Metadata-Version: 2.1
Name: spyglass-neuro
Version: 0.1.1
Summary: Neuroscience data analysis framework for reproducible research
Author-email: Loren Frank <loren.frank@ucsf.edu>, Kyu Hyun Lee <kyuhyun.lee@ucsf.edu>, Eric Denovellis <eric.denovellis@ucsf.edu>, Ryan Ly <rly@lbl.gov>
License: Copyright (c) 2020-present Loren Frank        
        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.        
Project-URL: Homepage, https://github.com/LorenFrankLab/spyglass
Project-URL: Bug Tracker, https://github.com/LorenFrankLab/spyglass/issues
Keywords: neuroscience,research,electrophysiology,reproducible,data analysis,spike sorting,spikeinterface,datajoint,nwb,kachery,sortingview
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: jupyterlab (>=3.*)
Requires-Dist: pydotplus (>=2.0.*)
Requires-Dist: dask (>=2.30)
Requires-Dist: position-tools
Requires-Dist: track-linearization
Requires-Dist: replay-trajectory-classification
Requires-Dist: ripple-detection
Requires-Dist: trajectory-analysis-tools
Requires-Dist: matplotlib
Requires-Dist: seaborn
Requires-Dist: skan
Requires-Dist: bottleneck
Requires-Dist: ipympl
Requires-Dist: tqdm
Requires-Dist: pubnub (<6.4.0)
Requires-Dist: pynwb (<3,>=2.0.0)
Requires-Dist: hdmf (>=3.4.5)
Requires-Dist: datajoint (>=0.13.6)
Requires-Dist: pymysql (>=1.0.*)
Requires-Dist: sortingview (>=0.8)
Requires-Dist: pyyaml
Requires-Dist: click
Requires-Dist: spikeinterface
Requires-Dist: ndx-franklab-novela (>=0.1.0)

[![Import test](https://github.com/LorenFrankLab/spyglass/actions/workflows/workflow.yml/badge.svg)](https://github.com/LorenFrankLab/spyglass/actions/workflows/workflow.yml)
[![Nightly Test](https://github.com/LorenFrankLab/spyglass/actions/workflows/nightly.yml/badge.svg)](https://github.com/LorenFrankLab/spyglass/actions/workflows/nightly.yml)

# spyglass

`spyglass` is a data analysis framework that facilitates the storage, analysis, visualization, and sharing of neuroscience data to support reproducible research. It is designed to be interoperable with the NWB format and integrates open-source tools into a coherent framework.

Documentation can be found at - [https://lorenfranklab.github.io/spyglass/](https://lorenfranklab.github.io/spyglass/)

### Installing from pip
Install spyglass
```bash
pip install spyglass-neuro
```

Some functions may take advantage of the latest changes to spike interface, which currently has a slow release cycle. To get the latest changes:
```bash
pip install git+https://github.com/SpikeInterface/spikeinterface.git
```

The Frank Lab typically uses mountainsort, although spyglass uses spikeinterface, which allows for any spike sorter. To install mountainsort:
```bash
pip install mountainsort4
```

Spyglass uses the package `ghostipy` for filtering of signals:
```bash
pip install ghostipy
```

WARNING: If you are on an M1 Mac, you need to install pyfftw via conda BEFORE installing ghostipy
```bash
conda install -c conda-forge pyfftw
```

## Setup
See the documentation for setup instructions - [https://lorenfranklab.github.io/spyglass/type/html/installation.html](https://lorenfranklab.github.io/spyglass/type/html/installation.html)

## Tutorials
The tutorials for `spyglass` is currently in the form of Jupyter Notebooks and can be found in the [notebooks](https://github.com/LorenFrankLab/spyglass/tree/master/notebooks) directory. We strongly recommend opening them in the context of `jupyterlab`.

## Contributing
See the [Developer's Note](https://lorenfranklab.github.io/spyglass/type/html/developer_notes.html) for contributing instructions found at - [https://lorenfranklab.github.io/spyglass/type/html/how_to_contribute.html](https://lorenfranklab.github.io/spyglass/type/html/how_to_contribute.html)

## License/Copyright
License and Copyright notice can be found at [https://lorenfranklab.github.io/spyglass/type/html/copyright.html](https://lorenfranklab.github.io/spyglass/type/html/copyright.html)

## Citation

Kyu Hyun Lee, Eric Denovellis, Ryan Ly, Jeremy Magland, Jeff Soules, Alison Comrie, Jennifer Guidera, Rhino Nevers, Daniel Gramling, Philip Adenekan, Ji Hyun Bak, Emily Monroe, Andrew Tritt, Oliver Rübel, Thinh Nguyen, Dimitri Yatsenko, Joshua Chu, Caleb Kemere, Samuel Garcia, Alessio Buccino, Emily Aery Jones, Lisa Giocomo, and Loren Frank. Spyglass: A Data Analysis Framework for Reproducible and Shareable Neuroscience Research. Neuroscience Meeting Planner. San Diego, CA: Society for Neuroscience, 2022.
