Metadata-Version: 2.4
Name: patpy
Version: 0.9.1
Summary: A toolbox for patient or sample representation from single-cell data
Project-URL: Documentation, https://patpy.readthedocs.io/
Project-URL: Homepage, https://github.com/lueckenlab/patpy
Project-URL: Source, https://github.com/lueckenlab/patpy
Author: Vladimir Shitov
Maintainer-email: Vladimir Shitov <vladimir.shitov@helmholtz-munich.de>
License: BSD 3-Clause License
        
        Copyright (c) 2023, Vladimir Shitov
        All rights reserved.
        
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License-File: LICENSE
Classifier: Programming Language :: Python :: 3 :: Only
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Description-Content-Type: text/markdown

# patpy – sample-level analysis framework for single-cell data

scverse-compatible package for sample (or patient) representation, representation methods evaluation, and sample-level analysis.

# ⚠️ Warning: Development in Progress ⚠️

> **This repository is currently under active development**
> Features and functionalities may change unexpectedly, and some aspects of the project are not yet complete.

---

**Please proceed with caution** and feel free to contribute, but be aware that:

-   The codebase is still evolving.
-   Documentation may be incomplete.
-   Some features may be unstable or subject to change.

If you have any questions or face bugs, feel free to open an [issue](https://github.com/lueckenlab/patpy/issues).

---

Thank you for your patience and interest. Stay tuned for updates!

---

[![Tests][badge-tests]][link-tests]
[![Documentation][badge-docs]][link-docs]

[badge-tests]: https://img.shields.io/github/actions/workflow/status/lueckenlab/patpy/test.yaml?branch=main
[link-tests]: https://github.com/lueckenlab/patpy/actions/workflows/test.yml
[badge-docs]: https://img.shields.io/readthedocs/patpy

## Getting started

Please refer to the [documentation][link-docs]. In particular, the

-   [API documentation][link-api].

## Installation

You need to have Python 3.9 or newer installed on your system. If you don't have
Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).

There are several alternative options to install patpy:

<!--
1) Install the latest release of `patpy` from `PyPI <https://pypi.org/project/patpy/>`_:

```bash
pip install patpy
```
-->

1. Install the latest development version:

```bash
pip install git+https://github.com/lueckenlab/patpy.git@main
```

To install specific dependencies for some sample representation tools, use the following command:

```bash
pip install git+https://github.com/lueckenlab/patpy.git@main[pilot]
```

All the available dependency groups: `diffusionemd`, `mrvi`, `pilot`, `scpoli`, `wassersteintsne`.

## Release notes

See the [changelog][changelog].

## Contact

For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].
If you found a bug, please use the [issue tracker][issue-tracker].

## Building docs

1. Install [sphinx](https://www.sphinx-doc.org/en/master/usage/installation.html)

You may need add path to `sphinx-doc` to the `$PATH`

2. Install other `doc` section dependencies from the [pyproject.toml](https://github.com/lueckenlab/patpy/blob/main/pyproject.toml)

3. Build the documentation pages:

```bash
cd docs
make html
```

4. Open `docs/_build/html/index.html`

## Citation

Preprint is coming soon. So far, you can refer to this repository as following:

### APA

Shitov, V. (2024). patpy – sample-level analysis framework for single-cell data (Version 0.1.29) [Computer software]. https://github.com/lueckenlab/patpy/

### BibTeX

```bibtex
@misc{shitov_patpy_2024,
  author = {Shitov, Vladimir},
  title = {patpy – sample-level analysis framework for single-cell data},
  year = {2024},
  url = {https://github.com/lueckenlab/patpy/},
  note = {Version 0.1.29}
}
```

[scverse-discourse]: https://discourse.scverse.org/
[issue-tracker]: https://github.com/lueckenlab/patpy/issues
[changelog]: https://patpy.readthedocs.io/latest/changelog.html
[link-docs]: https://patpy.readthedocs.io
[link-api]: https://patpy.readthedocs.io/latest/api.html
