[REVIEW]: TopologicalNumbers.jl: A Julia package for topological number computation

[editorialbot]

Submitting author: !--author-handle-->@KskAdch<!--end-author-handle-- (Keisuke Adachi) Repository: https://github.com/KskAdch/TopologicalNumbers.jl Branch with paper.md (empty if default branch): Version: v1.7.5 Editor: !--editor-->@olexandr-konovalov<!--end-editor-- Reviewers: @lf28, @michiexile Archive: Pending

Status

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Markdown: [![status](https://joss.theoj.org/papers/d5363597cf38cb06360482fbabb6d350/status.svg)](https://joss.theoj.org/papers/d5363597cf38cb06360482fbabb6d350)

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

@lf28 & @michiexile, 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 @olexandr-konovalov 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 @lf28

📝 Checklist for @michiexile

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (969.8 files/s, 191458.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           22           1267           1666           4419
Markdown                        17            523              0           1332
TeX                              2             16              0            264
Jupyter Notebook                 1              0            997            149
SVG                              3             14              0            146
YAML                             5              1             29            143
TOML                             6             12              1             76
-------------------------------------------------------------------------------
SUM:                            56           1833           2693           6529
-------------------------------------------------------------------------------

Commit count by author:

   316  Keisuke Adachi
   301  Minoru Kanega
     4  phjmsycc
     1  CompatHelper Julia

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 757

✅ The paper includes a Statement of need section

[editorialbot]

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

OK DOIs

- 10.1143/JPSJ.74.1674 is OK
- 10.48550/arXiv.2305.05615 is OK
- 10.1103/PhysRevB.96.235152 is OK
- 10.1103/PhysRevLett.114.206401 is OK
- 10.7566/JPSJ.87.041002 is OK
- 10.1103/PhysRevB.84.075129 is OK
- 10.1143/JPSJ.76.053702 is OK
- 10.1088/2058-9565/aae93b is OK
- 10.1145/2331130.2331138 is OK
- 10.1103/RevModPhys.82.3045 is OK
- 10.1103/RevModPhys.83.1057 is OK
- 10.1088/1367-2630/12/6/065010 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

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

[lf28]

Review checklist for @lf28

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/KskAdch/TopologicalNumbers.jl?
• [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 (@KskAdch) 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?
• [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?
• [x] 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?
• [x] 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?
• [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?

[michiexile]

Review checklist for @michiexile

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/KskAdch/TopologicalNumbers.jl?
• [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 (@KskAdch) 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?
• [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?
• [X] 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?
• [X] 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?
• [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?

[michiexile]

In my opinion, the two missing check-marks in my checklist are not blocking acceptance of the paper. The authors do describe what the software is doing, well enough for anyone who knows the domain they are writing for, and they do describe the lack of Julia packages for doing the same computations (however, no discussion of packages for other platforms).

[olexandr-konovalov]

Thank you @michiexile! Perhaps let's wait till @lf28 completes his review, to decide if this is acceptable, or some improvements would still be possible and make sense.

[olexandr-konovalov]

Hi @lf28, how are you getting on with this review? Do you think you will be able to complete it soon? It would be nice to see some checkboxes marked, to get an idea of the stage where you are in with your review.

[lf28]

Hi @olexandr-konovalov, apologies for the delay. I have now finished the review. I think I agree with the other reviewer's comments.

[olexandr-konovalov]

Thank you for your reviews @michiexile and @lf28 - also apologise to you and @KskAdch for the delay from my side in responding to you. I am glad that you agree in your opinions, and also that except the two remaining checkboxes, everything else looks good. But to accept the paper, we need also to be able to add those two ticks for the summary and the state of the field as well. As @michiexile says

The authors do describe what the software is doing, well enough for anyone who knows the domain they are writing for, and they do describe the lack of Julia packages for doing the same computations (however, no discussion of packages for other platforms).

but we indeed need a "clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience" and also "how this software compares to other commonly-used packages".

Can perhaps something still be done here, @KskAdch?