lamindb 1.11.2__tar.gz → 1.11.3__tar.gz

{lamindb-1.11.2 → lamindb-1.11.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamindb
-Version: 1.11.2
+Version: 1.11.3
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10,<3.14
@@ -10,8 +10,8 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: lamin_utils==0.15.0
-Requires-Dist: lamin_cli==1.7.1
-Requires-Dist: lamindb_setup[aws]==1.10.1
+Requires-Dist: lamin_cli==1.7.2
+Requires-Dist: lamindb_setup[aws]==1.10.2
 Requires-Dist: bionty>=1.7a1
 Requires-Dist: wetlab>=1.5a1
 Requires-Dist: nbproject==0.11.1

{lamindb-1.11.2 → lamindb-1.11.3}/lamindb/__init__.py

@@ -114,7 +114,7 @@ Backwards compatibility.
 
 # ruff: noqa: I001
 # denote a release candidate for 0.1.0 with 0.1rc1, 0.1a1, 0.1b1, etc.
-__version__ = "1.11.2"
+__version__ = "1.11.3"
 
 import warnings as _warnings
 

{lamindb-1.11.2 → lamindb-1.11.3}/lamindb/models/schema.py

@@ -258,6 +258,12 @@ class Schema(SQLRecord, CanCurate, TracksRun):
 
     Composite schemas can have multiple slots, e.g., for an `AnnData`, one schema for slot `obs` and another one for `var`.
 
+    To create a schema, one of the following must be passed:
+    - `features`: A list of :class:`~lamindb.Feature` records, e.g., `[Feature(...), Feature(...)]`.
+    - `itype`: A registry field, e.g., `Feature` or `bionty.Gene.ensembl_gene_id`, to constrain feature identifiers to be valid identifiers of the registry.
+    - `slots`: A dictionary mapping slot names to :class:`~lamindb.Schema` objects, e.g., `{"obs": Schema(...), "var": Schema(...), "obsm": Schema(...)}`.
+    - `is_type=True`: To create a schema type, e.g., `ln.Schema(name="ProteinPanel", is_type=True)`.
+
     Args:
         features: `list[SQLRecord] | list[tuple[Feature, dict]] | None = None` Feature
             records, e.g., `[Feature(...), Feature(...)]` or Features with their config, e.g., `[Feature(...).with_config(optional=True)]`.
@@ -565,6 +571,10 @@ class Schema(SQLRecord, CanCurate, TracksRun):
             coerce_dtype=coerce_dtype,
             n_features=n_features,
         )
+        if not features and not slots and not is_type and not itype:
+            raise InvalidArgument(
+                "Please pass features or slots or itype or set is_type=True"
+            )
         if not is_type:
             schema = (
                 Schema.objects.using(using)
@@ -1211,12 +1221,14 @@ def get_type_str(dtype: str | None) -> str | None:
     return type_str
 
 
-def _get_related_name(self: Schema) -> str:
+def _get_related_name(self: Schema) -> str | None:
     related_models = dict_related_model_to_related_name(self, instance=self._state.db)
-    related_name = related_models.get(
-        parse_cat_dtype(self.itype, is_itype=True)["registry_str"]
-    )
-    return related_name
+    if self.itype:
+        related_name = related_models.get(
+            parse_cat_dtype(self.itype, is_itype=True)["registry_str"]
+        )
+        return related_name
+    return None
 
 
 class SchemaFeature(BaseSQLRecord, IsLink):

{lamindb-1.11.2 → lamindb-1.11.3}/pyproject.toml

@@ -17,8 +17,8 @@ classifiers = [
 dependencies = [
     # Lamin PINNED packages
     "lamin_utils==0.15.0",
-    "lamin_cli==1.7.1",
-    "lamindb_setup[aws]==1.10.1",
+    "lamin_cli==1.7.2",
+    "lamindb_setup[aws]==1.10.2",
     # Lamin OPTIONAL packages, included to avoid users forgetting about passing extras,
     # which has happened very often these past years
     # these are small packages with few dependencies

{lamindb-1.11.2 → lamindb-1.11.3}/tests/core/test_schema.py

@@ -3,7 +3,7 @@ import lamindb as ln
 import pandas as pd
 import pytest
 from django.db.utils import IntegrityError
-from lamindb.errors import FieldValidationError, ValidationError
+from lamindb.errors import FieldValidationError, InvalidArgument, ValidationError
 from lamindb.models.schema import get_related_name, validate_features
 
 
@@ -548,7 +548,7 @@ def test_schema_already_saved_aux():
 
 
 def test_schema_not_saved_describe():
-    schema = ln.Schema()
+    schema = ln.Schema(name="NotSavedSchema", is_type=True)
     with pytest.raises(ValueError) as e:
         schema.describe()
     assert "Schema must be saved before describing" in str(e.value)
@@ -561,7 +561,10 @@ def test_schema_is_type():
     assert BioSample.hash is None
     assert BioSample.type == Sample
     assert BioSample.is_type
-
+    # create a schema without any features or slots or itype or is_type=True
+    with pytest.raises(InvalidArgument) as e:
+        ln.Schema(name="TechSample", type=Sample)
+    assert "Please pass features or slots or itype or set is_type=True" in str(e.value)
     # clean up
     BioSample.delete(permanent=True)
     Sample.delete(permanent=True)

{lamindb-1.11.2 → lamindb-1.11.3}/tests/curators/test_curators_examples.py

@@ -941,14 +941,15 @@ def test_tiledbsoma_curator(clean_soma_files):
     )
 
     # Test with invalid dataset
-    with pytest.raises(ln.errors.InvalidArgument):
+    with pytest.raises(ln.errors.InvalidArgument) as e:
         ln.curators.TiledbsomaExperimentCurator(adata, soma_schema)
+    assert "dataset must be SOMAExperiment-like." in str(e.value)
 
     # Test with invalid schema
-    min_schema = ln.Schema(features=[]).save()
     with tiledbsoma.Experiment.open("small_dataset.tiledbsoma") as experiment:
-        with pytest.raises(ln.errors.InvalidArgument):
-            ln.curators.TiledbsomaExperimentCurator(experiment, schema=min_schema)
+        with pytest.raises(ln.errors.InvalidArgument) as e:
+            ln.curators.TiledbsomaExperimentCurator(experiment, schema=var_schema)
+        assert "Schema otype must be 'tiledbsoma'." in str(e.value)
 
     with tiledbsoma.Experiment.open("small_dataset.tiledbsoma") as experiment:
         curator = ln.curators.TiledbsomaExperimentCurator(experiment, soma_schema)
@@ -994,7 +995,6 @@ def test_tiledbsoma_curator(clean_soma_files):
     # Clean up
     shutil.rmtree(typo_soma_path)
     artifact.delete(permanent=True)
-    min_schema.delete(permanent=True)
     soma_schema.delete(permanent=True)
     var_schema.delete(permanent=True)
     obs_schema.delete(permanent=True)