cap-anndata 0.4.0__py3-none-any.whl → 0.5.0__py3-none-any.whl

cap_anndata/cap_anndata.py

@@ -143,15 +143,19 @@ class BaseLayerMatrixAndDf:
         if not isinstance(group, h5py.Group):
             raise ValueError(f"The object {key} must be a group!")
 
-        for array_name in group.keys():
-            array = group[array_name]
-            if isinstance(array, h5py.Dataset):
-                cap_dict[array_name] = array
-            elif isinstance(array, h5py.Group):
-                cap_dict[array_name] = sparse_dataset(array)
+        for entity_name in group.keys():
+            entity = group[entity_name]
+            if isinstance(entity, h5py.Dataset):
+                cap_dict[entity_name] = entity
+            elif isinstance(entity, h5py.Group):
+                enc_type = dict(entity.attrs).get("encoding-type")
+                if enc_type == "dataframe":
+                    cap_dict[entity_name] = self._read_df(key="/".join([key, entity_name]), columns=None)
+                elif enc_type in ["csc_matrix", "csr_matrix"]:
+                    cap_dict[entity_name] = sparse_dataset(entity)
             else:
                 raise ValueError(
-                    f"Can't link array in {key} due to unsupported type of object: {type(array)}"
+                    f"Can't link array in {key} due to unsupported type of object: {type(entity)}"
                 )
 
     def _create_new_matrix(
@@ -260,11 +264,11 @@ class CapAnnData(BaseLayerMatrixAndDf):
     def raw(self) -> RawLayer:
         if self._raw is None:
             if "raw" not in self._file.keys():
-                logger.warning("Can't read raw.var since raw layer doesn't exist!")
+                logger.debug("Can't read raw.var since raw layer doesn't exist!")
                 return
 
             if len(self._file["raw"].keys()) == 0:
-                logger.warning("The raw layer is empty!")
+                logger.debug("The raw layer is empty!")
                 return
 
             self._raw = RawLayer(self._file)

{cap_anndata-0.4.0.dist-info → cap_anndata-0.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: cap_anndata
-Version: 0.4.0
+Version: 0.5.0
 Summary: Partial read/write of AnnData (h5ad) files for low-memory operations with large datasets.
 Home-page: https://github.com/cellannotation/cap-anndata
 Author: R. Mukhin, A. Isaev
@@ -26,6 +26,7 @@ Dynamic: classifier
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page
+Dynamic: license-file
 Dynamic: project-url
 Dynamic: provides-extra
 Dynamic: requires-dist
@@ -34,6 +35,8 @@ Dynamic: summary
 
 # CAP-AnnData: Partial I/O for AnnData (.h5ad) Files
 
+[![PyPI version](https://img.shields.io/pypi/v/cap-anndata)](https://pypi.org/project/cap-anndata/) [![Build Status](https://github.com/cellannotation/cap-anndata/actions/workflows/python-app.yml/badge.svg)](https://github.com/cellannotation/cap-anndata/actions)
+
 ## Overview
 CAP-AnnData offering functionalities for selective reading and writing of [AnnData](https://pypi.org/project/anndata/) 
 file fields without the need for loading entire dataset (or even entire field) into memory. 

cap_anndata-0.5.0.dist-info/RECORD

@@ -0,0 +1,10 @@
+cap_anndata/__init__.py,sha256=WRAQEDsWTvLbJWVUA5FmKCVrD2GN4oRd5I3c8jc9ajo,197
+cap_anndata/backed_df.py,sha256=2OVomvTY51V05sYwEXg-4JYBgd9iJCA2-Lt7nEAL1Ug,3255
+cap_anndata/backed_dict.py,sha256=Hb1SjnKuQ13mBUitQ5sL3kmcQ1j3GgB19r3yXkC0oIo,1019
+cap_anndata/cap_anndata.py,sha256=4sro4BIsaOuTBHrRXYCi0WlGtxsql_bnqIDEpT2tRhQ,21371
+cap_anndata/reader.py,sha256=UpZBCjaS4-K2w_9m6IuYetO9LwmEEJ5KvAw9aAoMRno,1609
+cap_anndata-0.5.0.dist-info/licenses/LICENSE,sha256=XXTH6JikkxH7Gqy9VEj4crSizuwxzv04ROzkQ-ZS6o4,1532
+cap_anndata-0.5.0.dist-info/METADATA,sha256=CbdJemeEOB1hIJ7tPrVOT7JldkVNOiJ6zkW8AFqTjqU,2825
+cap_anndata-0.5.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+cap_anndata-0.5.0.dist-info/top_level.txt,sha256=GKi_Uk4LUhXwWBfFCTIyJvEoJqFREt_4uH4CWgeLsg4,12
+cap_anndata-0.5.0.dist-info/RECORD,,

{cap_anndata-0.4.0.dist-info → cap_anndata-0.5.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

cap_anndata-0.4.0.dist-info/RECORD

@@ -1,10 +0,0 @@
-cap_anndata/__init__.py,sha256=WRAQEDsWTvLbJWVUA5FmKCVrD2GN4oRd5I3c8jc9ajo,197
-cap_anndata/backed_df.py,sha256=2OVomvTY51V05sYwEXg-4JYBgd9iJCA2-Lt7nEAL1Ug,3255
-cap_anndata/backed_dict.py,sha256=Hb1SjnKuQ13mBUitQ5sL3kmcQ1j3GgB19r3yXkC0oIo,1019
-cap_anndata/cap_anndata.py,sha256=-Lp6wxPncVcl_TaECnE6uHTfD9j_Ow_rScvpAWKK_fs,21081
-cap_anndata/reader.py,sha256=UpZBCjaS4-K2w_9m6IuYetO9LwmEEJ5KvAw9aAoMRno,1609
-cap_anndata-0.4.0.dist-info/LICENSE,sha256=XXTH6JikkxH7Gqy9VEj4crSizuwxzv04ROzkQ-ZS6o4,1532
-cap_anndata-0.4.0.dist-info/METADATA,sha256=IXvItMAdXH-CunN3fNlyHPNFmxfoF9dOrU58tl17eLQ,2539
-cap_anndata-0.4.0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-cap_anndata-0.4.0.dist-info/top_level.txt,sha256=GKi_Uk4LUhXwWBfFCTIyJvEoJqFREt_4uH4CWgeLsg4,12
-cap_anndata-0.4.0.dist-info/RECORD,,