lamindb 1.10.0__py3-none-any.whl → 1.10.1__py3-none-any.whl

lamindb/__init__.py

@@ -108,7 +108,7 @@ Backwards compatibility.
 
 # ruff: noqa: I001
 # denote a release candidate for 0.1.0 with 0.1rc1, 0.1a1, 0.1b1, etc.
-__version__ = "1.10.0"
+__version__ = "1.10.1"
 
 import warnings
 

lamindb/core/storage/_anndata_accessor.py

@@ -340,6 +340,12 @@ if ZARR_INSTALLED:
                 ds = sparse_dataset(elem)
                 return _subset_sparse(ds, indices)
             else:
+                indices = tuple(
+                    idim.tolist()
+                    if isinstance(idim, np.ndarray) and idim.dtype == "bool"
+                    else idim
+                    for idim in indices
+                )
                 return read_elem_partial(elem, indices=indices)
 
     # this is needed because accessing zarr.Group.keys() directly is very slow

lamindb/examples/datasets/__init__.py

@@ -36,11 +36,12 @@ Directories.
    dir_scrnaseq_cellranger
    dir_iris_images
 
-Dataframe, AnnData, MuData.
+Dictionary, Dataframe, AnnData, MuData, SpatialData.
 
 .. autosummary::
    :toctree: .
 
+   dict_cxg_uns
    df_iris
    df_iris_in_meter
    df_iris_in_meter_study1
@@ -55,6 +56,7 @@ Dataframe, AnnData, MuData.
    mudata_papalexi21_subset
    schmidt22_crispra_gws_IFNG
    schmidt22_perturbseq
+   spatialdata_blobs
 
 Other.
 
@@ -76,6 +78,7 @@ from ._core import (
     df_iris_in_meter,
     df_iris_in_meter_study1,
     df_iris_in_meter_study2,
+    dict_cxg_uns,
     dir_iris_images,
     dir_scrnaseq_cellranger,
     file_bam,

lamindb/examples/datasets/_core.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from pathlib import Path
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Any
 from urllib.request import urlretrieve
 
 import anndata as ad
@@ -418,6 +418,38 @@ def mudata_papalexi21_subset() -> MuData:  # pragma: no cover
     return mdata
 
 
+def dict_cxg_uns() -> dict[str, Any]:
+    """An example CELLxGENE AnnData `.uns` dictionary."""
+    uns = {
+        "organism_ontology_term_id": "NCBITaxon:9606",
+        "spatial": {
+            "is_single": True,
+            "library_1": {  # Dynamic library_id key
+                "images": {
+                    "fullres": "path/to/fullres.jpg",
+                    "hires": "path/to/hires.jpg",
+                },
+                "scalefactors": {
+                    "spot_diameter_fullres": 89.43,
+                    "tissue_hires_scalef": 0.177,
+                },
+            },
+            "library_2": {  # Another dynamic library_id key
+                "images": {
+                    "fullres": "path/to/fullres_2.jpg",
+                    "hires": "path/to/hires_2.jpg",
+                },
+                "scalefactors": {
+                    "spot_diameter_fullres": 120.34,
+                    "tissue_hires_scalef": 0.355,
+                },
+            },
+        },
+    }
+
+    return uns
+
+
 def df_iris() -> pd.DataFrame:
     """The iris collection as in sklearn.
 

lamindb/examples/schemas/_anndata.py

@@ -10,7 +10,7 @@ if TYPE_CHECKING:
 
 
 def anndata_ensembl_gene_ids_and_valid_features_in_obs() -> Schema:
-    """Return a schema for an AnnData with Ensembl gene IDs and valid features in obs.
+    """An `AnnData` schema validating Ensembl gene IDs and valid features in obs.
 
     .. literalinclude:: scripts/define_schema_anndata_ensembl_gene_ids_and_valid_features_in_obs.py
         :language: python

lamindb/examples/schemas/_simple.py

@@ -10,7 +10,7 @@ if TYPE_CHECKING:
 
 
 def valid_features() -> Schema:
-    """Return a schema for an AnnData with Ensembl gene IDs and valid features in obs.
+    """A `DataFrame` schema that validates that columns map on existing features.
 
