deerlab

Python package for data analysis for dipolar EPR spectroscopy

https://github.com/jeschkelab/deerlab

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
✓
Committers with academic emails
4 of 9 committers (44.4%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (15.4%) to scientific vocabulary

Keywords

data-analysis deer epr esr peldor python

Last synced: 6 months ago · JSON representation ·

Repository

Python package for data analysis for dipolar EPR spectroscopy

Basic Info

Host: GitHub
Owner: JeschkeLab
License: mit
Language: Python
Default Branch: main
Homepage: https://jeschkelab.github.io/DeerLab
Size: 98.9 MB

Statistics

Stars: 19
Watchers: 4
Forks: 11
Open Issues: 15
Releases: 21

Topics

data-analysis deer epr esr peldor python

Created over 5 years ago · Last pushed 11 months ago

Metadata Files

Readme License Citation

DeerLab

PyPI - Downloads

About

DeerLab is a comprehensive free scientific software package for Python focused on modeling, penalized least-squares regression, and uncertainty quantification. It provides highly specialized on the analysis of dipolar EPR (electron paramagnetic resonance) spectroscopy data. Dipolar EPR spectroscopy techniques include DEER (double electron-electron resonance), RIDME (relaxation-induced dipolar modulation enhancement), and others.

The documentation can be found here.

The early versions of DeerLab (up to version 0.9.2) are written in MATLAB. The old MATLAB codebase is archived and can be found here.

Requirements

DeerLab is available for Windows, Mac and Linux systems and requires Python 3.9, 3.10, 3.11, or 3.12.

All additional dependencies are automatically downloaded and installed during the setup.

Setup

A pre-built distribution can be installed from the PyPI repository using pip.

From a terminal (preferably with admin privileges) use the following command to install from PyPI:

python -m pip install deerlab

More details on the installation and updating of DeerLab can be found here.

Citing DeerLab

When you use DeerLab in your work, please cite the following publication:

DeerLab: a comprehensive software package for analyzing dipolar electron paramagnetic resonance spectroscopy data
Luis Fábregas Ibáñez, Gunnar Jeschke, Stefan Stoll
Magn. Reson., 1, 209–224, 2020
doi.org/10.5194/mr-1-209-2020

Here is the citation in bibtex format:

tex @article{FabregasIbanez2020_DeerLab, title = {{DeerLab}: a comprehensive software package for analyzing dipolar electron paramagnetic resonance spectroscopy data}, author = {Fábregas Ibáñez, Luis and Jeschke, Gunnar and Stoll, Stefan}, journal = {Magnetic Resonance}, year = {2020}, volume = {1}, number = {2}, pages = {209--224}, doi = {10.5194/mr-1-209-2020} }

License

DeerLab is licensed under the MIT License.

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software in your work, please cite it as below."
authors:
- family-names: "Fábregas Ibáñez"
  given-names: "Luis"
  orcid: "https://orcid.org/0000-0002-8085-1256"
- family-names: "Stoll"
  given-names: "Stefan"
  orcid: "https://orcid.org/0000-0003-4255-9550"
- family-names: "Jeschke"
  given-names: "Gunnar"
  orcid: "https://orcid.org/0000-0001-6853-8585"
title: "DeerLab"
url: "https://github.com/JeschkeLab/DeerLab"
preferred-citation:
  type: article
  authors:
  - family-names: "Fábregas Ibáñez"
    given-names: "Luis"
    orcid: "https://orcid.org/0000-0002-8085-1256"
  - family-names: "Stoll"
    given-names: "Stefan"
    orcid: "https://orcid.org/0000-0003-4255-9550"
  - family-names: "Jeschke"
    given-names: "Gunnar"
    orcid: "https://orcid.org/0000-0001-6853-8585"
  doi: "10.5194/mr-1-209-2020"
  journal: "Magnetic Resonance"
  start: 209 # First page number
  end: 224 # Last page number
  title: "DeerLab: a comprehensive software package for analyzing dipolar electron paramagnetic resonance spectroscopy data"
  volume: 1
  year: 2020

GitHub Events

Total

Issues event: 10
Watch event: 2
Delete event: 1
Issue comment event: 2
Push event: 4
Pull request event: 4
Pull request review event: 2
Pull request review comment event: 1
Fork event: 1

