[REVIEW]: MoSDeF-dihedral-fit: A lightweight software for fitting dihedrals within MoSDeF #6970

editorialbot · 2024-07-10T15:15:18Z

Submitting author: @jpotoff (Jeffrey Potoff)
Repository: https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/
Branch with paper.md (empty if default branch):
Version: 0.1.12
Editor: @phibeck
Reviewers: @naik-aakash, @RiesBen
Archive: 10.5281/zenodo.14271075

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/2d6869aa8dce990c7dec7267815a8efc/status.svg)](https://joss.theoj.org/papers/2d6869aa8dce990c7dec7267815a8efc)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@naik-aakash & @RiesBen, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @naik-aakash

📝 Checklist for @RiesBen

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-07-10T15:15:21Z

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editorialbot · 2024-07-10T15:15:39Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.11 s (394.5 files/s, 145376.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          11           1081           1961          10109
XML                              4              2             10            597
TeX                              3             31              6            373
reStructuredText                13            240            278            262
DOS Batch                        1             29              1            212
YAML                             6             23              3            182
Markdown                         2             59              0            147
make                             1             28              6            143
Dockerfile                       1             15              2             33
Bourne Shell                     1              2              0              9
-------------------------------------------------------------------------------
SUM:                            43           1510           2267          12067
-------------------------------------------------------------------------------

Commit count by author:

   186	bc118
    50	pre-commit-ci[bot]
    37	Brad Crawford
    28	CalCraven
    28	Co Quach
    10	Jeffrey Potoff
     6	GOMC

editorialbot · 2024-07-10T15:15:43Z

Paper file info:

📄 Wordcount for paper.md is 1354

✅ The paper includes a Statement of need section

editorialbot · 2024-07-10T15:15:45Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1002/jcc.23422 is OK
- 10.1007/s00894-008-0305-0 is OK
- 10.1021/jp972543 is OK
- 10.1098/rspa.1938.0173 is OK
- 10.1063/1.1740026 is OK
- 10.1021/ja00315a051 is OK
- 10.1002/jcc.540070216 is OK
- 10.1002/jcc.20035 is OK
- 10.1021/ja9621760 is OK
- 10.1002/andp.19033160802 is OK
- 10.1002/jcc.21287 is OK
- 10.1021/acs.jctc.5b00935 is OK
- 10.1063/1.1674022 is OK
- 10.1002/andp.18812480110 is OK
- 10.1002/aic.17206 is OK
- 10.1021/acs.jctc.9b01183 is OK
- 10.1021/acs.jcim.2c01498 is OK
- 10.1016/j.softx.2018.11.005 is OK
- 10.1016/j.softx.2020.100627 is OK
- 10.1021/jp990988n is OK
- 10.1021/jp9072137 is OK
- 10.1021/acs.jpcb.5b01354 is OK
- 10.1016/0263-7855(96)00018-5 is OK
- 10.1145/364338.364398 is OK

MISSING DOIs

- No DOI given, and none found for title: Sur le mélange des gaz
- No DOI given, and none found for title: Gaussian 16 Revision C.01
- No DOI given, and none found for title: GMSO: General Molecular Simulation Object
- No DOI given, and none found for title: forcefield-utilities
- No DOI given, and none found for title: MoSDeF-dihedral-fit: A simple software package to ...
- 10.1021/acs.jcim.2c01498.s001 may be a valid DOI for title: MoSDeF-GOMC: Python software for the creation of s...
- No DOI given, and none found for title: vmd-python

INVALID DOIs

- None

editorialbot · 2024-07-10T15:15:46Z

License info:

🟡 License found: Other (Check here for OSI approval)

editorialbot · 2024-07-10T15:17:01Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

naik-aakash · 2024-07-10T15:34:24Z

Review checklist for @naik-aakash

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@jpotoff) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

