Metadata-Version: 2.4
Name: py2rely
Version: 0.6.0
Summary: Command line tools to Run Automated Sub-Tomogram Averaging with Relion and CCPEM Pipeline.
Author-email: Jonathan Schwartz <jonathan.schwartz@czii.org>
License: # Legal
        
        ## License for the py2rely package
        
        This package is licensed under the MIT License:
        
        ```
        MIT License
        
        Copyright (c) 2025 Chan Zuckerberg Initiative
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        ```
        
        ## License Notice for Dependencies
        
        ```
        This repository is licensed under the MIT License; however, it relies on certain third-party dependencies that are licensed under the GNU General Public License (GPL). Specifically:
        
        - PyQt5 is licensed under the GNU General Public License v3 or later (GPLv3+).
        This library is not included in this repository but must be installed separately by users. Please be aware that the GPL license terms apply to these dependencies, and certain uses of GPL-licensed code may have licensing implications for your own software.
        ```
License-File: LICENSE
Requires-Python: >=3.9
Requires-Dist: ccpem-pipeliner
Requires-Dist: copick
Requires-Dist: fastmcp>=2.0.0
Requires-Dist: gradio
Requires-Dist: mrcfile
Requires-Dist: pydantic
Requires-Dist: rich-click
Requires-Dist: scipy
Requires-Dist: slabpick
Requires-Dist: starfile
Requires-Dist: submitit
Requires-Dist: zarr-particle-tools
Provides-Extra: dashboard
Requires-Dist: fastapi>=0.110.0; extra == 'dashboard'
Requires-Dist: uvicorn[standard]>=0.29.0; extra == 'dashboard'
Requires-Dist: watchdog>=4.0.0; extra == 'dashboard'
Requires-Dist: websockets>=12.0; extra == 'dashboard'
Provides-Extra: gui
Requires-Dist: pyqt5; extra == 'gui'
Requires-Dist: pyqtgraph; extra == 'gui'
Provides-Extra: web
Requires-Dist: gradio; extra == 'web'
Requires-Dist: pytz; extra == 'web'
Description-Content-Type: text/markdown

# py2rely - The Python Pipeline To Rely On 
Pythonic to Relion interface for streamlined sub-tomogram averaging on SLURM HPC clusters.

## Introduction

py2rely simplifies and accelerates the execution of RELION-based sub-tomogram averaging (STA) workflows on SLURM-based high-performance computing (HPC) systems. Designed for rapid iteration and evaluation of particle picking strategies, py2rely integrates with existing tilt series alignment from AreTomo and particle coordinate storage from [copick](https://github.com/copick/copick), making it ideal for automated benchmarking and structure validation.

## 💫 Key Features

* ⚙️ Automated job preparation: One-command setup of RELION STA workflows including particle extraction, classification, and refinement.
* 🔄 Copick integration: Seamless import of particle coordinates from copick metadata storage.
* 🧭 Tilt series-aware: Direct input of alignment and metadata from AreTomo processing pipelines.
* 🚀 SLURM-native execution: Jobs are launched, monitored, and managed directly on HPC SLURM environments.
* 🧠 Validation-ready: Quickly test new particle picking algorithms and assess their reconstruction outcomes with minimal setup.

## 🚀 Getting Started

### Installation

py2rely is availableon PyPI and can be installed using pip:
```bash
pip install py2rely
```

## 📚 Documentation 

For comprehensive guides, usage examples, and API references, visit the [documentation](https://chanzuckerberg.github.io/py2rely/).

## 🤝 Contributing 

This project adheres to the Contributor Covenant [code of conduct](https://github.com/chanzuckerberg/.github/blob/master/CODE_OF_CONDUCT.md).
By participating, you are expected to uphold this code. 
Please report unacceptable behavior to [opensource@chanzuckerberg.com](mailto:opensource@chanzuckerberg.com).

## 🔒 Security

If you believe you have discovered a security vulnerability, please report it responsibly to security@chanzuckerberg.com.
