lamindb 0.73.0__py3-none-any.whl → 0.73.2__py3-none-any.whl

lamindb/__init__.py

@@ -41,7 +41,7 @@ Modules & settings:
 """
 
 # denote a release candidate for 0.1.0 with 0.1rc1, 0.1a1, 0.1b1, etc.
-__version__ = "0.73.0"
+__version__ = "0.73.2"
 
 import os as _os
 

lamindb/_annotate.py

@@ -813,7 +813,10 @@ def standardize_and_inspect(
     values: Iterable[str], field: FieldAttr, registry: Registry, **kwargs
 ):
     """Standardize and inspect values using a registry."""
-    if hasattr(registry, "standardize"):
+    if hasattr(registry, "standardize") and hasattr(
+        registry,
+        "synonyms",  # https://github.com/laminlabs/lamindb/issues/1685
+    ):
         values = registry.standardize(values, field=field, mute=True, **kwargs)
     return registry.inspect(values, field=field, mute=True, **kwargs)
 
@@ -976,7 +979,7 @@ def save_artifact(
         except ImportError:
             pass
     if artifact is None:
-        raise ValueError("data must be a DataFrame, AnnData or MuData object")
+        raise ValueError("data must be a DataFrame, AnnData or MuData object.")
     artifact.save()
 
     feature_kwargs = check_registry_organism(

lamindb/_artifact.py

@@ -196,6 +196,8 @@ def get_stat_or_artifact(
     if not isinstance(path, LocalPathClasses):
         size, hash, hash_type = None, None, None
         if stat is not None:
+            # convert UPathStatResult to fsspec info dict
+            stat = stat.as_info()
             if "ETag" in stat:  # is file
                 size, hash, hash_type = get_stat_file_cloud(stat)
             elif stat["type"] == "directory":
@@ -1109,6 +1111,5 @@ for name in METHOD_NAMES:
 Artifact._delete_skip_storage = _delete_skip_storage
 Artifact._save_skip_storage = _save_skip_storage
 Artifact.path = path
-Artifact.stage = cache
 # this seems a Django-generated function
 delattr(Artifact, "get_visibility_display")

lamindb/_registry.py

@@ -54,7 +54,7 @@ def suggest_records_with_similar_names(record: Registry, kwargs) -> bool:
     """
     if kwargs.get("name") is None:
         return False
-    queryset = _search(record.__class__, kwargs["name"], truncate_words=True, limit=5)
+    queryset = _search(record.__class__, kwargs["name"], truncate_words=True, limit=20)
     if not queryset.exists():  # empty queryset
         return False
     for alternative_record in queryset:
@@ -549,24 +549,3 @@ if ln_setup._TESTING:  # type: ignore
 
 for name in METHOD_NAMES:
     attach_func_to_class_method(name, Registry, globals())
-
-
-@classmethod  # type: ignore
-def __get_schema_name__(cls) -> str:
-    schema_module_name = cls.__module__.split(".")[0]
-    schema_name = schema_module_name.replace("lnschema_", "")
-    return schema_name
-
-
-@classmethod  # type: ignore
-def __get_name_with_schema__(cls) -> str:
-    schema_name = cls.__get_schema_name__()
-    if schema_name == "core":
-        schema_prefix = ""
-    else:
-        schema_prefix = f"{schema_name}."
-    return f"{schema_prefix}{cls.__name__}"
-
-
-Registry.__get_schema_name__ = __get_schema_name__
-Registry.__get_name_with_schema__ = __get_name_with_schema__

lamindb/_view.py

@@ -1,14 +1,16 @@
 from __future__ import annotations
 
+import builtins
 import importlib
 import inspect
 
-from IPython.display import display
 from lamin_utils import colors, logger
 from lamindb_setup import settings
 from lamindb_setup._init_instance import get_schema_module_name
 from lnschema_core import Registry
 
+is_run_from_ipython = getattr(builtins, "__IPYTHON__", False)
+
 
 def view(
     n: int = 7, schema: str | None = None, registries: list[str] | None = None
@@ -25,6 +27,11 @@ def view(
     Examples:
         >>> ln.view()
     """
+    if is_run_from_ipython:
+        from IPython.display import display as show
+    else:
+        show = logger.print
+
     if schema is not None:
         schema_names = [schema]
     else:
@@ -60,4 +67,4 @@ def view(
                 df = orm.df().iloc[-n:]
             if df.shape[0] > 0:
                 logger.print(colors.blue(colors.bold(orm.__name__)))
-                display(df)
+                show(df)

lamindb/core/_label_manager.py

@@ -125,13 +125,13 @@ def validate_labels(labels: QuerySet | list | dict, parents: bool = True):
 
 
 class LabelManager:
-    """Label manager (:attr:`~lamindb.core.Data.labels`).
+    """Label manager (:attr:`~lamindb.core.HasFeatures.labels`).
 