RiesBen · 2024-07-16T14:53:21Z

Review checklist for @RiesBen

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@jpotoff) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

phibeck · 2024-08-05T14:30:35Z

Thanks @naik-aakash and @RiesBen for getting your reviews started! I see there's lots of activity also on the side of the authors in the respective issues, but please send us an note here when you have completed your updates or if any questions come up @jpotoff, thanks.

phibeck · 2024-09-16T06:58:54Z

Hi @jpotoff just checking in. When you have a moment, could you please let us know the status of addressing the reviewers' comments? Thank you.

jpotoff · 2024-10-11T16:45:54Z

@phibeck We have addressed all of the reviewers comments and are good to go!

jpotoff · 2024-10-11T16:56:56Z

@editorialbot generate pdf

editorialbot · 2024-10-11T16:58:26Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

phibeck · 2024-10-15T08:52:48Z

Hi @jpotoff thank you for letting us know you've completed working through the reviewers' comments. 🎉 I saw your change to the authorlist (#131), which does not seem to be reflected in the latest proof. Could you cross-check that please? Thanks.

@RiesBen I see you've completed your checklist, thank you! 🎉 Could you please confirm that you agree to the publication of this software in its current form?
@naik-aakash, could you please let me know if the changes are satisfactory, and if so, tick off the relevant items on your checklist?

naik-aakash · 2024-10-15T10:11:22Z

Hi @phibeck, Thanks. I forgot to update the checklist. I have just a few things left to go through the changes. I will try to wrap it up by the end of this week and update you here.

phibeck · 2024-12-04T10:35:41Z

Hi @bc118, @jpotoff thank you for catching this!

phibeck · 2024-12-04T10:36:15Z

@editorialbot set 10.5281/zenodo.14271075 as archive

editorialbot · 2024-12-04T10:36:18Z

Done! archive is now 10.5281/zenodo.14271075

phibeck · 2024-12-04T10:36:25Z

@editorialbot set 0.1.12 as version

editorialbot · 2024-12-04T10:36:28Z

Done! version is now 0.1.12

phibeck · 2024-12-04T10:36:36Z

@editorialbot recommend-accept

editorialbot · 2024-12-04T10:36:39Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-12-04T10:37:21Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1002/jcc.23422 is OK
- 10.1021/acs.jcim.2c01153 is OK
- 10.1007/s00894-008-0305-0 is OK
- 10.1021/jp972543 is OK
- 10.1098/rspa.1938.0173 is OK
- 10.1063/1.1740026 is OK
- 10.1021/ja00315a051 is OK
- 10.1002/jcc.540070216 is OK
- 10.1002/jcc.20035 is OK
- 10.1021/ja9621760 is OK
- 10.1021/acs.jctc.1c00302 is OK
- 10.1002/andp.19033160802 is OK
- 10.1063/1.1674022 is OK
- 10.1002/andp.18812480110 is OK
- 10.5281/zenodo.12533861 is OK
- 10.5281/zenodo.10494867 is OK
- 10.1002/aic.17206 is OK
- 10.1021/acs.jctc.9b01183 is OK
- 10.5281/zenodo.14107384 is OK
- 10.1021/acs.jcim.2c01498 is OK
- 10.5281/zenodo.14266177 is OK
- 10.1016/j.softx.2018.11.005 is OK
- 10.1016/j.softx.2020.100627 is OK
- 10.1021/jp990988n is OK
- 10.1021/jp9072137 is OK
- 10.1021/acs.jpcb.5b01354 is OK
- 10.1016/0263-7855(96)00018-5 is OK
- 10.1145/364338.364398 is OK
- 10.1021/jp048581s is OK
- 10.1021/acs.jpca.0c10845 is OK
- 10.1038/s41598-018-21070-0 is OK
- 10.1038/s42004-023-00944-z is OK
- 10.1007/s00249-011-0700-9 is OK
- 10.1021/ct4003477 is OK
- 10.1002/jcc.20082 is OK
- 10.1002/jcc.21367 is OK
- 10.2174/13816128113199990600 is OK
- 10.1002/jcc.23808 is OK
- 10.1007/978-3-030-26837-4_6 is OK
- 10.1007/978-3-658-07529-3_1 is OK
- 10.1080/23746149.2023.2235060 is OK
- 10.1140/epjs/s11734-022-00569-8 is OK
- 10.1007/s13202-020-01003-2 is OK
- 10.1016/j.neuron.2018.08.011 is OK
- 10.1039/c4fd90024c is OK
- 10.1007/978-981-19-3092-8_1 is OK
- 10.1038/s41563-021-01015-1 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Sur le mélange des gaz
- No DOI given, and none found for title: Gaussian 16 Revision C.01
- No DOI given, and none found for title: VMD-python
- No DOI given, and none found for title: Computer Simulation of Liquids (2nd ed.)
- No DOI given, and none found for title: Understanding Molecular Simulation From Algorithms...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-12-04T10:38:17Z

