cap-anndata 0.2.2__tar.gz → 0.3.1__tar.gz

{cap_anndata-0.2.2 → cap_anndata-0.3.1}/LICENSE

@@ -1,28 +1,28 @@
-BSD 3-Clause License
-
-Copyright (c) 2024, R. Mukhin, A. Isaev, Cell-Annotation Platform
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
-   list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice,
-   this list of conditions and the following disclaimer in the documentation
-   and/or other materials provided with the distribution.
-
-3. Neither the name of the copyright holder nor the names of its
-   contributors may be used to endorse or promote products derived from
-   this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+BSD 3-Clause License
+
+Copyright (c) 2024, R. Mukhin, A. Isaev, Cell-Annotation Platform
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

cap_anndata-0.3.1/PKG-INFO

@@ -0,0 +1,56 @@
+Metadata-Version: 2.1
+Name: cap_anndata
+Version: 0.3.1
+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
+Author-email: roman@ebookapplications.com
+Project-URL: Bug Tracker, https://github.com/cellannotation/cap-anndata/issues
+Project-URL: Changelog, https://github.com/cellannotation/cap-anndata/blob/main/CHANGELOG.md
+Project-URL: Documentation, https://github.com/cellannotation/cap-anndata/blob/main/HOWTO.md
+Classifier: Programming Language :: Python :: 3.9
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.23.5
+Requires-Dist: pandas>=2.2.0
+Requires-Dist: anndata>=0.10.0
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0.0; extra == "dev"
+Requires-Dist: setuptools~=69.1.1; extra == "dev"
+
+# CAP-AnnData: Partial I/O for AnnData (.h5ad) Files
+
+## 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. 
+For example, it allows to read and modify the single `obs` column taking nothing into memory except the column itself.
+Package eager to replicate the original AnnData API as much as possible, 
+while providing additional features for efficient data manipulation for heavy datasets.
+
+## Installation
+Install CAP-AnnData via pip:
+
+```commandline
+pip install -U cap-anndata
+```
+
+## Basic Example
+
+The example below displayes how to read a single `obs` column, create new obs column and propagate it to the `.h5ad` file.
+```python
+from cap_anndata import read_h5ad
+
+file_path = "your_data.h5ad"
+with read_h5ad(file_path=file_path, edit=True) as cap_adata:
+    print(cap_adata.obs_keys())  # ['a', 'b', 'c']
+    print(cap_adata.obs) # Empty DataFrame
+    cap_adata.read_obs(columns=['a'])
+    print(cap_adata.obs.columns) # ['a']
+    cap_adata.obs['new_col'] = cap_adata.obs['a']
+    cap_adata.overwrite(fields=['obs'])
+```
+
+More example can be found in the [How-TO](https://github.com/cellannotation/cap-anndata/blob/main/HOWTO.md) file. 

cap_anndata-0.3.1/README.md

@@ -0,0 +1,33 @@
+# CAP-AnnData: Partial I/O for AnnData (.h5ad) Files
+
+## 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. 
+For example, it allows to read and modify the single `obs` column taking nothing into memory except the column itself.
+Package eager to replicate the original AnnData API as much as possible, 
+while providing additional features for efficient data manipulation for heavy datasets.
+
+## Installation
+Install CAP-AnnData via pip:
+
+```commandline
+pip install -U cap-anndata
+```
+
+## Basic Example
+
+The example below displayes how to read a single `obs` column, create new obs column and propagate it to the `.h5ad` file.
+```python
+from cap_anndata import read_h5ad
+
+file_path = "your_data.h5ad"
+with read_h5ad(file_path=file_path, edit=True) as cap_adata:
+    print(cap_adata.obs_keys())  # ['a', 'b', 'c']
+    print(cap_adata.obs) # Empty DataFrame
+    cap_adata.read_obs(columns=['a'])
+    print(cap_adata.obs.columns) # ['a']
+    cap_adata.obs['new_col'] = cap_adata.obs['a']
+    cap_adata.overwrite(fields=['obs'])
+```
+
+More example can be found in the [How-TO](https://github.com/cellannotation/cap-anndata/blob/main/HOWTO.md) file. 

{cap_anndata-0.2.2 → cap_anndata-0.3.1}/cap_anndata/__init__.py

@@ -1,10 +1,10 @@
-from .backed_df import CapAnnDataDF
-from .backed_uns import CapAnnDataUns
-from .cap_anndata import CapAnnData
-from .reader import (
-    read_directly,
-    read_h5ad,
-)
-
-
-__all__ = ["CapAnnData"]
+from .backed_df import CapAnnDataDF
+from .backed_dict import CapAnnDataDict
+from .cap_anndata import CapAnnData
+from .reader import (
+    read_directly,
+    read_h5ad,
+)
+
+
+__all__ = ["CapAnnData"]

