pyprep

PyPREP: A Python implementation of the Preprocessing Pipeline (PREP) for EEG data

https://github.com/sappelhoff/pyprep

Science Score: 67.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 5 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
○
Committers with academic emails
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (14.3%) to scientific vocabulary

Keywords

artifact data eeg electroencephalogaphy mne neuroimaging neuroscience preprocessing python

Keywords from Contributors

ecog electrocorticography electroencephalography magnetoencephalography meg bids ieeg standardization interactive brain

Last synced: 4 months ago · JSON representation ·

Repository

PyPREP: A Python implementation of the Preprocessing Pipeline (PREP) for EEG data

Basic Info

Host: GitHub
Owner: sappelhoff
License: mit
Language: Python
Default Branch: main
Homepage: https://pyprep.readthedocs.io/en/latest/
Size: 26 MB

Statistics

Stars: 156
Watchers: 9
Forks: 35
Open Issues: 26
Releases: 7

Topics

artifact data eeg electroencephalogaphy mne neuroimaging neuroscience preprocessing python

Created over 7 years ago · Last pushed 4 months ago

Metadata Files

Readme Contributing License Citation

README.rst


.. image:: https://github.com/sappelhoff/pyprep/workflows/Python%20build/badge.svg
   :target: https://github.com/sappelhoff/pyprep/actions?query=workflow%3A%22Python+build%22
   :alt: Python build


.. image:: https://github.com/sappelhoff/pyprep/workflows/Python%20tests/badge.svg
   :target: https://github.com/sappelhoff/pyprep/actions?query=workflow%3A%22Python+tests%22
   :alt: Python tests


.. image:: https://codecov.io/gh/sappelhoff/pyprep/branch/main/graph/badge.svg
   :target: https://codecov.io/gh/sappelhoff/pyprep
   :alt: Test coverage

.. image:: https://readthedocs.org/projects/pyprep/badge/?version=latest
   :target: https://pyprep.readthedocs.io/en/latest/?badge=latest
   :alt: Documentation Status


.. image:: https://badge.fury.io/py/pyprep.svg
   :target: https://badge.fury.io/py/pyprep
   :alt: PyPI version

.. image:: https://img.shields.io/conda/vn/conda-forge/pyprep.svg
   :target: https://anaconda.org/conda-forge/pyprep
   :alt: Conda version

.. image:: https://zenodo.org/badge/129240824.svg
   :target: https://zenodo.org/badge/latestdoi/129240824
   :alt: Zenodo archive

PyPREP
======

For documentation, see the:

- `stable documentation `_
- `latest (development) documentation `_

.. docs_readme_include_label

``pyprep`` is a Python implementation of the
`Preprocessing Pipeline (PREP) `_
for EEG data, working with `MNE-Python `_.

Installation
============

``pyprep`` runs on Python version 3.9 or higher.

We recommend to run ``pyprep`` in a dedicated virtual environment
(for example using `conda `_).

For installing the **stable** version of ``pyprep``, call:

.. code-block:: Text

   python -m pip install --upgrade pyprep

or if you use `conda `_:

.. code-block:: Text

   conda install --channel conda-forge pyprep

For installing the **latest (development)** version of ``pyprep``, call:

.. code-block:: Text

   python -m pip install --upgrade https://github.com/sappelhoff/pyprep/archive/refs/heads/main.zip

Both the *stable* and the *latest* installation will additionally install
all required dependencies automatically.
The dependencies are defined in the ``pyproject.toml`` file under the
``dependencies`` and ``project.optional-dependencies`` sections.

Contributing
============

The development of ``pyprep`` is taking place on
`GitHub `_.

For more information, please see
`CONTRIBUTING.md `_.

Citing
======

If you use this software in academic work, please cite it using the `Zenodo entry `_.
Please also consider citing the original publication on PREP (see "References" below).
Metadata is encoded in the `CITATION.cff` file.

References
==========

1. Bigdely-Shamlo, N., Mullen, T., Kothe, C., Su, K.-M., & Robbins, K. A.
   (2015). The PREP pipeline: standardized preprocessing for large-scale EEG
   analysis. Frontiers in Neuroinformatics, 9, 16. doi:
   `10.3389/fninf.2015.00016 `_

Owner

Name: Stefan Appelhoff
Login: sappelhoff
Kind: user
Location: Germany
Company: @MPIB

Website: https://www.stefanappelhoff.com
Twitter: stefanappelhoff
Repositories: 18
Profile: https://github.com/sappelhoff

Citation (CITATION.cff)

