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

Submitting author: !--author-handle-->@jpotoff@phibeck<!--end-editor-- Reviewers: @naik-aakash, @RiesBen Archive: Pending

Status

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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. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @phibeck know.

✨ 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

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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

Paper file info:

📄 Wordcount for paper.md is 1354

✅ The paper includes a Statement of need section

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

License info:

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

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Review checklist for @naik-aakash

Conflict of interest

[x] 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

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

General checks

[x] Repository: Is the source code for this software available at the https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[ ] Functionality: Have the functional claims of the software been confirmed?
[x] 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?
[x] 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)?
[x] 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?

Review checklist for @RiesBen