     .. literalinclude:: scripts/define_valid_features.py
         :language: python

{lamindb-1.10.0.dist-info → lamindb-1.10.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamindb
-Version: 1.10.0
+Version: 1.10.1
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10,<3.14
@@ -11,7 +11,7 @@ Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: lamin_utils==0.15.0
 Requires-Dist: lamin_cli==1.6.1
-Requires-Dist: lamindb_setup[aws]==1.9.0
+Requires-Dist: lamindb_setup[aws]==1.9.1
 Requires-Dist: pyyaml
 Requires-Dist: pyarrow
 Requires-Dist: pandera>=0.24.0
@@ -19,7 +19,7 @@ Requires-Dist: typing_extensions!=4.6.0
 Requires-Dist: python-dateutil
 Requires-Dist: pandas>=2.0.0
 Requires-Dist: scipy<1.15.0
-Requires-Dist: anndata>=0.8.0,<=0.12.0
+Requires-Dist: anndata>=0.8.0,<=0.12.1
 Requires-Dist: fsspec
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary

{lamindb-1.10.0.dist-info → lamindb-1.10.1.dist-info}/RECORD

@@ -1,4 +1,4 @@
-lamindb/__init__.py,sha256=E2TEOJS9lT0g-yGTWuIdK6m0kyIF7prfBGxJTPhFHHA,2905
+lamindb/__init__.py,sha256=cWTeR7mqoNI5I8jjkRldYjJOqmaCsy7n8wCvbbWbeNI,2905
 lamindb/_finish.py,sha256=3HVKRw27rQs_S2ior-JX2IU0vUkeG5a6p8XgEgdT8-U,21219
 lamindb/_tracked.py,sha256=-wK7BJv30nf4v2_nH5qDCyxHvug7ih6duQNGxDrj3UE,4447
 lamindb/_view.py,sha256=cod1RnZoLyzMVJcjWjytg78Sf4qsR8IAdqpwzsi8FTw,4950
@@ -21,7 +21,7 @@ lamindb/core/exceptions.py,sha256=FMEoSvT3FvtLkxQAt2oDXPeaPem8V5x5UBbTsPFYU5w,53
 lamindb/core/loaders.py,sha256=QH3r3Q_aPrbkgiWaV30TmxcLCs6zZFQLRW442DsTrNU,5456
 lamindb/core/types.py,sha256=_u8amXATAZN-nNGNWYGmyqYDcHbT_i0NZeLRhm_-ygI,378
 lamindb/core/storage/__init__.py,sha256=2gJyn9w6rzv3oPHjY756OfQYrLEXb37YuKMqh6ZjbF8,542
-lamindb/core/storage/_anndata_accessor.py,sha256=zDg_ugdjtnEV1aenh1ePEadM9vLNGcIEZDP55TECF1o,26379
+lamindb/core/storage/_anndata_accessor.py,sha256=NOAqI-SHS8IwM0MwsZmRUtqG8r4tBTJ9T8888lhvQkw,26611
 lamindb/core/storage/_backed_access.py,sha256=5y3C_D1g89d831FAXr8-WashmmL3cdNfTR5s61vrMdA,7858
 lamindb/core/storage/_polars_lazy_df.py,sha256=_JhnU8RmoTzU2kp7kyHRSUTAkFhpCJo6NNnHxvBXQv4,2929
 lamindb/core/storage/_pyarrow_dataset.py,sha256=lRYYt7edUtwauhxd7RwFud6YPDbz2PFvYYgqLhfapfk,1398
@@ -43,16 +43,16 @@ lamindb/examples/cellxgene/_cellxgene.py,sha256=HP_skQJbNYDEYhiLUpaP9kfmtPivmgTu
 lamindb/examples/cellxgene/cxg_schema_versions.csv,sha256=Du_zk2rrMA4AbHwYp6vgLzZH1Krnmml_KVerc2IvvkI,2107
 lamindb/examples/croissant/__init__.py,sha256=a8LFsAvHzts_C2jlcbuF7kxwGEBWd4VERsluwDFh_iY,1418
 lamindb/examples/croissant/mini_immuno.anndata.zarr_metadata.json,sha256=XhY4wnFyMoK4Thkaolh2yJxtU6sX0bdFsJvRvt942k8,2921
