Joss-reviews: [REVIEW]: GIMS: Graphical Interface for Materials Simulations

Created on 23 Oct 2020 · 9Comments · Source: openjournals/joss-reviews

Submitting author: @kokookster (Sebastian Kokott)
Repository: https://gitlab.com/gims-developers/gims
Version: 1.0.0
Editor: @jgostick
Reviewer: @marshallmcdonnell, @arose, @marshallmcdonnell
Archive: Pending

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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

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Review checklist for @marshallmcdonnell

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@kokookster) 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

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] 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

[x] 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.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 @arose

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 repository url?
[ ] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[ ] Contribution and authorship: Has the submitting author (@kokookster) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[ ] 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?

Makefile Python Shell review

Source

whedon

All 9 comments

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @marshallmcdonnell, @arose, @marshallmcdonnell it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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whedon on 23 Oct 2020

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

OK DOIs

- None

MISSING DOIs

- 10.1016/j.cpc.2009.06.022 may be a valid DOI for title: Ab initio molecular simulations with numeric atom-centered orbitals
- 10.1088/0953-8984/26/36/363202 may be a valid DOI for title: Exciting: a full-potential all-electron package implementing density-functional theory and many-body perturbation theory
- 10.1016/j.commatsci.2010.05.010 may be a valid DOI for title: High-throughput electronic band structure calculations: Challenges and tools
- 10.1007/978-1-4842-2677-3_5 may be a valid DOI for title: pytest

INVALID DOIs

- None

whedon on 23 Oct 2020

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

whedon on 23 Oct 2020

@jgostick Small question, it looks like I've been added twice to the review above:

Reviewer: @marshallmcdonnell, @arose, @marshallmcdonnell

1) Does this matter?
2) Is this something that I need to use whedon to remove?

Thanks in advance!

marshallmcdonnell on 23 Oct 2020

I'm still leaning how to interact with the whedon thing. I thought I'd finally got it right this time :-( Anyway, it doesn't matter much, at the end of the day I just look at the check boxes above. I did remove the second set of check boxes for you though.

jgostick on 23 Oct 2020

👍1

Awesome, thanks!

marshallmcdonnell on 23 Oct 2020

@Kokookster really like your software package, see it as one of many needs to bring web-based solutions in the materials modeling and simulation domain! Great documentation and clean website design, very intuitive. I have went ahead and opened the following issues in the GIMS repository for my request of minor revisions. Besides that, I don't see any issues publishing in JOSS.

Minor revisions

I also added a "suggested revision" and merge requests that do not bar acceptance for me but think would be good to address / include.

Suggested revisions

I figured out the installation via "dockerizing" and the interface worked with everything I "threw at it" :grin:

Tests ran as expected for me (followed the GitLab CI yaml for instructions).
I encourage expanding the test suite but doing great so far.

My biggest issues are Python application API documentation, contribution guidelines, comparison to other similar softwares in the paper, and resolving the license clash in the OrthographicTrackballControls module.

Let me know if you have questions about these issues and happy to engage in a discussion.

marshallmcdonnell on 26 Oct 2020

Hi @marshallmcdonnell, thanks for a terrific review!

jgostick on 26 Oct 2020

👍1

Hi @marshallmcdonnell,
Thanks for your kind words and your constructive review! All points are really helpful. Thanks even for fixing small typos and adding the Docker!
Will start to address your MRs, today.

Kokookster on 28 Oct 2020

👍1

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