# YAML 1.2
---
# Metadata for citation of this software according to the CFF format (https://citation-file-format.github.io/)
cff-version: 1.2.0
title: 'PyPREP: A Python implementation of the preprocessing pipeline (PREP) for EEG data.'
abstract: 'PyPREP is a Python library to facilitate preprocessing of EEG data. More information can be found at <a href=\"https://pyprep.readthedocs.io\">pyprep.readthedocs.io</a>.'
authors:
    - given-names: Stefan
      family-names: Appelhoff
      affiliation: 'Center for Adaptive Rationality, Max Planck Institute for Human Development, Berlin, Germany'
      orcid: 'https://orcid.org/0000-0001-8002-0877'
    - given-names: Austin J.
      family-names: Hurst
      affiliation: 'Dalhousie University, Halifax, Nova Scotia'
      orcid: 'https://orcid.org/0000-0002-0219-4131'
    - given-names: Aamna
      family-names: Lawrence
      affiliation: 'Johns Hopkins University, Baltimore, MD, USA'
      orcid: 'https://orcid.org/0000-0002-0983-0997'
    - given-names: Adam
      family-names: Li
      affiliation: 'Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA'
      orcid: 'https://orcid.org/0000-0001-8421-365X'
    - given-names: Yorguin José
      family-names: Mantilla Ramos
      affiliation: 'Grupo Neuropsicología y Conducta, Universidad de Antioquia, Medellín, Colombia'
      orcid: 'https://orcid.org/0000-0003-4473-0876'
    - given-names: Christian
      family-names: O'Reilly
      affiliation: 'Azrieli Centre for Autism Research, McGill University, Montreal, Canada'
      orcid: 'https://orcid.org/0000-0002-3149-4934'
    - given-names: Liang
      family-names: Xiang
      affiliation: 'Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA'
      orcid: 'https://orcid.org/0000-0003-3191-9565'
    - given-names: Jonte
      family-names: Dancker
      affiliation: 'Institute of Electric Power Systems, Otto von Guericke University Magdeburg, Magdeburg, Germany'
      orcid: 'https://orcid.org/0000-0001-6486-6987'
    - given-names: Mathieu
      family-names: Scheltienne
      affiliation: 'Fondation Campus Biotech Geneva, Geneva, Switzerland'
      orcid: 'https://orcid.org/0000-0001-8316-7436'
    - given-names: Ole
      family-names: Bialas
      affiliation: 'Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA'
      orcid: 'https://orcid.org/0000-0003-4472-7626'
    - given-names: Nabil
      family-names: Alibou
      affiliation: 'Biotrial, Neuroscience Department, Rennes, France'
    - given-names: Ayush
      family-names: Agarwal
      affiliation: 'Techno India University, India'
    - given-names: John
      family-names: Veillette
      affiliation: 'Department of Psychology, University of Chicago, Chicago, IL, USA'
      orcid: 'https://orcid.org/0000-0002-0332-4372'
type: software
repository-code: 'https://github.com/sappelhoff/pyprep'
license: MIT
keywords:
  - EEG
  - artifact
  - preprocessing
  - data
  - neuroscience
  - neuroimaging
  - mne
  - python
  - electroencephalography
  - eeg
message: >-
  Please cite this software using the citation string you can
  find on the Zenodo archive page, or use the data provided
  in the CITATION.cff file.
identifiers:
  - description: "Code archive on Zenodo"
    type: doi
    value: 10.5281/zenodo.6363575
references:
  - authors:
      - name: "PREP developers"
    repository-code: "https://github.com/VisLab/EEG-Clean-Tools"
    title: Original PREP code
    type: software
  - authors:
      - family-names: Bigdely-Shamlo
        given-names: Nima
      - family-names: Mullen
        given-names: Tim
      - family-names: Kothe
        given-names: Christian
      - family-names: Su
        given-names: Kyungmin Su
      - family-names: Robbins
        given-names: Kay A.
    doi: 10.3389/fninf.2015.00016
    issue: 16
    journal: "Frontiers in Neuroinformatics"
    scope: "Cite this paper if you in addition to PyPREP, because it describes the original pipeline."
    title: "The PREP pipeline: standardized preprocessing for large-scale EEG analysis"
    type: article
    volume: 42
    year: 2015
...