     This allows to manage untyped labels :class:`~lamindb.ULabel` and arbitrary
     typed labels (e.g., :class:`~bionty.CellLine`) and associate labels
     with features.
 
-    See :class:`~lamindb.core.Data` for more information.
+    See :class:`~lamindb.core.HasFeatures` for more information.
     """
 
     def __init__(self, host: Artifact | Collection):

lamindb/core/schema.py

@@ -1,10 +1,10 @@
-from typing import Type
+from __future__ import annotations
 
 from django.db.models import ManyToManyField
 from lnschema_core.models import Feature, FeatureSet, LinkORM, Registry
 
 
-def dict_schema_name_to_model_name(orm: Type[Registry]) -> dict[str, Registry]:
+def dict_schema_name_to_model_name(orm: type[Registry]) -> dict[str, Registry]:
     d: dict = {
         i.related_model.__get_name_with_schema__(): i.related_model
         for i in orm._meta.related_objects
@@ -21,7 +21,7 @@ def dict_schema_name_to_model_name(orm: Type[Registry]) -> dict[str, Registry]:
 
 
 def dict_related_model_to_related_name(
-    orm: Type[Registry], links: bool = False
+    orm: type[Registry], links: bool = False
 ) -> dict[str, str]:
     def include(model: Registry):
         return not links != issubclass(model, LinkORM)

lamindb/core/versioning.py

@@ -138,7 +138,7 @@ def process_is_new_version_of(
     if is_new_version_of is not None and not isinstance(is_new_version_of, type):
         raise TypeError(f"is_new_version_of has to be of type {type}")
     if is_new_version_of is None:
-        uid = init_uid(version=version, n_full_id=type._len_stem_uid)
+        uid = init_uid(version=version, n_full_id=type._len_full_uid)
     else:
         uid, version = get_uid_from_old_version(is_new_version_of, version)
         if name is None:

lamindb/integrations/_vitessce.py

@@ -39,9 +39,13 @@ def save_vitessce_config(vitessce_config: VitessceConfig, description: str) -> A
             if "url" not in file:
                 raise ValueError("Each file must have a 'url' key.")
             filename = file["url"].split("/")[-1]
-            assert filename.endswith((".anndata.zarr", ".spatialdata.zarr"))
-            filestem = filename.replace(".anndata.zarr", "").replace(
-                ".spatialdata.zarr", ""
+            assert filename.endswith(
+                (".anndata.zarr", ".spatialdata.zarr", ".ome.zarr")
+            )
+            filestem = (
+                filename.replace(".anndata.zarr", "")
+                .replace(".spatialdata.zarr", "")
+                .replace(".ome.zarr", "")
             )
             artifact = Artifact.filter(uid__startswith=filestem).one_or_none()
             if artifact is None:

{lamindb-0.73.0.dist-info → lamindb-0.73.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.73.0
+Version: 0.73.2
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,8 +9,8 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Dist: lnschema_core==0.68.0
-Requires-Dist: lamindb_setup==0.73.0
+Requires-Dist: lnschema_core==0.69.0
+Requires-Dist: lamindb_setup==0.73.1
 Requires-Dist: lamin_utils==0.13.2
 Requires-Dist: lamin_cli==0.14.0
 Requires-Dist: rapidfuzz
@@ -25,7 +25,7 @@ Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
 Requires-Dist: psutil
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.43.1 ; extra == "bionty"
+Requires-Dist: bionty==0.44.0 ; extra == "bionty"
 Requires-Dist: pandas<2 ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"

