cap-anndata 0.2.0__py3-none-any.whl → 0.2.2__py3-none-any.whl

cap_anndata/backed_df.py

@@ -1,6 +1,6 @@
 import pandas as pd
 import numpy as np
-from typing import List, Any
+from typing import List, Any, Union
 import logging
 
 from pandas._typing import Self
@@ -65,5 +65,5 @@ class CapAnnDataDF(pd.DataFrame):
         column_order = np.append(self.column_order, new_columns)
         return self.from_df(result, column_order=column_order)
 
-    def copy(self, deep: bool_t | None = True) -> Self:
+    def copy(self, deep: Union[bool_t, None] = True) -> Self:
         return self.from_df(super().copy(deep=deep), column_order=self.column_order)

cap_anndata/cap_anndata.py

@@ -91,8 +91,8 @@ class BaseLayerMatrixAndDf:
             df.column_order = df.column_order.astype(object)
         return df
 
-    def _write_elem_lzf(self, dest_key: str, elem: any) -> None:
-        write_elem(self._file, dest_key, elem, dataset_kwargs={"compression": "lzf"})
+    def _write_elem(self, dest_key: str, elem: any, compression: str) -> None:
+        write_elem(self._file, dest_key, elem, dataset_kwargs={"compression": compression})
 
     def _validate_cap_df(self, cap_df: CapAnnDataDF, axis: int) -> None:
         if not isinstance(cap_df, CapAnnDataDF):
@@ -210,7 +210,7 @@ class CapAnnData(BaseLayerMatrixAndDf):
             for col in df.columns:
                 self._var[col] = df[col]
 
-    def overwrite(self, fields: List[str] = None) -> None:
+    def overwrite(self, fields: List[str] = None, compression: str = "lzf") -> None:
         field_to_entity = {
             "obs": self.obs,
             "var": self.var,
@@ -237,7 +237,7 @@ class CapAnnData(BaseLayerMatrixAndDf):
                 key = key.replace(".", "/") if key == "raw.var" else key
 
                 for col in entity.columns:
-                    self._write_elem_lzf(f"{key}/{col}", entity[col].values)
+                    self._write_elem(f"{key}/{col}", entity[col].values, compression=compression)
 
                 column_order = entity.column_order
                 if (
@@ -250,7 +250,7 @@ class CapAnnData(BaseLayerMatrixAndDf):
             for key in self.uns.keys():
                 if self.uns[key] is not NotLinkedObject:
                     dest = f"uns/{key}"
-                    self._write_elem_lzf(dest, self.uns[key])
+                    self._write_elem(dest, self.uns[key], compression=compression)
             for key in self.uns.keys_to_remove:
                 del self._file[f"uns/{key}"]
 
@@ -261,8 +261,8 @@ class CapAnnData(BaseLayerMatrixAndDf):
         for key in keys:
             existing_keys = self.uns.keys()
             if key in existing_keys:
-                sourse = self._file[f"uns/{key}"]
-                self.uns[key] = read_elem(sourse)
+                source = self._file[f"uns/{key}"]
+                self.uns[key] = read_elem(source)
 
     def _link_obsm(self) -> None:
         self._obsm = {}

{cap_anndata-0.2.0.dist-info → cap_anndata-0.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cap_anndata
-Version: 0.2.0
+Version: 0.2.2
 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
@@ -12,11 +12,13 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy >=1.26.3
-Requires-Dist: pandas >=2.2.0
-Requires-Dist: anndata >=0.10.5
+Requires-Dist: numpy ~=1.26.3
+Requires-Dist: pandas ~=2.2.0
+Requires-Dist: anndata ~=0.10.5
+Requires-Dist: h5py ~=3.5.0
 Provides-Extra: dev
 Requires-Dist: pytest >=8.0.0 ; extra == 'dev'
+Requires-Dist: setuptools ~=69.1.1 ; extra == 'dev'
 
 # CAP-AnnData: Enhanced Partial I/O for AnnData Files
 

cap_anndata-0.2.2.dist-info/RECORD

@@ -0,0 +1,10 @@
+cap_anndata/__init__.py,sha256=l9lvFpcMsQksp8_dI-fjUgrImoMdztbu3jVSdmxNPmA,205
+cap_anndata/backed_df.py,sha256=06wZwEjszFQ8lkvy6-GgD_SD14idu9857RtlfMQiBjE,2691
+cap_anndata/backed_uns.py,sha256=Tfxoz3RgcgENf4SvxFOox9w048K2QmBTh1VbAf4yqVI,854
+cap_anndata/cap_anndata.py,sha256=fEaIwWIKKDJpIsQ7cwOfUTmUReIyryv5qRDqRjRsWhU,10185
+cap_anndata/reader.py,sha256=kg9xoS_S0gY6WpsHE8PwGMa14VXh9Ibqjw4bwoerYsE,1267
+cap_anndata-0.2.2.dist-info/LICENSE,sha256=JAV0w7TBl6wQe9iFcCKjAWgpurym0f-Q0B75zm2PrKw,1560
+cap_anndata-0.2.2.dist-info/METADATA,sha256=h41dgoz3w2rDHnic828FahjEoKq1lt_Bi1jm-ZX-goA,9569
+cap_anndata-0.2.2.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+cap_anndata-0.2.2.dist-info/top_level.txt,sha256=GKi_Uk4LUhXwWBfFCTIyJvEoJqFREt_4uH4CWgeLsg4,12
+cap_anndata-0.2.2.dist-info/RECORD,,

cap_anndata-0.2.0.dist-info/RECORD

@@ -1,10 +0,0 @@
-cap_anndata/__init__.py,sha256=l9lvFpcMsQksp8_dI-fjUgrImoMdztbu3jVSdmxNPmA,205
-cap_anndata/backed_df.py,sha256=wKtQ_LkTpfPIfBod9kGlEUrmJMYe7TGs9TZexvmz7QI,2678
-cap_anndata/backed_uns.py,sha256=Tfxoz3RgcgENf4SvxFOox9w048K2QmBTh1VbAf4yqVI,854
-cap_anndata/cap_anndata.py,sha256=nv5f7A9jyK_rZ2kx54XvnX-V65MFlE3CYQC-n_zBhB8,10097
-cap_anndata/reader.py,sha256=kg9xoS_S0gY6WpsHE8PwGMa14VXh9Ibqjw4bwoerYsE,1267
-cap_anndata-0.2.0.dist-info/LICENSE,sha256=JAV0w7TBl6wQe9iFcCKjAWgpurym0f-Q0B75zm2PrKw,1560
-cap_anndata-0.2.0.dist-info/METADATA,sha256=xh25tmJOKCeTnWL3Cir-PXixFmZYIUcKuaUw4Uzrarg,9487
-cap_anndata-0.2.0.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-cap_anndata-0.2.0.dist-info/top_level.txt,sha256=GKi_Uk4LUhXwWBfFCTIyJvEoJqFREt_4uH4CWgeLsg4,12
-cap_anndata-0.2.0.dist-info/RECORD,,