gufe

core data models of the Open Free Energy ecosystem

Science Score: 77.0%

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 3 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
3 of 16 committers (18.8%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (10.3%) to scientific vocabulary

Keywords from Contributors

computational-chemistry free-energy-calculations molecular-dynamics drug-discovery distributed-computing alchemistry quantum-chemistry free-energy biophysics molecular-dynamics-simulation

Last synced: 6 months ago · JSON representation ·

Repository

core data models of the Open Free Energy ecosystem

Basic Info

Host: GitHub
Owner: OpenFreeEnergy
License: mit
Language: Python
Default Branch: main
Homepage: https://gufe.openfree.energy
Size: 2.03 MB

Statistics

Stars: 36
Watchers: 4
Forks: 10
Open Issues: 120
Releases: 28

Created almost 4 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Citation

gufe

gufe is a toolkit for developers of software related to alchemical free energy calculations, containing data models and abstract base classes.

Looking to run a free energy calculation? You're probably looking for openfe

License

This library is made available under the MIT open source license.

API stability

Our 1.0 releases follow semantic versioning and we will make an effort to keep the 1.0 API stable.

Installation

To install, run

conda install -c conda-forge gufe

Authors

The Open Free Energy development team.

Acknowledgements

Open Free Energy is an Open Molecular Software Foundation hosted project.

Owner

Name: Open Free Energy
Login: OpenFreeEnergy
Kind: organization

Website: https://openfree.energy
Repositories: 10
Profile: https://github.com/OpenFreeEnergy

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Gowers"
  given-names: "Richard J."
  orcid: "https://orcid.org/0000-0002-3241-1846"
- family-names: "Alibay"
  given-names: "Irfan"
  orcid: "https://orcid.org/0000-0001-5787-9130"
- family-names: "Dotson"
  given-names: "David L."
  orcid: "https://orcid.org/0000-0001-5879-2942"
- family-names: "Swenson"
  given-names: "David W.H."
  orcid: "https://orcid.org/0000-0001-9922-7923"
- family-names: "Henry"
  given-names: "Michael M."
  orcid: "https://orcid.org/0000-0002-3870-9993"
- family-names: "Ries"
  given-names: "Benjamin"
  orcid: "https://orcid.org/0000-0002-0945-8304"
- given-names: "Joshua A."
  family-names: "Mitchell"
  orcid: 'https://orcid.org/0000-0002-8246-5113'
- family-names: "Baumann"
  given-names: "Hannah M."
  orcid: "https://orcid.org/0000-0002-1736-7744"
- family-names: "Thompson"
  given-names: "Matthew W."
  orcid: "https://orcid.org/0000-0002-1460-3983"
- family-names: "Kenney"
  given-names: "Ian M."
  orcid: "https://orcid.org/0000-0002-9749-8866"
- family-names: "MacDermott-Opeskin"
  given-names: "Hugo"
  orcid: "https://orcid.org/0000-0002-7393-7457"
- family-names: "Horton"
  given-names: "Joshua T."
  orcid: "https://orcid.org/0000-0001-8694-7200"
- family-names: "Andreev"
  given-names: "Georgy"
  orcid: "https://orcid.org/0009-0004-8126-6085"
- family-names: "Travitz"
  given-names: "Alyssa"
  orcid: "https://orcid.org/0000-0001-5953-8807"
- family-names: "Pulido"
  given-names: "Iván J."
  orcid: "https://orcid.org/0000-0002-7178-8136"

title: "gufe"
version: 1.3.0
date-released: 2025-03-10
url: "https://gufe.openfree.energy/"
repository-code: "https://github.com/OpenFreeEnergy/gufe"
doi: "10.5281/zenodo.8296913"

Committers

Last synced: 11 months ago

All Time

Total Commits: 865
Total Committers: 16
Avg Commits per committer: 54.063
Development Distribution Score (DDS): 0.662

Past Year

Commits: 117
Committers: 12
Avg Commits per committer: 9.75
Development Distribution Score (DDS): 0.769

Top Committers

Name	Email	Commits
richard	r**s@g**m	292
David Dotson	d**l@g**m	169
David W.H. Swenson	d**n@o**o	163
IAlibay	i**y@m**g	90
Mike Henry	1****y	65
Alyssa Travitz	a**z@u**u	22
Josh Horton	J**n@n**k	18
Josh Mitchell	y**i@g**m	14
Ian Kenney	i**y@g**m	12
Benjamin Ries	b**s@o**m	9
hannahbaumann	h**n@u**u	4
hmacdope	h**t@g**m	2
Matt Thompson	m**n@o**g	2
George	3****d	1
Iván Pulido	2****s	1
pre-commit-ci[bot]	6****]	1