👋 @openjournals/pe-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#6214, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

bc118 · 2024-12-04T10:54:34Z

@editorialbot accept

editorialbot · 2024-12-04T10:54:37Z

I'm sorry @bc118, I'm afraid I can't do that. That's something only eics are allowed to do.

bc118 · 2024-12-04T10:55:06Z

@phibeck This version looks good to me!

GOMC-WSU · 2024-12-04T16:21:21Z

@bc118 @phibeck The proof looks good to me.

jpotoff · 2024-12-04T16:23:26Z

Looks good to me. @bc118 @phibeck

kyleniemeyer · 2024-12-05T23:43:22Z

Hi @jpotoff, in the paper, can the equations be moved to where they are actually mentioned in the text, rather than grouped together at the end (without the appropriate context)?

It also appears that they have some unnecessary linebreaks, and are missing appropriate \text{} commands around some subscripts and words ("where", "periodic", etc.). In addition, functions like cos should be expressed as \cos so they appear in the appropriate font and are not interpreted as a sequence of variables.

bc118 · 2024-12-06T12:00:43Z

@kyleniemeyer @jpotoff @phibeck

I have made the additional changes that were suggested by @kyleniemeyer above.

It is now updated to version 0.1.13 as GitHub, conda-forge, and Zenodo packages. I have listed the relevant information below:

zenodo DOI for version 0.1.13 = 10.5281/zenodo.14288503 and link is here.

kyleniemeyer · 2024-12-06T15:19:31Z

@bc118 ah, changes to the paper only don't actually require updating the version / archives, if the software didn't change. But that's fine.

kyleniemeyer · 2024-12-06T15:19:36Z

@editorialbot generate pdf

editorialbot · 2024-12-06T15:21:10Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