GitHub Events

Total

Create event: 6
Release event: 1
Issues event: 1
Watch event: 20
Delete event: 3
Issue comment event: 6
Push event: 18
Pull request event: 11
Fork event: 1

Last Year

Create event: 6
Release event: 1
Issues event: 1
Watch event: 20
Delete event: 3
Issue comment event: 6
Push event: 18
Pull request event: 11
Fork event: 1

Committers

Last synced: almost 2 years ago

All Time

Total Commits: 347
Total Committers: 11
Avg Commits per committer: 31.545
Development Distribution Score (DDS): 0.331

Past Year

Commits: 16
Committers: 2
Avg Commits per committer: 8.0
Development Distribution Score (DDS): 0.125

Top Committers

Name	Email	Commits
Stefan Appelhoff	s**f@m**g	232
Austin Hurst	m**t@g**m	43
Aamna Lawrence	a**e@g**m	21
Victor Xiang	x**1@g**m	21
Yorguin Mantilla	y**a@g**m	10
Adam Li	a**2@g**m	9
dependabot[bot]	4****]	7
Christian O'Reilly	c**y@g**m	1
Mathieu Scheltienne	m**e@g**m	1
Jonte Dancker	8****r	1
Ole Bialas	3****s	1

Committer Domains (Top 20 + Academic)

mailbox.org: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 69
Total pull requests: 63
Average time to close issues: about 2 months
Average time to close pull requests: 7 days
Total issue authors: 19
Total pull request authors: 11
Average comments per issue: 5.59
Average comments per pull request: 3.41
Merged pull requests: 55
Bot issues: 0
Bot pull requests: 11

Past Year

Issues: 6
Pull requests: 9
Average time to close issues: about 2 months
Average time to close pull requests: 3 days
Issue authors: 1
Pull request authors: 3
Average comments per issue: 1.17
Average comments per pull request: 2.22
Merged pull requests: 6
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

a-hurst (23)
sappelhoff (22)
yjmantilla (4)
sunshineinsandiego (2)
john-veillette (2)
SebastianSpeer (2)
nabilalibou (2)
walkerped (1)
gael-vanderlee (1)
mscheltienne (1)
guishuyunye-lyw (1)
OleBialas (1)
neerajww (1)
m4sp3 (1)
hoechenberger (1)

Pull Request Authors

a-hurst (26)
sappelhoff (18)
dependabot[bot] (13)
Ayush-Devs (6)
yjmantilla (4)
nabilalibou (3)
john-veillette (2)
joDancker (1)
OleBialas (1)
mscheltienne (1)
sourcery-ai[bot] (1)

Top Labels

Issue Labels

enhancement (6) documentation/example (4) bug (4) Matlab PREP (3) refactor (3) API (2) maintenance (2) MNE-Python (1) needs investigation (1) good first issue (1)

Pull Request Labels

dependencies (13) github_actions (8) documentation/example (1)

Packages

Total packages: 2
Total downloads:
- pypi 4,224 last-month

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 5
(may contain duplicates)
Total versions: 16
Total maintainers: 2

pypi.org: pyprep

PyPREP: A Python implementation of the preprocessing pipeline (PREP) for EEG data.

Homepage: https://pyprep.readthedocs.io/en/latest
Documentation: https://pyprep.readthedocs.io/en/latest
License: MIT License Copyright (c) 2018 PyPREP developers 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.
Latest release: 0.5.0
published 5 months ago

Versions: 12
Dependent Packages: 0
Dependent Repositories: 4
Downloads: 4,224 Last month

Rankings

Stargazers count: 7.2%

Dependent packages count: 7.3%

Dependent repos count: 7.6%

Forks count: 8.0%

Average: 8.7%

Downloads: 13.5%

Maintainers (2)

sappelhoff a-hurst

Last synced: 4 months ago

conda-forge.org: pyprep

Homepage: https://github.com/sappelhoff/pyprep
License: MIT
Latest release: 0.4.2
published almost 4 years ago

Versions: 4
Dependent Packages: 0
Dependent Repositories: 1

Rankings

Dependent repos count: 24.1%

Forks count: 34.1%

Stargazers count: 34.6%

Average: 36.1%

Dependent packages count: 51.5%

Last synced: 4 months ago

Dependencies

requirements-dev.txt pypi

black * development
check-manifest * development
flake8 * development
flake8-docstrings * development
isort * development
matplotlib * development
numpydoc * development
pillow * development
pooch * development
pre-commit * development
pymatreader * development
pytest * development
pytest-cov * development
pytest-sugar * development
sphinx >3 development
sphinx-copybutton * development
sphinx_bootstrap_theme * development
sphinx_gallery * development
tdqm * development

.github/workflows/cffconvert.yml actions

actions/checkout v3 composite
citation-file-format/cffconvert-github-action 2.0.0 composite

.github/workflows/python_build.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite

.github/workflows/python_publish.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite

.github/workflows/python_tests.yml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/setup-python v4 composite
actions/upload-artifact v3 composite
codecov/codecov-action v3 composite