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Pyret

Pyret: A Python package for analysis of neurophysiology data - Published in JOSS (2017)

https://github.com/baccuslab/pyret

Science Score: 98.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ✓
    Committers with academic emails
    3 of 6 committers (50.0%) from academic institutions
  • ✓
    Institutional organization owner
    Organization baccuslab has institutional domain (sites.stanford.edu)
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

electrophysiology neuroscience python scientific-computing tools

Scientific Fields

Mathematics Computer Science - 84% confidence
Artificial Intelligence and Machine Learning Computer Science - 83% confidence
Last synced: 4 months ago · JSON representation

Repository

Python tools for analysis of neurophysiology data

Basic Info
Statistics
  • Stars: 37
  • Watchers: 15
  • Forks: 8
  • Open Issues: 3
  • Releases: 0
Topics
electrophysiology neuroscience python scientific-computing tools
Created almost 12 years ago · Last pushed about 2 years ago
Metadata Files
Readme License Codemeta

README.md

pyret

Build Status Coverage Status Documentation Status PyPi version status

A Python package for analyzing sensory electrophysiology data

Benjamin Naecker, Niru Maheswaranthan

Brief description

The pyret package provides a set of tools for analyzing electrophysiology data, especially data recorded from sensory systems driven by an external stimulus. It was originally written and is mainly used for the analysis of multi-electrode array (MEA) recordings from the retina in the Baccus lab at Stanford University. It contains routines for manipulating spike trains, performing basic spike-triggered analyses, and visualization tools.

Documentation

For more info and documentation, see the pyret documentation.

Contributing

Pull requests are welcome! We follow the Numpy/Scipy documentation standards, and Sphinx for generating documentation.

Testing

Testing is done via py.test. Once installed (e.g. with pip install pytest) then simply run make test at the top level directory to run the tests. Test functions are located in the tests/ folder.

Owner

  • Name: Baccus Lab
  • Login: baccuslab
  • Kind: organization
  • Email: thebaccuslab@gmail.com

JOSS Publication

Pyret: A Python package for analysis of neurophysiology data
Published
January 06, 2017
DOI
Volume 2, Issue 9, Page 137
Authors
Benjamin Naecker ORCID
Neurosciences Graduate Program, Stanford University
Niru Maheswaranathan ORCID
Neurosciences Graduate Program, Stanford University
Surya Ganguli
Department of Applied Physics, Stanford University, Department of Neurobiology, Stanford University
Stephen Baccus
Department of Neurobiology, Stanford University
Editor
Ariel Rokem ORCID
Tags
neuroscience sensory retina
View PDF Review Thread Software Archive

CodeMeta (codemeta.json) 

{
  "@context": "https://raw.githubusercontent.com/mbjones/codemeta/master/codemeta.jsonld",
  "@type": "Code",
  "author": [],
  "identifier": "",
  "codeRepository": "https://github.com/baccuslab/pyret",
  "datePublished": "2016-12-01",
  "dateModified": "2016-12-01",
  "dateCreated": "2016-12-01",
  "description": "A Python package for analyzing sensory electrophysiology",
  "keywords": "sensory, neuroscience, retina",
  "license": "MIT",
  "title": "pyret",
  "version": "v0.5.0"
}

Papers & Mentions

Total mentions: 1

Inferring hidden structure in multilayered neural circuits
Last synced: 2 months ago

GitHub Events

Total
  • Watch event: 2
Last Year
  • Watch event: 2

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 357
  • Total Committers: 6
  • Avg Commits per committer: 59.5
  • Development Distribution Score (DDS): 0.373
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Niru Maheswaranathan n****m@s****u 224
Benjamin Naecker b****r@g****m 110
Niru Maheswaranathan n****m 14
lmcintosh l****h@s****u 5
Pablo D. Jadzinsky j****z@s****u 3
Arfon Smith a****n 1
Committer Domains (Top 20 + Academic)
stanford.edu: 3

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 77
  • Total pull requests: 21
  • Average time to close issues: 2 months
  • Average time to close pull requests: 10 days
  • Total issue authors: 6
  • Total pull request authors: 4
  • Average comments per issue: 1.39
  • Average comments per pull request: 1.38
  • Merged pull requests: 19
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • nirum (39)
  • bnaecker (26)
  • kdesimone (5)
  • lmcintosh (3)
  • pabloj100000 (3)
  • bongsoos (1)
Pull Request Authors
  • nirum (9)
  • bnaecker (8)
  • lmcintosh (3)
  • arfon (1)
Top Labels
Issue Labels
enhancement (24) bug (13) question (6) discussion (5) documentation (1) wontfix (1)
Pull Request Labels
enhancement (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 107 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 2
  • Total versions: 13
  • Total maintainers: 2
pypi.org: pyret

Tools for the analysis of neural electrophysiology data

  • Versions: 13
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 107 Last month
Rankings
Dependent packages count: 10.0%
Stargazers count: 10.8%
Dependent repos count: 11.6%
Forks count: 11.9%
Average: 13.4%
Downloads: 22.7%
Maintainers (2)
nirum bnaecker
Last synced: 4 months ago

Dependencies

requirements-dev.txt pypi
  • coverage * development
  • flake8 * development
  • pytest * development
requirements.txt pypi
  • matplotlib >=1.5
  • numpy >=1.11
  • pip >=8.1
  • scikit-image >=0.12
  • scikit-learn >=0.18
  • scipy >=0.18
setup.py pypi
  • matplotlib >=1.5
  • numpy >=1.11
  • scikit-image >=0.12
  • scikit-learn >=0.18
  • scipy >=0.18