kyleniemeyer · 2024-12-06T15:26:13Z

@editorialbot accept

editorialbot · 2024-12-06T15:26:15Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2024-12-06T15:33:16Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Crawford
  given-names: Brad
  orcid: "https://orcid.org/0000-0003-0638-7333"
- family-names: Quach
  given-names: Co D.
  orcid: "https://orcid.org/0000-0002-1255-4161"
- family-names: Craven
  given-names: Nicholas C.
  orcid: "https://orcid.org/0000-0002-4607-4377"
- family-names: Iacovella
  given-names: Christopher R.
  orcid: "https://orcid.org/0000-0003-0557-0427"
- family-names: McCabe
  given-names: Clare
  orcid: "https://orcid.org/0000-0002-8552-9135"
- family-names: Cummings
  given-names: Peter T.
  orcid: "https://orcid.org/0000-0002-9766-2216"
- family-names: Potoff
  given-names: Jeffrey J.
  orcid: "https://orcid.org/0000-0002-4421-8787"
doi: 10.5281/zenodo.14271075
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Crawford
    given-names: Brad
    orcid: "https://orcid.org/0000-0003-0638-7333"
  - family-names: Quach
    given-names: Co D.
    orcid: "https://orcid.org/0000-0002-1255-4161"
  - family-names: Craven
    given-names: Nicholas C.
    orcid: "https://orcid.org/0000-0002-4607-4377"
  - family-names: Iacovella
    given-names: Christopher R.
    orcid: "https://orcid.org/0000-0003-0557-0427"
  - family-names: McCabe
    given-names: Clare
    orcid: "https://orcid.org/0000-0002-8552-9135"
  - family-names: Cummings
    given-names: Peter T.
    orcid: "https://orcid.org/0000-0002-9766-2216"
  - family-names: Potoff
    given-names: Jeffrey J.
    orcid: "https://orcid.org/0000-0002-4421-8787"
  date-published: 2024-12-06
  doi: 10.21105/joss.06970
  issn: 2475-9066
  issue: 104
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6970
  title: "MoSDeF-dihedral-fit: A lightweight software for fitting
    dihedrals within MoSDeF"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06970"
  volume: 9
title: "MoSDeF-dihedral-fit: A lightweight software for fitting
  dihedrals within MoSDeF"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2024-12-06T15:33:21Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-12-06T15:33:22Z

🦋🦋🦋 👉 Bluesky post for this paper 👈 🦋🦋🦋

editorialbot · 2024-12-06T15:33:23Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06970 joss-papers#6230
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06970
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer · 2024-12-06T15:42:02Z

Congratulations @jpotoff @bc118 on your article's publication in JOSS! Please consider signing up as a reviewer if you haven't already.

Many thanks to @naik-aakash and @RiesBen for reviewing this, and @phibeck for editing it.

editorialbot · 2024-12-06T15:42:04Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following

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[![DOI](https://joss.theoj.org/papers/10.21105/joss.06970/status.svg)](https://doi.org/10.21105/joss.06970)

HTML:
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</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06970/status.svg
   :target: https://doi.org/10.21105/joss.06970

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editorialbot added Python review Shell TeX Track: 3 (PE) Physics and Engineering labels Jul 10, 2024

editorialbot assigned phibeck Jul 10, 2024

editorialbot mentioned this issue Jul 10, 2024

[PRE REVIEW]: MoSDeF-dihedral-fit: A lightweight software for fitting dihedrals within MoSDeF #6811

Closed

RiesBen mentioned this issue Jul 21, 2024

Review JOSS - BR GOMC-WSU/MoSDeF-dihedral-fit#100

Closed

16 tasks

bc118 mentioned this issue Jul 21, 2024

Team checklist of JOSS reviewer requests GOMC-WSU/MoSDeF-dihedral-fit#101

Closed

25 tasks

editorialbot added accepted published Papers published in JOSS labels Dec 6, 2024

kyleniemeyer closed this as completed Dec 6, 2024

[REVIEW]: MoSDeF-dihedral-fit: A lightweight software for fitting dihedrals within MoSDeF #6970

[REVIEW]: MoSDeF-dihedral-fit: A lightweight software for fitting dihedrals within MoSDeF #6970

Comments

editorialbot commented Jul 10, 2024 • edited Loading

Status

Reviewer instructions & questions

Checklists

editorialbot commented Jul 10, 2024

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naik-aakash commented Jul 10, 2024 • edited Loading

Review checklist for @naik-aakash

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

RiesBen commented Jul 16, 2024 • edited Loading

Review checklist for @RiesBen

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

phibeck commented Aug 5, 2024

phibeck commented Sep 16, 2024

jpotoff commented Oct 11, 2024 • edited Loading

jpotoff commented Oct 11, 2024

editorialbot commented Oct 11, 2024

phibeck commented Oct 15, 2024

naik-aakash commented Oct 15, 2024

phibeck commented Dec 4, 2024

phibeck commented Dec 4, 2024

editorialbot commented Dec 4, 2024

phibeck commented Dec 4, 2024

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phibeck commented Dec 4, 2024

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