: "3.62.0"
-    Ethnicity:
-      hancestro:
-        human: "3.0"
-    DevelopmentalStage:
-      hsapdv:
-        human: "2020-03-10"
-      mmusdv:
-        mouse: "2020-03-10"
-    Disease:
-      mondo:
-        all: "2024-01-03"
-    Organism:
-      ncbitaxon:
-        all: "2023-06-20"
-      ensembl:
-        vertebrates: "release-110"
-    Phenotype:
-      pato:
-        all: "2023-05-18"
-    Tissue:
-      uberon:
-        all: "2024-01-18"
-    Gene:
-      genecode:
-        human: "v44"
-        mouse: "vM33"
-      ensembl:
-        human: "release-110"
-        mouse: "release-110"
-  5.1.0:
-    CellType:
-      cl:
-        all: "2024-04-05"
-    ExperimentalFactor:
-      efo:
-        all: "3.65.0"
-    Ethnicity:
-      hancestro:
-        human: "3.0"
-    DevelopmentalStage:
-      hsapdv:
-        human: "2020-03-10"
-      mmusdv:
-        mouse: "2020-03-10"
-    Disease:
-      mondo:
-        all: "2024-05-08"
-    Organism:
-      ncbitaxon:
-        all: "2023-06-20"
-      ensembl:
-        vertebrates: "release-110"
-    Phenotype:
-      pato:
-        all: "2023-05-18"
-    Tissue:
-      uberon:
-        all: "2024-03-22"
-    Gene:
-      genecode:
-        human: "v44"
-        mouse: "vM33"
-      ensembl:
-        human: "release-110"
-        mouse: "release-110"