Metadata-Version: 2.4
Name: moscot
Version: 0.5.0
Summary: Multi-omic single-cell optimal transport tools
Author: Dominik Klein, Giovanni Palla, Michal Klein, Zoe Piran, Marius Lange
Maintainer-email: Dominik Klein <dominik.klein@helmholtz-muenchen.de>, Giovanni Palla <giovanni.palla@helmholtz-muenchen.de>, Michal Klein <michal.klein@helmholtz-muenchen.de>
License: BSD 3-Clause License
        
        Copyright (c) 2022, Theis Lab
        All rights reserved.
        
        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.
        
Project-URL: Homepage, https://github.com/theislab/moscot
Project-URL: Download, https://moscot.readthedocs.io/en/latest/installation.html
Project-URL: Bug Tracker, https://github.com/theislab/moscot/issues
Project-URL: Documentation, https://moscot.readthedocs.io
Project-URL: Source Code, https://github.com/theislab/moscot
Keywords: single-cell,bio-informatics,optimal transport
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Typing :: Typed
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Mathematics
Requires-Python: >=3.10
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: numpy>=1.20.0
Requires-Dist: scipy>=1.7.0
Requires-Dist: pandas>=2.0.1
Requires-Dist: networkx>=3.2
Requires-Dist: matplotlib>=3.5.0
Requires-Dist: anndata>=0.9.1
Requires-Dist: scanpy>=1.9.3
Requires-Dist: wrapt>=1.13.2
Requires-Dist: docrep>=0.3.2
Requires-Dist: jax>=0.6.1
Requires-Dist: ott-jax>=0.6.0
Requires-Dist: cloudpickle>=2.2.0
Requires-Dist: rich>=13.5
Requires-Dist: docstring_inheritance>=2.0.0
Requires-Dist: mudata>=0.2.2
Requires-Dist: optax
Requires-Dist: flax
Requires-Dist: diffrax
Requires-Dist: ott-jax[neural]>=0.5.0
Provides-Extra: spatial
Requires-Dist: squidpy>=1.2.3; extra == "spatial"
Provides-Extra: dev
Requires-Dist: pre-commit>=3.0.0; extra == "dev"
Requires-Dist: tox>=4; extra == "dev"
Provides-Extra: test
Requires-Dist: pytest>=7; extra == "test"
Requires-Dist: pytest-xdist>=3; extra == "test"
Requires-Dist: pytest-mock>=3.5.0; extra == "test"
Requires-Dist: pytest-cov>=4; extra == "test"
Requires-Dist: coverage[toml]>=7; extra == "test"
Requires-Dist: moscot[neural]; extra == "test"
Provides-Extra: docs
Requires-Dist: sphinx>=5.1.1; extra == "docs"
Requires-Dist: sphinx_copybutton>=0.5.0; extra == "docs"
Requires-Dist: sphinxcontrib-bibtex>=2.3.0; extra == "docs"
Requires-Dist: sphinxcontrib-spelling>=7.6.2; extra == "docs"
Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
Requires-Dist: furo>=2022.09.29; extra == "docs"
Requires-Dist: sphinx-tippy>=0.4.1; extra == "docs"
Requires-Dist: myst-nb>=0.17.1; extra == "docs"
Requires-Dist: ipython>=7.20.0; extra == "docs"
Requires-Dist: sphinx_design>=0.3.0; extra == "docs"
Dynamic: license-file

|PyPI| |Downloads| |CI| |Pre-commit| |Codecov| |Docs|

Moscot - Multiomics Single-cell Optimal Transport
=======================================================

.. image:: docs/_static/img/light_mode_concept_revised.png
    :width: 800px
    :align: center
    :class: only-light

.. image:: docs/_static/img/dark_mode_concept_revised.png
    :width: 800px
    :align: center
    :class: only-dark


**moscot** is a framework for Optimal Transport (OT) applications in
single-cell genomics. It scales to large datasets and can be used for a
variety of applications across different modalities.

moscot's key applications
---------------------------
- Trajectory inference (incorporating spatial and lineage information).
- Mapping cells to their spatial organisation.
- Aligning spatial transcriptomics slides.
- Translating modalities.
- prototyping of new OT models in single-cell genomics.
- ... and more, check out the `documentation <https://moscot.readthedocs.io>`_ for more information.


**moscot** is powered by
`OTT <https://ott-jax.readthedocs.io>`_ which is a JAX-based Optimal
Transport toolkit that supports just-in-time compilation, GPU acceleration, automatic
differentiation and linear memory complexity for OT problems.

Installation
------------
Install **moscot** by running::

    pip install moscot

In order to install **moscot** from in editable mode, run::

    git clone https://github.com/theislab/moscot
    cd moscot
    pip install -e .

For further instructions how to install jax, please refer to https://github.com/google/jax.

Citing moscot
-------------
If you find a model useful for your research, please consider citing the `Klein et al., 2025`_ manuscript as
well as the publication introducing the model, which can be found in the corresponding documentation.

.. |Codecov| image:: https://codecov.io/gh/theislab/moscot/branch/master/graph/badge.svg?token=Rgtm5Tsblo
    :target: https://codecov.io/gh/theislab/moscot
    :alt: Coverage

.. |PyPI| image:: https://img.shields.io/pypi/v/moscot.svg
    :target: https://pypi.org/project/moscot/
    :alt: PyPI

.. |CI| image:: https://img.shields.io/github/actions/workflow/status/theislab/moscot/test.yml?branch=main
    :target: https://github.com/theislab/moscot/actions
    :alt: CI

.. |Pre-commit| image:: https://results.pre-commit.ci/badge/github/theislab/moscot/main.svg
   :target: https://results.pre-commit.ci/latest/github/theislab/moscot/main
   :alt: pre-commit.ci status

.. |Docs| image:: https://img.shields.io/readthedocs/moscot
    :target: https://moscot.readthedocs.io/en/stable/
    :alt: Documentation

.. |Downloads| image:: https://static.pepy.tech/badge/moscot
    :target: https://pepy.tech/project/moscot
    :alt: Downloads

.. _Klein et al., 2025: https://www.nature.com/articles/s41586-024-08453-2
