Metadata-Version: 2.4
Name: scphylo-tools
Version: 0.1.0
Summary: A python toolkit for single-cell tumor phylogenetic analysis
Author-email: Farid Rashidi <farid.rsh@gmail.com>
Maintainer-email: Farid Rashidi <farid.rsh@gmail.com>
License: BSD-3-Clause
Project-URL: Homepage, https://github.com/faridrashidi/scphylo-tools
Project-URL: Documentation, https://scphylo-tools.readthedocs.io/en/latest
Project-URL: Source Code, https://github.com/faridrashidi/scphylo-tools
Project-URL: Download, https://github.com/faridrashidi/scphylo-tools
Keywords: tumor phylogeny,single cell,tools
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Framework :: Jupyter
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
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: >=3.11
Description-Content-Type: text/x-rst
License-File: LICENSE.md
Requires-Dist: anndata
Requires-Dist: apted
Requires-Dist: biopython
Requires-Dist: click
Requires-Dist: cyvcf2
Requires-Dist: ete3
Requires-Dist: graphviz
Requires-Dist: ipython
Requires-Dist: joblib
Requires-Dist: legacy-cgi; python_version >= "3.13"
Requires-Dist: matplotlib
Requires-Dist: natsort
Requires-Dist: networkx
Requires-Dist: numba
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: pybnb
Requires-Dist: pydot<2.0.0
Requires-Dist: python_sat
Requires-Dist: pyyaml
Requires-Dist: scikit_learn
Requires-Dist: scipy
Requires-Dist: seaborn
Requires-Dist: termcolor
Requires-Dist: tqdm
Provides-Extra: dev
Requires-Dist: pre-commit; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"
Requires-Dist: pytest-xdist; extra == "dev"
Requires-Dist: bump-my-version; extra == "dev"
Requires-Dist: ipykernel; extra == "dev"
Provides-Extra: docs
Requires-Dist: furo; extra == "docs"
Requires-Dist: ipython; extra == "docs"
Requires-Dist: memory_profiler; extra == "docs"
Requires-Dist: nbsphinx; extra == "docs"
Requires-Dist: nbsphinx-link; extra == "docs"
Requires-Dist: pydata_sphinx_theme; extra == "docs"
Requires-Dist: pyenchant; extra == "docs"
Requires-Dist: pypandoc; extra == "docs"
Requires-Dist: sphinx<6; extra == "docs"
Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
Requires-Dist: sphinx-click; extra == "docs"
Requires-Dist: sphinx-paramlinks; extra == "docs"
Requires-Dist: sphinx_copybutton; extra == "docs"
Requires-Dist: sphinx_gallery; extra == "docs"
Requires-Dist: sphinx_rtd_theme; extra == "docs"
Requires-Dist: sphinxcontrib-bibtex; extra == "docs"
Requires-Dist: truststore; extra == "docs"
Requires-Dist: typing_extensions; extra == "docs"
Dynamic: license-file

|Tests| |Docs| |PyPI| |Python Version| |License|


scphylo-tools: a python toolkit for single-cell tumor phylogenetic analysis
===========================================================================

.. image:: https://raw.githubusercontent.com/faridrashidi/scphylo-tools/main/docs/source/_static/images/overview.png
   :target: https://github.com/faridrashidi/scphylo-tools
   :alt: overview
   :align: center

**scphylo-tools** is a comprehensive Python toolkit designed for single-cell tumor
phylogenetic analysis. It integrates efficient implementations of state-of-the-art
methods to infer evolutionary trees from single-cell genotype data.

Features
--------

*   **Phylogenetic Inference**: Wrappers and implementations for state-of-the-art
    inference methods.

*   **API & CLI**: Provides a Python API as well as command-line tools.

*   **Visualization**: Built-in visualization tools.

*   **Datasets**: Access to available datasets.

*   **Ease of Use**: A unified Python interface for complex phylogenetic workflows.

Installation
------------

Install the Python package from PyPI:

.. code-block:: bash

    pip install scphylo-tools

For development and the complete native stack, use `Pixi
<https://pixi.prefix.dev/latest/installation/>`_. Pixi installs Python together
with Graphviz, R, ``rpy2``, ``ggtree``, ``ggtreeExtra``, ``graph-tool``, and
MPI from the lockfile:

.. code-block:: bash

    git clone https://github.com/faridrashidi/scphylo-tools
    cd scphylo-tools
    pixi install --locked
    pixi run test

The locked Pixi environments support Linux and macOS. On Windows, use WSL for
the complete native and R plotting stack.

The regular PyPI wheel and source distribution remain available for users who
only need the Python package. See the `installation guide
<https://scphylo-tools.readthedocs.io/en/latest/installation.html>`_ for the
complete development environment and plotting details.

Documentation
-------------

Detailed documentation and tutorials are available at `Read the Docs <https://scphylo-tools.readthedocs.io>`_.

.. |Tests| image:: https://img.shields.io/github/actions/workflow/status/faridrashidi/scphylo-tools/ci.yml?branch=main&logo=github&logoColor=white&style=flat-square&label=tests&labelColor=000000&cacheSeconds=0
    :target: https://github.com/faridrashidi/scphylo-tools/actions/workflows/ci.yml
    :alt: Tests

.. |Docs| image:: https://img.shields.io/website?url=https%3A%2F%2Fscphylo-tools.readthedocs.io%2F&up_message=online&down_message=offline&logo=readthedocs&logoColor=white&style=flat-square&label=docs&labelColor=000000&cacheSeconds=0
    :target: https://scphylo-tools.readthedocs.io/
    :alt: Docs

.. |PyPI| image:: https://img.shields.io/pypi/v/scphylo-tools?logo=pypi&logoColor=white&style=flat-square&labelColor=000000&cacheSeconds=0
    :target: https://pypi.org/project/scphylo-tools/
    :alt: PyPI

.. |Python Version| image:: https://img.shields.io/pypi/pyversions/scphylo-tools?logo=python&logoColor=white&style=flat-square&labelColor=000000&cacheSeconds=0
    :target: https://pypi.org/project/scphylo-tools/
    :alt: Python Version

.. |License| image:: https://img.shields.io/pypi/l/scphylo-tools?logo=creativecommons&logoColor=white&style=flat-square&labelColor=000000&color=blueviolet&cacheSeconds=0
    :target: https://github.com/faridrashidi/scphylo-tools/blob/main/LICENSE.md
    :alt: License
