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physical_validation

physical_validation: A Python package to assess the physical validity of molecular simulation results - Published in JOSS (2022)

https://github.com/shirtsgroup/physical_validation

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 8 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ✓
    Committers with academic emails
    5 of 14 committers (35.7%) from academic institutions
  • ✓
    Institutional organization owner
    Organization shirtsgroup has institutional domain (www.colorado.edu)
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

molecular-dynamics molecular-mechanics molecular-simulation physical-validation python

Keywords from Contributors

mesh hydrology energy-system exoplanet hydraulic-modelling polygon gravitational-lensing geoscience ode

Scientific Fields

Mathematics Computer Science - 84% confidence
Last synced: 4 months ago · JSON representation

Repository

Physical validation of molecular simulations

Basic Info
Statistics
  • Stars: 56
  • Watchers: 13
  • Forks: 20
  • Open Issues: 17
  • Releases: 6
Topics
molecular-dynamics molecular-mechanics molecular-simulation physical-validation python
Created over 8 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License Zenodo

README.md

GitHub Actions Test Status GitHub Actions Lint Status Documentation Status codecov
DOI DOI
MIT license

physical_validation: A Python package to assess the physical validity of molecular simulation results

physical_validation is a package testing results obtained by molecular simulations for their physical validity.

Please cite

Merz PT, Shirts MR (2018) Testing for physical validity in molecular simulations. PLoS ONE 13(9): e0202764. https://doi.org/10.1371/journal.pone.0202764
Merz et al., (2022). physical_validation: A Python package to assess the physical validity of molecular simulation results. Journal of Open Source Software, 7(69), 3981, https://doi.org/10.21105/joss.03981

physical_validation incorporates the functionality of checkensemble.

This software is developed in the Shirts group at University of Colorado in Boulder.

Documentation

Please check https://physical-validation.readthedocs.io for the full reference.

Owner

  • Name: Shirts Research Group
  • Login: shirtsgroup
  • Kind: organization
  • Location: University of Colorado Boulder

JOSS Publication

physical_validation: A Python package to assess the physical validity of molecular simulation results
Published
January 06, 2022
DOI
Volume 7, Issue 69, Page 3981
Authors
Pascal T. Merz ORCID
Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309, United States of America
Wei-Tse Hsu
Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309, United States of America
Matt W. Thompson
Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309, United States of America
Simon Boothroyd
Boothroyd Scientific Consulting Ltd., 71-75 Shelton Street, London, United Kingdom
Chris C. Walker
Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309, United States of America
Michael R. Shirts ORCID
Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309, United States of America
Editor
Rachel Kurchin ORCID
Tags
molecular simulation molecular dynamics molecular mechanics statistical mechanics physical validation
View PDF Review Thread Software Archive

GitHub Events

Total
  • Issues event: 2
  • Watch event: 1
  • Issue comment event: 3
  • Push event: 3
  • Pull request review event: 2
  • Pull request event: 2
  • Fork event: 1
  • Create event: 1
Last Year
  • Issues event: 2
  • Watch event: 1
  • Issue comment event: 3
  • Push event: 3
  • Pull request review event: 2
  • Pull request event: 2
  • Fork event: 1
  • Create event: 1

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 429
  • Total Committers: 14
  • Avg Commits per committer: 30.643
  • Development Distribution Score (DDS): 0.259
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Pascal Merz p****z@c****u 318
mrshirts m****s@3****5 47
dependabot[bot] 4****] 22
Michael Shirts m****s@g****m 9
pre-commit-ci[bot] 6****] 8
Matthew W. Thompson m****n@p****m 7
Michael Shirts m****s@v****u 6
SimonBoothroyd s****d@c****u 5
Wei-Tse Hsu 4****1 2
lgtm-com[bot] 4****] 1
Theodore Fobe t****e@c****u 1
MKiesel 3****e 1
Chris Walker 6****7 1
Nate n****m@c****u 1
Committer Domains (Top 20 + Academic)
colorado.edu: 4 virginia.edu: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 30
  • Total pull requests: 94
  • Average time to close issues: over 1 year
  • Average time to close pull requests: 19 days
  • Total issue authors: 8
  • Total pull request authors: 9
  • Average comments per issue: 3.4
  • Average comments per pull request: 1.59
  • Merged pull requests: 76
  • Bot issues: 0
  • Bot pull requests: 42
Past Year
  • Issues: 4
  • Pull requests: 4
  • Average time to close issues: about 12 hours
  • Average time to close pull requests: N/A
  • Issue authors: 3
  • Pull request authors: 3
  • Average comments per issue: 1.5
  • Average comments per pull request: 0.25
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 3
View more stats
Top Authors
Issue Authors
  • ptmerz (16)
  • mrshirts (5)
  • EidRashed (2)
  • mattwthompson (2)
  • wehs7661 (2)
  • lilyminium (1)
  • Efrem-Braun (1)
  • cwalker7 (1)
Pull Request Authors
  • ptmerz (39)
  • dependabot[bot] (37)
  • pre-commit-ci[bot] (13)
  • mrshirts (5)
  • mattwthompson (5)
  • lilyminium (2)
  • lgtm-com[bot] (1)
  • wehs7661 (1)
  • cwalker7 (1)
Top Labels
Issue Labels
documentation (8) deployment (5) improvement (3) new feature (3) question (1) workflow (1) testing (1)
Pull Request Labels
dependencies (37)

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 124 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 1
    (may contain duplicates)
  • Total versions: 18
  • Total maintainers: 1
pypi.org: physical-validation
  • Versions: 14
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 124 Last month
Rankings
Forks count: 8.7%
Stargazers count: 9.3%
Dependent packages count: 10.0%
Average: 17.3%
Dependent repos count: 21.8%
Downloads: 36.8%
Maintainers (1)
ptmerz
Last synced: 4 months ago
conda-forge.org: physical_validation

physical_validation is a package aimed at testing results obtained by molecular dynamics simulations for their physical validity.

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 34.0%
Forks count: 34.7%
Average: 40.1%
Stargazers count: 40.5%
Dependent packages count: 51.2%
Last synced: 4 months ago

Dependencies

.github/workflows/continous_integration.yaml actions
  • actions/checkout v3 composite
  • codecov/codecov-action v3 composite
  • conda-incubator/setup-miniconda v2.2.0 composite
.github/workflows/lint.yaml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
doc/requirements.txt pypi
  • nbsphinx ==0.8.7
  • sphinx ==4.2.0
  • sphinx_rtd_theme ==1.0.0
requirements.txt pypi
  • matplotlib *
  • numpy *
  • pymbar *
  • scipy *
setup.py pypi
  • matplotlib *
  • numpy *
  • pymbar *
  • scipy *
.github/workflows/codeql.yml actions
  • actions/checkout v3 composite
  • github/codeql-action/analyze v2 composite
  • github/codeql-action/autobuild v2 composite
  • github/codeql-action/init v2 composite