pyglotaran

A Python library for Global and Target Analysis of time-resolved spectroscopy data

Science Score: 59.0%

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

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 10 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Committers with academic emails
4 of 22 committers (18.2%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (15.9%) to scientific vocabulary

Keywords

data-analysis glotaran modelling pyglotaran python-library target-analysis

Keywords from Contributors

kinetic-modeling chinese biochemical-networks condensed-matter-physics defects density-functional-theory electronic-structure forschungszentrum-juelich full-potential greens-functions

Last synced: 6 months ago · JSON representation

Repository

A Python library for Global and Target Analysis of time-resolved spectroscopy data

Basic Info

Host: GitHub
Owner: glotaran
License: lgpl-3.0
Language: Python
Default Branch: main
Homepage:
Size: 30 MB

Statistics

Stars: 57
Watchers: 4
Forks: 18
Open Issues: 11
Releases: 16

Topics

data-analysis glotaran modelling pyglotaran python-library target-analysis

Created almost 10 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Codeowners Authors Zenodo

pyglotaran

A framework written in Python for global and target analysis; commonly used for the analysis of time-resolved spectroscopy measurements in the study of energy transfer pathways in photosynthesis, or the characterization of energy transfer (in-)efficiencies in photovoltaics.

The Future of Global and Target Analysis

A scientific publication titled "pyglotaran: a lego-like Python framework for global and target analysis of time-resolved spectra" (DOI: 10.1007/s43630-023-00460-y) covers aspects of the architecture and the design of the software while illustrating its flexibility as an analysis tool through some exciting case studies. This publication, along with other pyglotaran-publications demonstrates why we believe this framework is the future of global and target analysis.

Usage of pyglotaran

If you just want to get started analyzing your data, jump straight to the getting started guide that is part of our documentation.

Afterwards, you may also want to have a look at our comprehensive collection of real-world examples in the pyglotaran-examples repository. There most like is an example that aligns well with your use case.

For state of the art usage of this framework you may want to check out the list of pyglotaran-publications.

Example analysis results

Results of a target analysis of Photosystem I (see study_florescence in the examples.)

overview plot of the fluorescence case study from the pyglotaran-examples _{Plot created with the plot_overview function of the pyglotaran-extras package.}

_{Notice: This is (still) an early access release, please refer to the usage notice prior to committing to use pyglotaran to avoid surprises down the line.}

Glotaran legacy

The pyglotaran package derives its name from the Glotaran software package (now called glotaran-legacy), first released in 2011 and described in a highly-cited publication in the Journal of Statistical Software, under the title Glotaran: A Java-Based Graphical User Interface for the R Package TIMP (DOI: 10.18637/jss.v049.i03).

The pyglotaran framework can be considered the spiritual successor of the glotaran-legacy software and has the backing of many of its original creators.

Community Support

For questions / suggestion please reach out to us via:

Credits

The credits can be found in the documentation authors section

Owner

Name: GloTarAn
Login: glotaran
Kind: organization
Email: github@glotaran.org
Location: Amsterdam

Website: http://www.glotaran.org
Twitter: glotaran
Repositories: 28
Profile: https://github.com/glotaran

Modeling frameworks for global and target analysis (GloTarAn)

GitHub Events

Total

Issues event: 5
Watch event: 1
Delete event: 36
Issue comment event: 180
Push event: 39
Pull request review event: 31
Pull request event: 69
Create event: 36

Last Year

Issues event: 5
Watch event: 1
Delete event: 36
Issue comment event: 180
Push event: 39
Pull request review event: 31
Pull request event: 69
Create event: 36

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 1,428
Total Committers: 22
Avg Commits per committer: 64.909
Development Distribution Score (DDS): 0.658

Past Year

Commits: 138
Committers: 8
Avg Commits per committer: 17.25
Development Distribution Score (DDS): 0.594

Top Committers

Name	Email	Commits
Joern Weissenborn	j**n@g**m	488
Sebastian Weigand	s**y@g**m	424
Joris Snellenburg	j**g@v**l	119
Joris Snellenburg	j**l@u**m	117
dependabot[bot]	4**]@u**m	109
Joern Weissenborn	j**n@v**l	66
pre-commit-ci[bot]	6**]@u**m	29
dependabot-preview[bot]	2**]@u**m	24
pyup-bot	g**t@p**o	13
Stefan Schütz	y**n@g**m	12
Joern Weissenborn	j**n@l**n	5
s-weigand	s**d@u**m	4
Joris Snellenburg	j**g@i**m	3
Joris Snellenburg	j**s@d**n	3
ism200	i**o@f**l	3
sourcery-ai[bot]	5**]@u**m	2
Joern Weissenborn	j**n@w**e	2
Ivo van Stokkum	1**0@u**m	1
Patrick Hätti	4**0@u**m	1
Patrick Hätti	9**i@u**m	1
lgtm-com[bot]	4**]@u**m	1
s-weigand	4**]@u**m	1