Last Year

Issues event: 10
Watch event: 2
Delete event: 1
Issue comment event: 2
Push event: 4
Pull request event: 4
Pull request review event: 2
Pull request review comment event: 1
Fork event: 1

Committers

Last synced: over 1 year ago

All Time

Total Commits: 477
Total Committers: 9
Avg Commits per committer: 53.0
Development Distribution Score (DDS): 0.593

Past Year

Commits: 23
Committers: 2
Avg Commits per committer: 11.5
Development Distribution Score (DDS): 0.217

Top Committers

Name	Email	Commits
Luis Fabregas	4****b	194
Luis Fabregas	l**s@p**h	178
Stefan Stoll	s****l	42
Hugo Karas	h**s@e**h	19
Stefan Stoll	s**t@u**u	19
Maxx Tessmer	m**r@g**m	14
Luis Fabregas	l**f@s**h	9
Dennis Bücker	d**r@k**e	1
edmundxcvi	5****i	1

Committer Domains (Top 20 + Academic)

kaissiber.de: 1 student.ethz.ch: 1 uw.edu: 1 ethz.ch: 1 phys.chem.ethz.ch: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 69
Total pull requests: 102
Average time to close issues: about 2 months
Average time to close pull requests: 5 days
Total issue authors: 10
Total pull request authors: 5
Average comments per issue: 0.62
Average comments per pull request: 0.1
Merged pull requests: 95
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 8
Pull requests: 8
Average time to close issues: about 1 hour
Average time to close pull requests: 9 days
Issue authors: 3
Pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.0
Merged pull requests: 5
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

HKaras (28)
luisfabib (21)
stestoll (6)
sergeqzin (3)
mtessmer (3)
schmidtnedlitz (1)
gjeschke (1)
BeneshJ (1)
andreaegg (1)
abehersan (1)

Pull Request Authors

luisfabib (57)
HKaras (45)
stestoll (5)
edmundxcvi (1)
mtessmer (1)

Top Labels

Issue Labels

bug (30) docs (14) enhancement (13) dev (4) design (3) decision (2) bugfix (1) performance (1) fundamental (1) refactor (1) question (1) help wanted (1) wontfix (1)

Pull Request Labels

bugfix (52) docs (20) enhancement (17) release (10) dev (8) refactor (4) performance (4) Overhaul (2) design (1) decision (1)

Packages

Total packages: 1
Total downloads:
- pypi 467 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 21
Total maintainers: 2

pypi.org: deerlab

Comprehensive package for data analysis of dipolar EPR spectroscopy

Homepage: https://github.com/JeschkeLab/DeerLab
Documentation: https://jeschkelab.github.io/DeerLab/
License: LICENSE.txt
Latest release: 1.1.4
published over 1 year ago

Versions: 21
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 467 Last month

Rankings

Dependent packages count: 10.1%

Forks count: 10.9%

Downloads: 14.4%

Average: 14.5%

Stargazers count: 15.6%

Dependent repos count: 21.5%

Maintainers (2)

luisfabib JeschkeLab

Last synced: 6 months ago

Dependencies

.github/workflows/ci_PR.yml actions

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

.github/workflows/ci_scheduled.yml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/deploy_ghpages.yml actions

actions/cache v2 composite
actions/checkout v1 composite
actions/setup-python v1 composite
peaceiris/actions-gh-pages v3 composite

.github/workflows/docs_PR.yml actions

actions/cache v2 composite
actions/checkout v1 composite
actions/setup-python v1 composite

.github/workflows/examples_PR.yml actions

actions/cache v2 composite
actions/checkout v1 composite
actions/setup-python v1 composite

.github/workflows/package_upload.yml actions

actions/checkout v1 composite
actions/setup-python v1 composite
pypa/gh-action-pypi-publish release/v1 composite

docsrc/package-lock.json npm

commander 2.20.0
katex 0.11.0

setup.py pypi

cvxopt >=1.0.0
dill >=0.3.0
joblib >
matplotlib >=3.3.4
memoization >=0.3.1
numexpr >=2.7.3
numpy >=1.22.4
pytest >=6.2.2
quadprog >=0.1.11
scipy >=1.6.3
setuptools >=53.0.0
tqdm >=4.51.0

deerlab

Science Score: 67.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

DeerLab

About

Requirements

Setup

Citing DeerLab

License

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: deerlab

Rankings

Maintainers (2)

Dependencies