lamindb 0.69.6__py3-none-any.whl → 0.69.7__py3-none-any.whl

lamindb/__init__.py

@@ -40,7 +40,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.69.6"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.69.7"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 

lamindb/_finish.py

@@ -34,7 +34,7 @@ def finish(i_saved_the_notebook: bool = False):
 
         if not i_saved_the_notebook and not ln_setup._TESTING:
             logger.error(
-                "Save the notebook, pass `i_saved_the_notebook=True`, and re-run this cell."
+                "Please save the notebook, pass `i_saved_the_notebook=True`, and re-run this cell."
             )
             return None
         notebook_content = read_notebook(run_context.path)  # type: ignore

lamindb/core/_mapped_collection.py

@@ -45,19 +45,28 @@ class _Connect:
 class MappedCollection:
     """Map-style collection for use in data loaders.
 
-    This currently only works for collections of `AnnData` objects.
+    This class virtually concatenates `AnnData` arrays as a `pytorch map-style dataset
+    <https://pytorch.org/docs/stable/data.html#map-style-datasets>`__.
 
-    For an example, see :meth:`~lamindb.Collection.mapped`.
+    If your `AnnData` collection is in the cloud, move them into a local cache
+    first for faster access.
 
     .. note::
 
-        A similar data loader exists `here
-        <https://github.com/Genentech/scimilarity>`__.
+        For a guide, see :doc:`docs:scrna5`.
+
+        For more convenient use within :class:`~lamindb.core.MappedCollection`,
+        see :meth:`~lamindb.Collection.mapped`.
+
+        This currently only works for collections of `AnnData` objects.
+
+        The implementation was influenced by the `SCimilarity
+        <https://github.com/Genentech/scimilarity>`__ data loader.
+
 
     Args:
-        path_list: A list of paths to `AnnData` objects stored in `h5ad` or `zrad` formats.
-        label_keys: Columns of the ``.obs`` slot - the names of the metadata
-            features storing labels.
+        path_list: A list of paths to `AnnData` objects stored in `.h5ad` or `.zarr` formats.
+        label_keys: Columns of the ``.obs`` slot that store labels.
         join: `"inner"` or `"outer"` virtual joins. If ``None`` is passed,
             does not join.
         encode_labels: Encode labels into integers.

{lamindb-0.69.6.dist-info → lamindb-0.69.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.69.6
+Version: 0.69.7
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -12,12 +12,13 @@ Classifier: Programming Language :: Python :: 3.11
 Requires-Dist: lnschema_core==0.64.4
 Requires-Dist: lamindb_setup==0.68.4
 Requires-Dist: lamin_utils==0.13.1
-Requires-Dist: lamin_cli==0.11.0
+Requires-Dist: lamin_cli==0.12.0
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
 Requires-Dist: python-dateutil
 Requires-Dist: anndata>=0.8.0,<0.10.6
+Requires-Dist: scipy<1.13.0rc1
 Requires-Dist: fsspec
 Requires-Dist: pandas
 Requires-Dist: graphviz