Committer Domains (Top 20 + Academic)

vu.nl: 2 wlan-141-23-185-17.tubit.tu-berlin.de: 1 few.vu.nl: 1 i-optics.com: 1 localhost.localdomain: 1 pyup.io: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 71
Total pull requests: 427
Average time to close issues: almost 2 years
Average time to close pull requests: 16 days
Total issue authors: 8
Total pull request authors: 9
Average comments per issue: 2.86
Average comments per pull request: 4.21
Merged pull requests: 213
Bot issues: 0
Bot pull requests: 299

Past Year

Issues: 1
Pull requests: 76
Average time to close issues: N/A
Average time to close pull requests: 25 days
Issue authors: 1
Pull request authors: 5
Average comments per issue: 0.0
Average comments per pull request: 3.41
Merged pull requests: 3
Bot issues: 0
Bot pull requests: 72

View more stats

Top Authors

Issue Authors

jsnel (33)
s-weigand (29)
joernweissenborn (7)
luccablois (1)
ism200 (1)
SanjoyPatraIISc (1)
ankit7540 (1)
anmolbhatia05 (1)

Pull Request Authors

dependabot[bot] (348)
s-weigand (100)
jsnel (38)
pre-commit-ci[bot] (33)
joernweissenborn (16)
sourcery-ai[bot] (9)
snyk-bot (2)
ism200 (2)
gdrosos (1)

Top Labels

Issue Labels

Status: Lack of interest (49) Type: Enhancement (24) Type: Refactor (13) Type: Bug (13) Type: Documentation (7) Type: Tooling (4) Priority: Low (4) staging (4) Type: Question (3) Status: Available (3) Priority: Medium (1)

Pull Request Labels

dependencies (349) python (269) github_actions (73) staging (49) Status: Lack of interest (7) submodules (7) Type: Invalid (1)

Packages

Total packages: 4
Total downloads:
- pypi 1,553 last-month

Total dependent packages: 2
(may contain duplicates)
Total dependent repositories: 7
(may contain duplicates)
Total versions: 44
Total maintainers: 2

pypi.org: pyglotaran

The Glotaran fitting engine.

Homepage: https://github.com/glotaran/pyglotaran
Documentation: https://pyglotaran.readthedocs.io
License: LGPL-3.0
Latest release: 0.7.3
published over 1 year ago

Versions: 16
Dependent Packages: 1
Dependent Repositories: 5
Downloads: 1,302 Last month

Rankings

Dependent repos count: 6.7%

Downloads: 7.2%

Dependent packages count: 7.3%

Average: 8.1%

Forks count: 8.9%

Stargazers count: 10.2%

Maintainers (2)

s-weigand jsnel

Last synced: 6 months ago

pypi.org: glotaran

The Glotaran fitting engine.

Homepage: https://github.com/glotaran/pyglotaran
Documentation: https://glotaran.readthedocs.io
License: GPLv3
Latest release: 0.1.0
published over 5 years ago

Versions: 13
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 218 Last month

Rankings

Dependent packages count: 7.3%

Forks count: 8.9%

Stargazers count: 10.2%

Average: 13.7%

Downloads: 19.9%

Dependent repos count: 22.1%

Maintainers (2)

s-weigand jsnel

Last synced: 6 months ago

pypi.org: pyglotaran-alias

Convenience module, which allows to use pyglotaran as alias in the CLI and imports

Homepage: https://github.com/glotaran/pyglotaran-alias
Documentation: https://pyglotaran-alias.readthedocs.io/
License: Apache-2.0
Latest release: 0.0.5
published almost 5 years ago

Versions: 5
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 33 Last month

Rankings

Dependent packages count: 10.1%

Forks count: 19.1%

Dependent repos count: 21.5%

Average: 22.3%

Stargazers count: 27.8%

Downloads: 32.9%

Maintainers (2)

s-weigand jsnel

Last synced: 6 months ago

conda-forge.org: pyglotaran

Pyglotaran is a python library for global analysis of time-resolved spectroscopy data. It is designed to provide a state of the art modeling toolbox to researchers, in a user-friendly manner. Its features are: - user-friendly modeling with a custom YAML (*.yml) based modeling language - parameter optimization using variable projection and non-negative least-squares algorithms - easy to extend modeling framework - battle-hardened model and algorithms for fluorescence dynamics - build upon and fully integrated in the standard Python science stack (NumPy, SciPy, Jupyter) pyglotaran is ideal for researchers and scientists who require a powerful, yet user-friendly tool for analyzing complex systems, from time-resolved spectroscopy to broader applications in scientific modeling.

Homepage: https://github.com/glotaran/pyglotaran
License: LGPL-3.0-only
Latest release: 0.6.0
published over 3 years ago

Versions: 10
Dependent Packages: 1
Dependent Repositories: 0

Rankings

Dependent packages count: 28.8%

Dependent repos count: 34.0%

Average: 34.8%

Forks count: 37.3%

Stargazers count: 39.1%

Last synced: 6 months ago

Dependencies

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pyglotaran

Science Score: 59.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

pyglotaran

The Future of Global and Target Analysis

Usage of pyglotaran

Example analysis results

Glotaran legacy

Community Support

Credits

Owner

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: pyglotaran

Rankings

Maintainers (2)

pypi.org: glotaran

Rankings

Maintainers (2)

pypi.org: pyglotaran-alias

Rankings

Maintainers (2)

conda-forge.org: pyglotaran

Rankings

Dependencies