{lamindb-0.73.0.dist-info → lamindb-0.73.2.dist-info}/RECORD

@@ -1,6 +1,6 @@
-lamindb/__init__.py,sha256=J7AraTNN8zk-iL_9_WY9zTUtEPPmvRdOK1r1-96jSfA,2207
-lamindb/_annotate.py,sha256=_2DeWFQ4pNaPtUYOqHzNPNrkvhPdxpl6i0OwynQ0jME,44271
-lamindb/_artifact.py,sha256=HnaCSfeW_1Knesvkz2loJH4AY7WBrm_pFRd-ZgVz6Pg,40747
+lamindb/__init__.py,sha256=ewJ0w3ggVARCnYyCLLJ_24n2eQDgjK3TXkzjyBn67sE,2207
+lamindb/_annotate.py,sha256=CScyKVB3k_x5p0pihxO1UrTFBCvPcSSjBXvGY3YgTLs,44381
+lamindb/_artifact.py,sha256=uMUlXCGU1JYSnOYMxCwEe_1MslbcnZACP9SYL-a4zRk,40816
 lamindb/_can_validate.py,sha256=s1q0lxplqnhytrVgArBTm05XKMMmpreK0ZlVCsd2jjk,14849
 lamindb/_collection.py,sha256=AGiztgM_OIet617aF86muL6lIv6GEDcmXorize6V62U,14657
 lamindb/_feature.py,sha256=Aawz4jCgjhuneZnmoty7JkZI3zjA_50vr_0dnFjSN3U,7348
@@ -12,18 +12,18 @@ lamindb/_is_versioned.py,sha256=0PgRCmxEmYDcAjllLSOYZm132B1lW6QgmBBERhRyFt0,1341
 lamindb/_parents.py,sha256=kb5AHkntpTP5g2lk1aPL0FmIilYZYVZvj6stddFOI40,15075
 lamindb/_query_manager.py,sha256=qxwrBM8UmNQnUiNOfe84YN6NpfJBg2wQ2JqUfH6HHhc,4225
 lamindb/_query_set.py,sha256=JgdJY2pACCqjC4AHjFiMAdq_qjeuhEo2NUX68f6ODwk,11597
-lamindb/_registry.py,sha256=ukzQaMtfySnirfk6XMQKFLyaLIVxIp61TI3Y0WoE6og,19346
+lamindb/_registry.py,sha256=hoBkVl8D4yLQKMoOhVIDTNkO_401yCoVHI4MlNHDZgI,18756
 lamindb/_run.py,sha256=b7A52M1On3QzFgIYyfQoz5Kk7V3wcu9p_Prq5bzd8v8,1838
 lamindb/_save.py,sha256=It4XO448D8NG2cReo9Xy0lQBQdkMm_rCx_TGD1qZWWc,11864
 lamindb/_storage.py,sha256=VW8xq3VRv58-ciholvOdlcgvp_OIlLxx5GxLt-e2Irs,614
 lamindb/_transform.py,sha256=E9C7psuOnsNrUQpWRuGgEUM8_pc7YhDn7n4ieHzB4X0,3169
 lamindb/_ulabel.py,sha256=XDSdZBXX_ki5s1vOths3MjF2x5DPggBR_PV_KF4SGyg,1611
 lamindb/_utils.py,sha256=LGdiW4k3GClLz65vKAVRkL6Tw-Gkx9DWAdez1jyA5bE,428
-lamindb/_view.py,sha256=GV1FrqIMmdooEkA-5zvcTWgV1nqx1sehi6WdWEaFpxM,2171
+lamindb/_view.py,sha256=NdWWF75rmkCHefqBViUnsHLu3OViJ1z_bEvfcedydsw,2330
 lamindb/core/__init__.py,sha256=RkE5BrdOWNHQIz60z1npYoRim-Ot24-L7JTmLXd2WTU,1363
 lamindb/core/_data.py,sha256=xkjEvAhWeEEYRIZIi9Qbb0aEWiUPttq-qnCLx_2xy48,16172
 lamindb/core/_feature_manager.py,sha256=h7puH83LjaiJrBlmw3wSkUVO5c_LVfubCJKklPryP84,26205
-lamindb/core/_label_manager.py,sha256=uRwzRVXBN-3B6EFCR2oox3p3lfxtICcAipG-1zVIN9w,9626
+lamindb/core/_label_manager.py,sha256=d9r3tiNDFbpZQmxE1jmgdgnMYPOfTPpAKGKtRRLmVj8,9640
 lamindb/core/_mapped_collection.py,sha256=_OwFZh5SePDUD70XIK5kngv3we_Z5-YdGHNfpUSatSQ,19469