{cap_anndata-0.2.2 → cap_anndata-0.3.1}/cap_anndata/backed_df.py

@@ -1,69 +1,69 @@
-import pandas as pd
-import numpy as np
-from typing import List, Any, Union
-import logging
-
-from pandas._typing import Self
-from pandas.core.generic import bool_t
-
-logger = logging.getLogger(__name__)
-
-
-class CapAnnDataDF(pd.DataFrame):
-    """
-    The class to expand the pandas DataFrame behaviour to support partial
-    reading and writing of AnnData obs and var (raw.var) fields.
-    The main feature of the class is handling <column-order> attribute
-    which must be a copy of h5py.Group attribute
-    """
-
-    _metadata = ["column_order"]
-
-    def rename_column(self, old_name: str, new_name: str) -> None:
-        i = np.where(self.column_order == old_name)[0]
-        self.column_order[i] = new_name
-        self.rename(columns={old_name: new_name}, inplace=True)
-
-    def remove_column(self, col_name: str) -> None:
-        i = np.where(self.column_order == col_name)[0]
-        self.column_order = np.delete(self.column_order, i)
-        self.drop(columns=[col_name], inplace=True)
-
-    def __setitem__(self, key, value) -> None:
-        if key not in self.column_order:
-            self.column_order = np.append(self.column_order, key)
-        return super().__setitem__(key, value)
-
-    @classmethod
-    def from_df(cls, df: pd.DataFrame, column_order: List[str] = None) -> Self:
-        if column_order is None:
-            column_order = df.columns.to_numpy()
-
-        new_inst = cls(df)
-        new_inst.column_order = column_order
-        return new_inst
-
-    def join(self, other: Any, **kwargs) -> Self:
-        result = super().join(other=other, **kwargs)
-        if isinstance(other, CapAnnDataDF):
-            new_columns = [
-                col for col in other.column_order if col not in self.column_order
-            ]
-        else:
-            new_columns = [col for col in other.columns if col not in self.column_order]
-        column_order = np.append(self.column_order, new_columns)
-        return self.from_df(result, column_order=column_order)
-
-    def merge(self, right, **kwargs) -> Self:
-        result = super().merge(right=right, **kwargs)
-        if isinstance(right, CapAnnDataDF):
-            new_columns = [
-                col for col in right.column_order if col not in self.column_order
-            ]
-        else:
-            new_columns = [col for col in right.columns if col not in self.column_order]
-        column_order = np.append(self.column_order, new_columns)
-        return self.from_df(result, column_order=column_order)
-
-    def copy(self, deep: Union[bool_t, None] = True) -> Self:
-        return self.from_df(super().copy(deep=deep), column_order=self.column_order)
+import pandas as pd
+import numpy as np
+from typing import List, Any, Union
+import logging
+
+from pandas._typing import Self
+from pandas.core.generic import bool_t
+
+logger = logging.getLogger(__name__)
+
+
+class CapAnnDataDF(pd.DataFrame):
+    """
+    The class to expand the pandas DataFrame behaviour to support partial
+    reading and writing of AnnData obs and var (raw.var) fields.
+    The main feature of the class is handling <column-order> attribute
+    which must be a copy of h5py.Group attribute
+    """
+
+    _metadata = ["column_order"]
+
+    def rename_column(self, old_name: str, new_name: str) -> None:
+        i = np.where(self.column_order == old_name)[0]
+        self.column_order[i] = new_name
+        self.rename(columns={old_name: new_name}, inplace=True)
+
+    def remove_column(self, col_name: str) -> None:
+        i = np.where(self.column_order == col_name)[0]
+        self.column_order = np.delete(self.column_order, i)
+        self.drop(columns=[col_name], inplace=True)
+
+    def __setitem__(self, key, value) -> None:
+        if key not in self.column_order:
+            self.column_order = np.append(self.column_order, key)
+        return super().__setitem__(key, value)
+
+    @classmethod
+    def from_df(cls, df: pd.DataFrame, column_order: List[str] = None) -> Self:
+        if column_order is None:
+            column_order = df.columns.to_numpy()
+
+        new_inst = cls(df)
+        new_inst.column_order = column_order
+        return new_inst
+
+    def join(self, other: Any, **kwargs) -> Self:
+        result = super().join(other=other, **kwargs)
+        if isinstance(other, CapAnnDataDF):
+            new_columns = [
+                col for col in other.column_order if col not in self.column_order
+            ]
+        else:
+            new_columns = [col for col in other.columns if col not in self.column_order]
+        column_order = np.append(self.column_order, new_columns)
+        return self.from_df(result, column_order=column_order)
+
+    def merge(self, right, **kwargs) -> Self:
+        result = super().merge(right=right, **kwargs)
+        if isinstance(right, CapAnnDataDF):
+            new_columns = [
+                col for col in right.column_order if col not in self.column_order
+            ]
+        else:
+            new_columns = [col for col in right.columns if col not in self.column_order]
+        column_order = np.append(self.column_order, new_columns)
+        return self.from_df(result, column_order=column_order)
+
+    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-0.3.1/cap_anndata/backed_dict.py

@@ -0,0 +1,34 @@
+from typing import Set, Any
+
+
+class CapAnnDataDict(dict):
+    __keys_to_remove: Set[str] = None
+
+    def __delitem__(self, __key: Any) -> None:
+        self.keys_to_remove.add(__key)
+        return super().__delitem__(__key)
+
+    def __setitem__(self, __key: Any, __value: Any) -> None:
+        if __value is not None:
+            if __key in self.keys_to_remove:
+                self.keys_to_remove.remove(__key)
+        else:
+            self.keys_to_remove.add(__key)
+        return super().__setitem__(__key, __value)
+
+    @property
+    def keys_to_remove(self) -> Set[str]:
+        if self.__keys_to_remove is None:
+            self.__keys_to_remove = set()
+        return self.__keys_to_remove
+
+    def pop(self, __key: Any, __default: Any = None) -> Any:
+        if __key in self:
+            self.keys_to_remove.add(__key)
+        return super().pop(__key, __default)
+
+    def popitem(self) -> Any:
+        item = super().popitem()
+        key = item[0]
+        self.keys_to_remove.add(key)
+        return item