-lamindb/examples/datasets/__init__.py,sha256=JsFd-nXGyBWV7VjvqCAT7Si5T4jBCqkzBkU3gzqi-5Y,1896
-lamindb/examples/datasets/_core.py,sha256=uaP0snoKuAE5nDTL_XIgPeEoXSp5sTrNNAyOPDciZRU,20286
+lamindb/examples/datasets/__init__.py,sha256=TI91CjNMh0MqcZVcruO6xLGPYqqQ5o3p_E37huOV3GI,1976
+lamindb/examples/datasets/_core.py,sha256=o_Kaz-i1W7ldXP2d1arUix_JvxPS9n2bpDAiW0M_yxA,21302
 lamindb/examples/datasets/_fake.py,sha256=BZF9R_1iF0HDnvtZNqL2FtsjSMuqDIfuFxnw_LJYIh4,953
 lamindb/examples/datasets/_small.py,sha256=60WKs6Oo2NE7HUqe6PLfiPxH_5TYUjr_iZdtFWiOeAA,3460
 lamindb/examples/datasets/mini_immuno.py,sha256=ZEL9T4zhCKm8ggqU7VVhuihVKPR3MmlkJNOtdygH2v4,6107
 lamindb/examples/fixtures/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 lamindb/examples/fixtures/sheets.py,sha256=2oRAY2jQYCJuW_gCTGAs90XerYQHIe3pivoi0vzgXpc,9035
 lamindb/examples/schemas/__init__.py,sha256=NPDp7VjMOHStEIthx3xW9NSHtY7jnnMzrNPcSDgxT3M,241
-lamindb/examples/schemas/_anndata.py,sha256=XpoEI52FIv_hv5Is8lXrxfkBbYgsQ6ZCHIBuci0_AU0,1215
-lamindb/examples/schemas/_simple.py,sha256=rNzjKYRQ2t7LnLbT24MjQUVpEZQxgPM1gtsate0hBXc,916
+lamindb/examples/schemas/_anndata.py,sha256=TAQrnBLZhH4TgbznrJDdGK_Gze6cf1MvyXuCcKIvb1g,1210
+lamindb/examples/schemas/_simple.py,sha256=Dspj5QRmv241IstBxuc1E1Q5YeEqTOnOvakg7ChPj1k,911
 lamindb/integrations/__init__.py,sha256=Zh0ROuRmob1QGV2mCo3A7cFmdheJGq4CUdo7G16pRHU,286
 lamindb/integrations/_croissant.py,sha256=9zRkOg2pkaiylKslfKfxYzZ5I5813qhCfA4Er3Q3bB4,4166
 lamindb/integrations/_vitessce.py,sha256=s2F8KPpYVG0zUOTaDJgH1XAJtQDg1zrD_SxC4ZHUkHk,4035
@@ -137,7 +137,7 @@ lamindb/setup/_switch.py,sha256=njZJN__JOhVrBFGClQG1wobdhJJp6l_XzPGKtKSCrfU,434
 lamindb/setup/core/__init__.py,sha256=SevlVrc2AZWL3uALbE5sopxBnIZPWZ1IB0NBDudiAL8,167
 lamindb/setup/errors/__init__.py,sha256=bAHTxOUJW1rm4zpF0Pvqkftn8W6iMGnQ-uyNBu13Nfg,171
 lamindb/setup/types/__init__.py,sha256=ATaosOi6q-cDWB52T69_sRmLMqj8cHfc-vljzZsrJNw,169
-lamindb-1.10.0.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-lamindb-1.10.0.dist-info/WHEEL,sha256=CpUCUxeHQbRN5UGRQHYRJorO5Af-Qy_fHMctcQ8DSGI,82
-lamindb-1.10.0.dist-info/METADATA,sha256=Z3G73ZpT3c9KDMhhW6SWsW55CxFsqh93MCl2LUB2PH4,5199
-lamindb-1.10.0.dist-info/RECORD,,
+lamindb-1.10.1.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+lamindb-1.10.1.dist-info/WHEEL,sha256=CpUCUxeHQbRN5UGRQHYRJorO5Af-Qy_fHMctcQ8DSGI,82
+lamindb-1.10.1.dist-info/METADATA,sha256=UYl8nK7xlSZg0L4GaKYNkMjXuNs36LvfgSJFq-StSho,5199
+lamindb-1.10.1.dist-info/RECORD,,