pertpy 0.10.0__py3-none-any.whl → 0.11.1__py3-none-any.whl

{pertpy-0.10.0.dist-info → pertpy-0.11.1.dist-info}/METADATA

@@ -1,15 +1,16 @@
 Metadata-Version: 2.4
 Name: pertpy
-Version: 0.10.0
+Version: 0.11.1
 Summary: Perturbation Analysis in the scverse ecosystem.
 Project-URL: Documentation, https://pertpy.readthedocs.io
 Project-URL: Source, https://github.com/scverse/pertpy
 Project-URL: Home-page, https://github.com/scverse/pertpy
-Author: Lukas Heumos, Yuge Ji, Lilly May, Alejandro Tejada, Johannes Köster, Emma Dann, Xinyue Zhang, Xichen Wu, Tessa Green, Stefan Peidli, Antonia Schumacher, Gregor Sturm
+Author: Lukas Heumos, Lilly May, Stefan Peidli, Johannes Ostner, Gregor Sturm, Emma Dann, Yuge Ji, Xinyue Zhang, Xichen Wu, Tessa Green, Antonia Schumacher
 Maintainer-email: Lukas Heumos <lukas.heumos@posteo.net>
 License: MIT License
         
         Copyright (c) 2021, Lukas Heumos
+        Copyright (c) 2025, scverse®
         
         Permission is hereby granted, free of charge, to any person obtaining a copy
         of this software and associated documentation files (the "Software"), to deal
@@ -29,7 +30,7 @@ License: MIT License
         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
         SOFTWARE.
 License-File: LICENSE
-Classifier: Development Status :: 4 - Beta
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
 Classifier: Framework :: Jupyter
 Classifier: Intended Audience :: Developers
@@ -39,66 +40,67 @@ Classifier: Natural Language :: English
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: POSIX :: Linux
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Visualization
-Requires-Python: <3.13,>=3.10
+Requires-Python: <3.14,>=3.11
 Requires-Dist: adjusttext
+Requires-Dist: arviz
 Requires-Dist: blitzgsea
 Requires-Dist: decoupler
+Requires-Dist: fast-array-utils
 Requires-Dist: lamin-utils
-Requires-Dist: muon
+Requires-Dist: mudata
 Requires-Dist: openpyxl
 Requires-Dist: ott-jax
 Requires-Dist: pubchempy
 Requires-Dist: pyarrow
 Requires-Dist: requests
 Requires-Dist: rich
-Requires-Dist: scanpy[leiden]
+Requires-Dist: scanpy
 Requires-Dist: scikit-learn>=1.4
 Requires-Dist: scikit-misc
 Requires-Dist: scvi-tools
 Requires-Dist: sparsecca
-Provides-Extra: coda
-Requires-Dist: arviz; extra == 'coda'
-Requires-Dist: ete3; extra == 'coda'
-Requires-Dist: pyqt5; extra == 'coda'
-Requires-Dist: toytree; extra == 'coda'
 Provides-Extra: de
 Requires-Dist: formulaic; extra == 'de'
 Requires-Dist: formulaic-contrasts>=0.2.0; extra == 'de'
-Requires-Dist: pydeseq2>=v0.5.0pre1; extra == 'de'
+Requires-Dist: pydeseq2>=v0.5.0; extra == 'de'
 Provides-Extra: dev
 Requires-Dist: pre-commit; extra == 'dev'
 Provides-Extra: doc
-Requires-Dist: docutils!=0.18.*,!=0.19.*,>=0.8; extra == 'doc'
-Requires-Dist: furo; extra == 'doc'
+Requires-Dist: docutils>=0.8; extra == 'doc'
 Requires-Dist: ipykernel; extra == 'doc'
 Requires-Dist: ipython; extra == 'doc'
 Requires-Dist: myst-nb; extra == 'doc'
-Requires-Dist: myst-parser; extra == 'doc'
 Requires-Dist: nbsphinx; extra == 'doc'
 Requires-Dist: nbsphinx-link; extra == 'doc'
-Requires-Dist: pyenchant; extra == 'doc'
 Requires-Dist: pygments; extra == 'doc'
+Requires-Dist: scanpydoc; extra == 'doc'
 Requires-Dist: sphinx-autodoc-typehints; extra == 'doc'
 Requires-Dist: sphinx-automodapi; extra == 'doc'
+Requires-Dist: sphinx-book-theme; extra == 'doc'
 Requires-Dist: sphinx-copybutton; extra == 'doc'
 Requires-Dist: sphinx-design; extra == 'doc'
 Requires-Dist: sphinx-gallery; extra == 'doc'
+Requires-Dist: sphinx-issues; extra == 'doc'
 Requires-Dist: sphinx-last-updated-by-git; extra == 'doc'
 Requires-Dist: sphinx-remove-toctrees; extra == 'doc'
-Requires-Dist: sphinx>=4; extra == 'doc'
+Requires-Dist: sphinx>=8.1; extra == 'doc'
 Requires-Dist: sphinxcontrib-bibtex>=1.0.0; extra == 'doc'
 Requires-Dist: sphinxext-opengraph; extra == 'doc'
+Provides-Extra: tcoda
+Requires-Dist: ete4; extra == 'tcoda'
+Requires-Dist: pyqt6; extra == 'tcoda'
+Requires-Dist: toytree; extra == 'tcoda'
 Provides-Extra: test
 Requires-Dist: coverage; extra == 'test'
+Requires-Dist: leidenalg; extra == 'test'
 Requires-Dist: pytest; extra == 'test'
 Description-Content-Type: text/markdown
 