{lamindb-0.69.6.dist-info → lamindb-0.69.7.dist-info}/RECORD

@@ -1,4 +1,4 @@
-lamindb/__init__.py,sha256=VcBG2i-qatWgu0eGNmmXfcGz5YInNKYXovMB80wzqq0,2163
+lamindb/__init__.py,sha256=areEfsBBfhAkUcjShkBTCquB5iBRUmTwb_Ycmz4E3tk,2163
 lamindb/_annotate.py,sha256=mM-GCej7i9eUH0cU5AcxWZ916k8NRI41WF84dfjJfu4,29955
 lamindb/_artifact.py,sha256=RV36tcHMZ6wH6u65jOAQ_H4rfmFiIzZmAr8IY7kFhm0,35817
 lamindb/_can_validate.py,sha256=w7lrUGTWldpvwaRiXBRrjfU_ZRidA7CooOu_r5MbocY,14569
@@ -6,7 +6,7 @@ lamindb/_collection.py,sha256=SdNNhhMh2O4q0hG4Hf_y1bcwcbkMF_sqk6MIYc-hLZo,14525
 lamindb/_feature.py,sha256=ahRv87q1tcRLQ0UM5FA3KtcMQvIjW__fZq1yAdRAV7s,6728
 lamindb/_feature_set.py,sha256=G_Ss6mKh4D0Eji-xSfLRbKVFXwgUE82YOqIUmkV0CAA,8767
 lamindb/_filter.py,sha256=_PjyQWQBR3ohDAvJbR3hMvZ-2p2GvzFxLfKGC-gPnHI,1320
-lamindb/_finish.py,sha256=8lfJzRedTDCA_XXBUf4ECOevpPhVxKqMMj9qgVkmF8M,8672
+lamindb/_finish.py,sha256=XXJb44gKuj-9trEqjgAa_wm2FvuTr0uveWwFbY0ywl0,8679
 lamindb/_from_values.py,sha256=Ei11ml77Q1xubVekt2C4-mbox2-qnC7kP18B-LhCdSc,11886
 lamindb/_is_versioned.py,sha256=DXp5t-1DwErpqqMc9eb08kpQPCHOC2fNzaozMoBunR4,1337
 lamindb/_parents.py,sha256=pTDsW8HjQ_txFbPKrBU0WjjtCNH6sx2LASUuGWpJuYE,14742
@@ -24,7 +24,7 @@ lamindb/core/__init__.py,sha256=Mw4sI-xgnMXNsu84oYFQBZOF8mxxxhp6-e3BjTQqjlA,1131
 lamindb/core/_data.py,sha256=SCyUjS9bL7MMqyZTJl8PxnNtLKL7eNiUcLvmwFrqP-k,17260
 lamindb/core/_feature_manager.py,sha256=_Bicjal2DQbpl6tR7p5o7Alb9rq0XYzAxrF_bV9sTjE,13894
 lamindb/core/_label_manager.py,sha256=zrWDSd2AkR6fKsGDxLSWqHC9fz9BcGlavPZEh92Wzjg,9063
-lamindb/core/_mapped_collection.py,sha256=e4P3AoykIMjD4_88BWbISWvKyWWTklwHl-_WLa72ZG4,16841
+lamindb/core/_mapped_collection.py,sha256=8meS0hiXa3CKmg7TG2Lej6pcI4YQXHMJyDQMxOBqm_E,17215
 lamindb/core/_run_context.py,sha256=EK0lFJWx32NY2FdqFR1YozR9zioC-BjA394nPu-KwLQ,17510
 lamindb/core/_settings.py,sha256=kHL5e20dWKSbf7mJOAddvS7SQBrr1D0ZTeG_5sj5RpY,5735
 lamindb/core/_sync_git.py,sha256=Bn_ofx2ynaw6etmskgEUNW8n7LDJs-7r2aB41BgCvdA,3928
@@ -48,7 +48,7 @@ lamindb/integrations/__init__.py,sha256=aH2PmO2m4-vwIifMYTB0Fyyr_gZWtVnV71jT0tVW
 lamindb/integrations/_vitessce.py,sha256=n85g8YRP8Y2sfU5DPJdbU84BGPrTfU3Dg2jStdmBBRI,1637
 lamindb/setup/__init__.py,sha256=OwZpZzPDv5lPPGXZP7-zK6UdO4FHvvuBh439yZvIp3A,410
 lamindb/setup/core/__init__.py,sha256=LqIIvJNcONxkqjbnP6CUaP4d45Lbd6TSMAcXFp4C7_8,231
-lamindb-0.69.6.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-lamindb-0.69.6.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
-lamindb-0.69.6.dist-info/METADATA,sha256=eH8bPo_rAfxl_e3fChr1gwMFLkt5-TqWELqNnuIFJp8,2856
-lamindb-0.69.6.dist-info/RECORD,,
+lamindb-0.69.7.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+lamindb-0.69.7.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+lamindb-0.69.7.dist-info/METADATA,sha256=35W5tzc2RHeY7REqSwzIgC1B2EqoAUncIVlg2rHVhsA,2887
+lamindb-0.69.7.dist-info/RECORD,,