 lamindb/core/_run_context.py,sha256=aGdZv4IeYo7QpXl9H9U7RNwpgzqGeCDKPuoSdtP-CAE,18988
 lamindb/core/_settings.py,sha256=rW1KfEXfT56XErwcnSuQxaCytpOy1kJ-u7tVmkmNmxY,6131
@@ -32,9 +32,9 @@ lamindb/core/_track_environment.py,sha256=xLZ6kgzxWS6MWZ5LQ_wkbJX99vmYOT8iQ-Fz4O
 lamindb/core/_transform_settings.py,sha256=eV96QKX9jOojjzF-a0oo0wXQsMXN2F6QV7orE06oFC8,161
 lamindb/core/exceptions.py,sha256=bbm-PeSy24qFcqh2HpucZWpwGAvk-TL_3FUoAPb3e3E,867
 lamindb/core/fields.py,sha256=Jgi_XI-iTe6cT7oD8FV_JqEpjN1Q9rZWwL8VLtj4jkA,164
-lamindb/core/schema.py,sha256=CshQ80Sau8yIeWC_hbP0E476EJx4-BzVv75wf5vW2No,1850
+lamindb/core/schema.py,sha256=BbG7JGrXVLwEX_6eQb8ouJc9Q-MgazwqHvAM5dtrWtM,1861
 lamindb/core/types.py,sha256=xeQF2x40p2pR9eIVQrXT74RrS810z2fbjmTRTSQUqPM,230
-lamindb/core/versioning.py,sha256=eEnLPW7lumrkZY-EovZfaQWU44vnuWs4bFGZWrgNSGc,4943
+lamindb/core/versioning.py,sha256=zbp3wAWOqU1uDF9wRrpaS9JfmRglUQtVHvFpWWoJHZk,4943
 lamindb/core/datasets/__init__.py,sha256=zRP98oqUAaXhqWyKMiH0s_ImVIuNeziQQ2kQ_t0f-DI,1353
 lamindb/core/datasets/_core.py,sha256=bMNtx2tXhzvjLkHmg9I5jE1xMTxPH68hovnX6_NjT6g,19858
 lamindb/core/datasets/_fake.py,sha256=BZF9R_1iF0HDnvtZNqL2FtsjSMuqDIfuFxnw_LJYIh4,953
@@ -46,10 +46,10 @@ lamindb/core/storage/_zarr.py,sha256=5ceEz6YIvgvUnVVNWhK5Z4W0WfrvyvY82Yna5jSX1_E
 lamindb/core/storage/objects.py,sha256=OzvBCS-Urz5mr-O95qYt6RGBDDX5HmjfRRKWPPDn1ZE,1797
 lamindb/core/storage/paths.py,sha256=H9OPCuI7fPNRmvtQRFda92VIi6whnW6Q9BAZ6U8VWI4,8203
 lamindb/integrations/__init__.py,sha256=aH2PmO2m4-vwIifMYTB0Fyyr_gZWtVnV71jT0tVWSw0,123
-lamindb/integrations/_vitessce.py,sha256=b0FqTBsP-M6Q7xCYXVwFwM8DOIeeOBZEhYbryhtq4gk,2535
+lamindb/integrations/_vitessce.py,sha256=Qd39OuNsL0GXU7nMvEWLRRESFQ0mwGf_ePMJE_FDYm8,2639
 lamindb/setup/__init__.py,sha256=OwZpZzPDv5lPPGXZP7-zK6UdO4FHvvuBh439yZvIp3A,410
 lamindb/setup/core/__init__.py,sha256=SevlVrc2AZWL3uALbE5sopxBnIZPWZ1IB0NBDudiAL8,167
-lamindb-0.73.0.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-lamindb-0.73.0.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
-lamindb-0.73.0.dist-info/METADATA,sha256=4HwOjMczVyTTooI8kH_aUPPO9rE-4gaCCUT86z7qExc,2735
-lamindb-0.73.0.dist-info/RECORD,,
+lamindb-0.73.2.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+lamindb-0.73.2.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+lamindb-0.73.2.dist-info/METADATA,sha256=bsHf6jMyHwkf2btB1WlAnrsfjN-9ue3xBK0thFSQt_s,2735
+lamindb-0.73.2.dist-info/RECORD,,