-[![Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![Build](https://github.com/scverse/pertpy/actions/workflows/build.yml/badge.svg)](https://github.com/scverse/pertpy/actions/workflows/build.yml)
 [![codecov](https://codecov.io/gh/scverse/pertpy/graph/badge.svg?token=1dTpIPBShv)](https://codecov.io/gh/scverse/pertpy)
 [![License](https://img.shields.io/github/license/scverse/pertpy)](https://opensource.org/licenses/Apache2.0)
@@ -108,13 +110,16 @@ Description-Content-Type: text/markdown
 [![Test](https://github.com/scverse/pertpy/actions/workflows/test.yml/badge.svg)](https://github.com/scverse/pertpy/actions/workflows/test.yml)
 [![PyPI](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
 
-# pertpy
+# pertpy - Perturbation Analysis in Python
+
+Pertpy is a scverse ecosystem framework for analyzing large-scale single-cell perturbation experiments.
+It provides tools for harmonizing perturbation datasets, automating metadata annotation, calculating perturbation distances, and efficiently analyzing how cells respond to various stimuli like genetic modifications, drug treatments, and environmental changes.
 
 ![fig1](https://github.com/user-attachments/assets/d2e32d69-b767-4be3-a938-77a9dce45d3f)
 
 ## Documentation
 
-Please read the [documentation](https://pertpy.readthedocs.io/en/latest).
+Please read the [documentation](https://pertpy.readthedocs.io/en/latest) for installation, tutorials, use cases, and more.
 
 ## Installation
 
@@ -127,10 +132,10 @@ You can install _pertpy_ in less than a minute via [pip] from [PyPI]:
 pip install pertpy
 ```
 
-if you want to use scCODA or tascCODA, please install pertpy as follows:
+if you want to use tascCODA, please install pertpy as follows:
 
 ```console
-pip install 'pertpy[coda]'
+pip install 'pertpy[tcoda]'
 ```
 
 If you want to use the differential gene expression interface, please install pertpy by running:
@@ -146,4 +151,17 @@ bioRxiv 2024.08.04.606516; doi: https://doi.org/10.1101/2024.08.04.606516](https
 
 [pip]: https://pip.pypa.io/
 [pypi]: https://pypi.org/
-[usage]: https://pertpy.readthedocs.io/en/latest/usage/usage.html
+[api]: https://pertpy.readthedocs.io/en/latest/api/api.html
+[//]: # "numfocus-fiscal-sponsor-attribution"
+
+pertpy is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
+If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
+
+<div align="center">
+<a href="https://numfocus.org/project/scverse">
+  <img
+    src="https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png"
+    width="200"
+  >
+</a>
+</div>

pertpy-0.11.1.dist-info/RECORD

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{pertpy-0.10.0.dist-info → pertpy-0.11.1.dist-info}/licenses/LICENSE

@@ -1,6 +1,7 @@
 MIT License
 
 Copyright (c) 2021, Lukas Heumos
+Copyright (c) 2025, scverse®
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

pertpy/tools/_kernel_pca.py

@@ -1,50 +0,0 @@
-from __future__ import annotations
-
-from typing import TYPE_CHECKING
-
-from sklearn.decomposition import KernelPCA
-
-if TYPE_CHECKING:
-    from anndata import AnnData
-
-
-def kernel_pca(
-    adata: AnnData,
-    n_comps: int = 50,
-    kernel: str = "linear",
-    copy: bool = False,
-    return_transformer: bool = False,
-    **kwargs,
-):
-    """Compute kernel PCA on `adata.X`.
-
-    Compute Kernel Principal component analysis (KPCA) using sklearn.
-    See also :class:`~sklearn.decomposition.KernelPCA`.
-
-    Args:
-        adata: The annotated data object.
-        n_comps: Number of components. If None, all non-zero components are kept.
-        kernel: Kernel used for PCA.
-        copy: Determines whether a copy of the `adata` is returned.
-        return_transformer: Determines if the `KernelPCA` transformer is returned.
-        **kwargs: Additional arguments for the `KernelPCA` transformer.
-
-    Returns:
-        If `copy=True`, returns the copy of `adata` with kernel pca in `.obsm["X_kpca"]`.
-        Otherwise, writes kernel pca directly to `.obsm["X_kpca"]` of the provided `adata`.
-        If `return_transformer=True`, returns also the fitted `KernelPCA` transformer.
-    """
-    if copy:
-        adata = adata.copy()
-    transformer = KernelPCA(n_components=n_comps, kernel=kernel, **kwargs)
-    X_kpca = transformer.fit_transform(adata.X)
-    adata.obsm["X_kpca"] = X_kpca
-
-    if copy:
-        if return_transformer:
-            return adata, transformer
-        else:
-            return adata
-    else:
-        if return_transformer:
-            return transformer

pertpy-0.10.0.dist-info/RECORD

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