Metadata-Version: 2.4
Name: autocleaneeg-pipeline
Version: 3.2.1
Summary: A modular framework for automated EEG data processing, built on MNE-Python
Project-URL: Homepage, https://github.com/cincibrainlab/autoclean_pipeline
Project-URL: Repository, https://github.com/cincibrainlab/autoclean_pipeline
Project-URL: Documentation, https://cincibrainlab.github.io/autoclean_pipeline/
Project-URL: Issues, https://github.com/cincibrainlab/autoclean_pipeline/issues
Author-email: Ernest Pedapati <ernest.pedapati@cchmc.org>, Gavin Gammoh <gavin.gammoh@cchmc.org>
License: # MIT License
        
        Copyright (c) 2024 Cincinnati Children's Hospital Medical Center
        
        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-File: LICENSE.md
Keywords: bids,eeg,electrophysiology,mne-python,neuroscience,preprocessing,signal-processing
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Requires-Python: <3.14,>=3.11
Requires-Dist: auth0-python==4.13.0
Requires-Dist: autoclean-eeg2source==0.3.7
Requires-Dist: autocleaneeg-icvision>=0.2.1
Requires-Dist: autocleaneeg-mne-qt-browser-fork>0.7.2
Requires-Dist: autocleaneeg-view==0.1.6
Requires-Dist: autoreject==0.4.3
Requires-Dist: bctpy==0.6.1
Requires-Dist: cryptography==46.0.1
Requires-Dist: cython==3.1.4
Requires-Dist: defusedxml==0.7.1
Requires-Dist: eeglabio==0.1.2
Requires-Dist: fastapi>=0.115.0
Requires-Dist: fastparquet==2024.11.0
Requires-Dist: inquirer==3.4.1
Requires-Dist: jinja2==3.1.6
Requires-Dist: loguru==0.7.3
Requires-Dist: matplotlib==3.10.6
Requires-Dist: mne-bids==0.17.0
Requires-Dist: mne-connectivity==0.7.0
Requires-Dist: mne-icalabel==0.8.1
Requires-Dist: mne==1.10.2
Requires-Dist: networkx==3.5
Requires-Dist: nibabel==5.3.2
Requires-Dist: numpy==2.3.3
Requires-Dist: onnxruntime==1.22.1
Requires-Dist: openai==1.109.0
Requires-Dist: pandas==2.3.3
Requires-Dist: platformdirs==4.4.0
Requires-Dist: pybv==0.7.6
Requires-Dist: pydantic==2.11.9
Requires-Dist: pyjsonviewer==1.6.0
Requires-Dist: pyopengl-accelerate==3.1.10
Requires-Dist: pyprep==0.5.0
Requires-Dist: pyqt6==6.7.1
Requires-Dist: python-dotenv==1.1.1
Requires-Dist: python-picard==0.8
Requires-Dist: python-ulid==3.1.0
Requires-Dist: pyvistaqt==0.11.3
Requires-Dist: pywavelets==1.9.0
Requires-Dist: pyyaml==6.0.2
Requires-Dist: qtpy==2.4.3
Requires-Dist: redis>=5.2.0
Requires-Dist: reportlab==4.4.4
Requires-Dist: requests==2.32.5
Requires-Dist: rich==14.1.0
Requires-Dist: rq>=2.0.0
Requires-Dist: schema==0.7.8
Requires-Dist: scipy==1.16.2
Requires-Dist: seaborn==0.13.2
Requires-Dist: specparam>=2.0.0rc3
Requires-Dist: textual-dev==1.7.0
Requires-Dist: textual==6.1.0
Requires-Dist: torch==2.8.0
Requires-Dist: uvicorn>=0.32.0
Requires-Dist: watchfiles>=0.24.0
Requires-Dist: websockets>=14.0
Provides-Extra: blocks-all
Requires-Dist: meegkit>=0.1.9; extra == 'blocks-all'
Provides-Extra: blocks-analysis
Provides-Extra: blocks-signal
Requires-Dist: meegkit>=0.1.9; extra == 'blocks-signal'
Description-Content-Type: text/markdown

# AutoCleanEEG Pipeline

[![Python](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org/downloads/)
[![License](https://img.shields.io/badge/license-MIT-green.svg)](LICENSE.md)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)

A modular framework for automated EEG data processing, built on MNE‑Python.

## Features

- Framework for automated EEG preprocessing with "lego block" modularity
- Support for multiple EEG paradigms (ASSR, Chirp, MMN, Resting State) 
- BIDS-compatible data organization and comprehensive quality control
- Extensible plugin system for file formats, montages, and event processing
- Research-focused workflow: single file testing → parameter tuning → batch processing
- Detailed output: BIDS‑compatible derivatives, single task log file, stage files, exports, and QA visualizations

## Installation (uv)

Use Astral's uv for fast, isolated installs. If you don't have uv yet, see https://docs.astral.sh/uv/

- Install CLI (recommended for users):

```bash
uv tool install autocleaneeg-pipeline
autocleaneeg-pipeline --help
```

- Upgrade or remove:

```bash
uv tool upgrade autocleaneeg-pipeline
uv tool uninstall autocleaneeg-pipeline
```

- Development install from source (editable install):

```bash
git clone https://github.com/cincibrainlab/autocleaneeg_pipeline.git
cd autocleaneeg_pipeline
uv tool install -e --upgrade . --force
autocleaneeg-pipeline --help # Slow on first run!
```

## Documentation

Full documentation is available at [https://docs.autocleaneeg.org](https://docs.autocleaneeg.org)

## Development

For contributors, we provide a Makefile with convenient development commands:

```bash
make help          # Show all available commands
make check         # Run code quality checks
make format        # Auto-format code
make lint          # Run linting and type checking
make test          # Run unit tests
make test-cov      # Run tests with coverage
make ci-check      # Run CI-equivalent checks locally
```

See [CONTRIBUTING.md](CONTRIBUTING.md) for full development guidelines.

## Contributing

We welcome contributions! Please see our [Contributing Guide](CONTRIBUTING.md) for details.
For branch workflow and cleanup expectations, see [BRANCHING.md](BRANCHING.md).

## License

This project is licensed under the MIT License - see the [LICENSE](LICENSE.md) file for details.

## Acknowledgments

- Cincinnati Children's Hospital Research Foundation
- Built with [MNE-Python](https://mne.tools/)