Committer Domains (Top 20 + Academic)

openforcefield.org: 1 uci.edu: 1 newcastle.ac.uk: 1 umich.edu: 1 mdanalysis.org: 1 omsf.io: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 279
Total pull requests: 314
Average time to close issues: about 2 months
Average time to close pull requests: 27 days
Total issue authors: 21
Total pull request authors: 16
Average comments per issue: 0.8
Average comments per pull request: 2.82
Merged pull requests: 231
Bot issues: 85
Bot pull requests: 4

Past Year

Issues: 161
Pull requests: 154
Average time to close issues: 22 days
Average time to close pull requests: 11 days
Issue authors: 14
Pull request authors: 10
Average comments per issue: 0.4
Average comments per pull request: 2.81
Merged pull requests: 107
Bot issues: 60
Bot pull requests: 4

View more stats

Top Authors

Issue Authors

github-actions[bot] (85)
dotsdl (50)
IAlibay (35)
richardjgowers (22)
atravitz (17)
jthorton (13)
mikemhenry (10)
ijpulidos (8)
dwhswenson (7)
RiesBen (6)
ianmkenney (6)
LilDojd (5)
hannahbaumann (4)
jchodera (2)
jameseastwood (2)

Pull Request Authors

richardjgowers (58)
atravitz (44)
mikemhenry (40)
dotsdl (35)
IAlibay (31)
dwhswenson (28)
jthorton (20)
ianmkenney (18)
RiesBen (13)
mattwthompson (6)
Yoshanuikabundi (5)
LilDojd (4)
pre-commit-ci[bot] (4)
hannahbaumann (4)
Mert-csrg (2)

Top Labels

Issue Labels

docs-developer (14) enhancement (8) question (6) priority:medium (3) good first issue (3) documentation (2) priority-high (1) bug (1) wontfix (1) ecosystem-standards (1) module-tokenization (1) serialization (1)

Pull Request Labels

enhancement (3) ecosystem-standards (2) bug (2)

Packages

Total packages: 2
Total downloads:
- pypi 35 last-month
Total docker downloads: 8

Total dependent packages: 2
(may contain duplicates)
Total dependent repositories: 1
(may contain duplicates)
Total versions: 5
Total maintainers: 6

pypi.org: gufe

Homepage: https://github.com/OpenFreeEnergy/gufe
Documentation: https://gufe.readthedocs.io/
License: MIT
Latest release: 0.4
published about 3 years ago

Versions: 1
Dependent Packages: 1
Dependent Repositories: 0
Downloads: 35 Last month
Docker Downloads: 8

Rankings

Dependent packages count: 6.6%

Stargazers count: 15.7%

Forks count: 19.6%

Average: 22.7%

Dependent repos count: 30.6%

Downloads: 41.1%

Maintainers (6)

mmh richard.j.gowers IAlibay riesb dwhswenson alyssatravitz

Last synced: 7 months ago

conda-forge.org: gufe

Abstract base classes for free energy calculations by Open Free Energy

Homepage: https://github.com/OpenFreeEnergy/gufe
License: MIT
Latest release: 0.4
published over 3 years ago

Versions: 4
Dependent Packages: 1
Dependent Repositories: 1

Rankings

Dependent repos count: 24.4%

Dependent packages count: 29.0%

Average: 41.4%

Stargazers count: 52.9%

Forks count: 59.3%

Last synced: 6 months ago

Dependencies

.github/workflows/ci.yaml actions

actions/checkout v2 composite
codecov/codecov-action v3 composite
conda-incubator/setup-miniconda v2 composite

.github/workflows/mypy.yaml actions

actions/checkout v2 composite
conda-incubator/setup-miniconda v2 composite

.github/workflows/clean_cache.yaml actions

actions/checkout v3 composite

.github/workflows/conda_cron.yaml actions

actions/checkout v4 composite
mamba-org/setup-micromamba v1 composite

docs/environment.yaml pypi

environment.yml pypi

autodoc_pydantic <2.0.0

pyproject.toml pypi

networkx *
numpy *

gufe

Science Score: 77.0%

Keywords from Contributors

Repository

Basic Info

Statistics

Metadata Files

README.md

gufe

License

API stability

Installation

Authors

Acknowledgements

Owner

Citation (CITATION.cff)

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: gufe

Rankings

Maintainers (6)

conda-forge.org: gufe

Rankings

Dependencies