cap-anndata 0.2.0__tar.gz → 0.2.2__tar.gz

{cap_anndata-0.2.0 → cap_anndata-0.2.2}/PKG-INFO

@@ -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-0.2.0 → cap_anndata-0.2.2}/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-0.2.0 → cap_anndata-0.2.2}/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 → cap_anndata-0.2.2}/cap_anndata.egg-info/PKG-INFO

@@ -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/cap_anndata.egg-info/requires.txt

@@ -0,0 +1,8 @@
+numpy~=1.26.3
+pandas~=2.2.0
+anndata~=0.10.5
+h5py~=3.5.0
+
+[dev]
+pytest>=8.0.0
+setuptools~=69.1.1

{cap_anndata-0.2.0 → cap_anndata-0.2.2}/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='cap_anndata',
-    version='0.2.0',
+    version='0.2.2',
     author='R. Mukhin, A. Isaev',
     author_email='roman@ebookapplications.com',
     packages=find_packages(exclude=["test"]),
@@ -20,9 +20,13 @@ setup(
     ],
     python_requires='>=3.9',
     install_requires=[
-        "numpy>=1.26.3",
-        "pandas>=2.2.0",
-        "anndata>=0.10.5",
+        "numpy~=1.26.3",
+        "pandas~=2.2.0",
+        "anndata~=0.10.5",
+        "h5py~=3.5.0",
     ],
-    extras_require={"dev": ["pytest>=8.0.0"]}
+    extras_require={"dev": [
+        "pytest>=8.0.0",
+        "setuptools~=69.1.1"
+    ]}
 )

{cap_anndata-0.2.0 → cap_anndata-0.2.2}/test/test_cap_anndata.py

@@ -102,7 +102,8 @@ def test_partial_read():
     pd.testing.assert_index_equal(adata.raw.var.index, cap_adata.raw.var.index)
 
 
-def test_overwrite_df():
+@pytest.mark.parametrize("compression", ["gzip", "lzf"])
+def test_overwrite_df(compression):
     adata = get_filled_anndata()
     temp_folder = tempfile.mkdtemp()
     file_path = os.path.join(temp_folder, "test_overwrite_df.h5ad")
@@ -132,7 +133,7 @@ def test_overwrite_df():
         cap_adata.raw.var["extra_info"] = np.random.rand(cap_adata.shape[1])
         ref_raw_var = cap_adata.raw.var.copy()
 
-        cap_adata.overwrite(["obs", "var", "raw.var"])
+        cap_adata.overwrite(["obs", "var", "raw.var"], compression=compression)
 
     adata = ad.read_h5ad(file_path)
     os.remove(file_path)
@@ -253,7 +254,8 @@ def test_read_uns():
     os.remove(file_path)
 
 
-def test_modify_uns():
+@pytest.mark.parametrize("compression", ["gzip", "lzf"])
+def test_modify_uns(compression):
     adata = get_base_anndata()
     adata.uns = {
         "field_to_ignore": list(range(100)),
@@ -278,7 +280,7 @@ def test_modify_uns():
         cap_adata.uns["field_to_expand"]["key1"] = d_to_exp
         cap_adata.uns["field_to_modify"] = v_to_mod
 
-        cap_adata.overwrite(["uns"])
+        cap_adata.overwrite(["uns"], compression=compression)
 
     adata = ad.read_h5ad(file_path)
 

cap_anndata-0.2.0/cap_anndata.egg-info/requires.txt

@@ -1,6 +0,0 @@
-numpy>=1.26.3
-pandas>=2.2.0
-anndata>=0.10.5
-
-[dev]
-pytest>=8.0.0