Joss-reviews: [REVIEW]: J2suscep: Calculation of magnetic exchange coupling and temperature dependence of magnetic susceptibility

[whedon]

Submitting author: @Swetanshu (Swetanshu Tandon)
Repository: https://github.com/WatsonGroupTCD/J2suscep
Version: 1.0
Editor: @dpsanders
Reviewer: @mturiansky, @mfherbst
Archive: Pending

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Status

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Reviewers and authors:

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Reviewer instructions & questions

@mturiansky & @mfherbst, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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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 ✨

Review checklist for @mturiansky

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 (@Swetanshu) 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

• [ ] 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

• [x] 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).
• [x] 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)?
• [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 @mfherbst

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 (@Swetanshu) 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

• [ ] 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

• [x] 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).
• [x] 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

• [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?
• [ ] 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?

[whedon]

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

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[whedon]

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

OK DOIs

- 10.1002/jcc.23234 is OK
- 10.1021/ic900992r is OK
- 10.1039/B902745A is OK
- 10.1007/128_2015_645 is OK
- 10.1016/j.ccr.2008.05.014 is OK
- 10.1021/ic502651w is OK
- 10.1016/j.cpc.2010.09.007 is OK
- 10.1039/D0SE00701C is OK
- 10.1039/D0DT01404D is OK
- 10.1002/chem.201405679 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[mturiansky]

@dpsanders a few quick questions: with regards to the "software paper" section, how strict is JOSS? Does there need to be an explicit section labeled "summary" or "state of the field". I feel that overall the paper covers these two topics, but not directly in their own section.

How about with writing quality? The paper gets its point across, but there are grammatical errors (run-on sentences, missing commas) that could be addressed.

I would say at this point that I have completed my review. I have opened several issues, and I would recommend major revisions. There is no installation instructions, so without major effort on my part, I cannot compile, run, or verify the output of the code. Also, there are no unit tests, which will likely require a not-insignificant effort to develop.

[mfherbst]

@dpsanders I am now also done with my review and would recommend major revisions. I opened up various issues with respect to my points of critique or added some comments to the earlier ones of @mturiansky.

Similar to @mturiansky I wonder a little about the Software paper section. I found the summary and statement of need addressed
to a satisfactory point, albeit not in particularly labelled sections. In contrast I am not so sure about the description of the state of the art. While I am not an expert in this particular subfield of quantum chemistry, it seems to me the authors solve a common enough problem, such that it could be worth expanding on the relationship of their code compared to other solutions in the field. Since JOSS is more centred around the code rather than the scientific methods, I am not sure how strict JOSS is in this respect, though.

Another aspect is the quality of the code itself. From the snippets I read the code makes use of some features that might make it difficult to maintain in the long run. Despite clearly involving some effort I think the code at its present stage could benefit a lot from taking the time to come up with a better structure, such that e.g. code duplication or global variables are avoided. This would not only make it more accessible for others, but also easier to maintain and test.
How much is this a concern for JOSS? Is it about the functionality of the present stage of the code or is it also about the long-term maintainability and the value a project adds to the open-source community?

[whedon]

:wave: @mturiansky, please update us on how your review is going.

[whedon]

:wave: @mfherbst, please update us on how your review is going.

[dpsanders]

👋 Hi @mturiansky and @mfherbst: Many thanks for your comments and sorry for the delay in getting to them (and for the automated reminders!). I hope to get to look through them carefully today or tomorrow.