cap-anndata 0.3.0__py3-none-any.whl → 0.4.0__py3-none-any.whl

cap_anndata/reader.py

@@ -1,57 +1,57 @@
-import logging
-import h5py
-import warnings
-
-from cap_anndata import CapAnnData
-
-
-logger = logging.getLogger(__name__)
-
-
-def read_h5ad(file_path: str, edit: bool = False):
-    """
-    This is the main read method for CapAnnData.
-    Must be used in 'with' context.
-    """
-    mode = "r+" if edit else "r"
-    logger.debug(f"Read file {file_path} mode={mode} in context...")
-
-    try:
-        file = h5py.File(file_path, mode)
-        cap_adata = CapAnnData(file)
-        logger.debug(f"Successfully read anndata file path {file_path}")
-        return cap_adata
-
-    except Exception as error:
-        logger.error(
-            f"Error during read anndata file at path: {file_path}, error = {error}!"
-        )
-        raise error
-
-
-def deprecated(message):
-    def deprecated_decorator(func):
-        def deprecated_func(*args, **kwargs):
-            warnings.warn(
-                "{} is a deprecated function. {}".format(func.__name__, message),
-                category=DeprecationWarning,
-                stacklevel=2,
-            )
-            warnings.simplefilter("default", DeprecationWarning)
-            return func(*args, **kwargs)
-
-        return deprecated_func
-
-    return deprecated_decorator
-
-
-# TODO: remove deprecated function
-@deprecated(
-    "It will be removed in the next version of package. Please replace it with `read_h5ad`."
-)
-def read_directly(file_path: str, edit: bool = False) -> CapAnnData:
-    """
-    Must be used only in specific cases.
-    User is responsible to close the h5py file when the work with CapAnnData instance done.
-    """
-    return read_h5ad(file_path, edit)
+import logging
+import h5py
+import warnings
+
+from cap_anndata import CapAnnData
+
+
+logger = logging.getLogger(__name__)
+
+
+def read_h5ad(file_path: str, edit: bool = False):
+    """
+    This is the main read method for CapAnnData.
+    Must be used in 'with' context.
+    """
+    mode = "r+" if edit else "r"
+    logger.debug(f"Read file {file_path} mode={mode} in context...")
+
+    try:
+        file = h5py.File(file_path, mode)
+        cap_adata = CapAnnData(file)
+        logger.debug(f"Successfully read anndata file path {file_path}")
+        return cap_adata
+
+    except Exception as error:
+        logger.error(
+            f"Error during read anndata file at path: {file_path}, error = {error}!"
+        )
+        raise error
+
+
+def deprecated(message):
+    def deprecated_decorator(func):
+        def deprecated_func(*args, **kwargs):
+            warnings.warn(
+                "{} is a deprecated function. {}".format(func.__name__, message),
+                category=DeprecationWarning,
+                stacklevel=2,
+            )
+            warnings.simplefilter("default", DeprecationWarning)
+            return func(*args, **kwargs)
+
+        return deprecated_func
+
+    return deprecated_decorator
+
+
+# TODO: remove deprecated function
+@deprecated(
+    "It will be removed in the next version of package. Please replace it with `read_h5ad`."
+)
+def read_directly(file_path: str, edit: bool = False) -> CapAnnData:
+    """
+    Must be used only in specific cases.
+    User is responsible to close the h5py file when the work with CapAnnData instance done.
+    """
+    return read_h5ad(file_path, edit)

{cap_anndata-0.3.0.dist-info → cap_anndata-0.4.0.dist-info}/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-0.3.0.dist-info → cap_anndata-0.4.0.dist-info}/METADATA

@@ -1,54 +1,67 @@
-Metadata-Version: 2.1
-Name: cap_anndata
-Version: 0.3.0
-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
-Author-email: roman@ebookapplications.com
-Project-URL: Bug Tracker, https://github.com/cellannotation/cap-anndata/issues
-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. 
+Metadata-Version: 2.2
+Name: cap_anndata
+Version: 0.4.0
+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
+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"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: project-url
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# 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-0.4.0.dist-info/RECORD

@@ -0,0 +1,10 @@
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+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,,

{cap_anndata-0.3.0.dist-info → cap_anndata-0.4.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.1.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

cap_anndata-0.3.0.dist-info/RECORD

@@ -1,10 +0,0 @@
-cap_anndata/__init__.py,sha256=m-iyYXl6oIgczQMXr_rqhoObblRAs37YYxMoWidm7i4,207
-cap_anndata/backed_df.py,sha256=06wZwEjszFQ8lkvy6-GgD_SD14idu9857RtlfMQiBjE,2691
-cap_anndata/backed_dict.py,sha256=jPJl7RxPxV7s5ywD23ZxkInWPrgValyKHmlKZplDuTE,1053
-cap_anndata/cap_anndata.py,sha256=RDozLa-RZoNq_-CWNbrEoLbrNfaD8GkIU8vmAkxFuoQ,21197
-cap_anndata/reader.py,sha256=yiY8kButhg5TDc_OcXNOZkJv5Bbdht3XOzswjgDogdQ,1666
-cap_anndata-0.3.0.dist-info/LICENSE,sha256=JAV0w7TBl6wQe9iFcCKjAWgpurym0f-Q0B75zm2PrKw,1560
-cap_anndata-0.3.0.dist-info/METADATA,sha256=Fj4jPwlPbFr_u-e8-cW2KX5H0bUyhiZ5wcNACGrwK9w,2172
-cap_anndata-0.3.0.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-cap_anndata-0.3.0.dist-info/top_level.txt,sha256=GKi_Uk4LUhXwWBfFCTIyJvEoJqFREt_4uH4CWgeLsg4,12
-cap_anndata-0.3.0.dist-info/RECORD,,