[REVIEW]: lys: interactive multi-dimensional data analysis and visualization platform

[editorialbot]

Submitting author: @lys-devel (Asuka Nakamura)
Repository: https://github.com/lys-devel/lys
Branch with paper.md (empty if default branch): review
Version: v0.3.3_zenodo
Editor: @emdupre
Reviewers: @kuadrat, @ziatdinovmax, @pr4deepr
Archive: 10.5281/zenodo.10241638

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/f6eb85c0c03099f7ec91db24ffcef3e1"><img src="https://joss.theoj.org/papers/f6eb85c0c03099f7ec91db24ffcef3e1/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/f6eb85c0c03099f7ec91db24ffcef3e1/status.svg)](https://joss.theoj.org/papers/f6eb85c0c03099f7ec91db24ffcef3e1)

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

@kuadrat & @ziatdinovmax & @pr4deepr, 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 @emdupre 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 @kuadrat

📝 Checklist for @pr4deepr

📝 Checklist for @ziatdinovmax

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.52 s (862.9 files/s, 243710.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                           200           9160            600          57612
Python                         154           5336           4225          18475
JavaScript                      16           4511           4394          16122
SVG                              1              0              0           2671
reStructuredText                67            764            646           1000
CSS                              4            187             35            756
Markdown                         6            167              0            650
TeX                              1             16              0            204
DOS Batch                        1             23              1            166
make                             1             24              5            124
Bourne Shell                     1              8              3             34
YAML                             1              1              4             21
-------------------------------------------------------------------------------
SUM:                           453          20197           9913          97835
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.25080/majora-7b98e3ed-013 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1109/mcse.2011.35 is OK
- 10.7567/APEX.11.092601 is OK
- 10.1021/acs.nanolett.0c01006 is OK
- 10.1063/4.0000059 is OK
- 10.1021/acs.nanolett.2c03938 is OK
- 10.1126/sciadv.abg1322 is OK
- 10.1063/5.0106517 is OK
- 10.1093/jmicro/dfad021 is OK
- 10.1039/D2FD00062H is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 1294

[editorialbot]

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

[emdupre]

👋 Hi @kuadrat, @ziatdinovmax, and @pr4deepr, and thank you again for agreeing to review this submission for lys !

The review will take place in this issue, and you can generate your individual reviewer checklists by asking editorialbot directly with @editorialbot generate my checklist.

In working through the checklist, you're likely to have specific feedback on lys. Whenever possible, please open relevant issues on the linked software repository (and cross-link them with this issue) rather than discussing them here. This helps to make sure that feedback is translated into actionable items to improve the software !

If you aren't sure how to get started, please see the Reviewing for JOSS guide -- and, of course, feel free to ping me with any questions !

[pr4deepr]

Review checklist for @pr4deepr

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/lys-devel/lys?
• 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 (@lys-devel) 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?

[pr4deepr]

Regarding "Contribution and authorship", I'm not sure how to judge this as there seems to be multiple accounts that have contributed to the code and I cannot ascertain who they belong to. Commit history.

There are multiple acccounts: @LabviewShare, @lys-devel which is the current account.

@emdupre, how do you suggest I proceed?
@lys-devel

[lys-devel]

@pr4deepr , @emdupre
I'm sorry for confusing commit history. "LabviewShare" is my private account.
Since lys have been private repository in our lab, I used it until very recently.
If it is needed, I will comment here from "LabviewShare" account for verification.

[pr4deepr]

Thanks @lys-devel . Perhaps that should be enough for now, unless anyone has other concerns..

[kuadrat]

Review checklist for @kuadrat

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/lys-devel/lys?
• 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 (@lys-devel) 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?

[emdupre]

👋 Hi @ziatdinovmax, I noticed that you had not yet generated your reviewer checklist, so I wanted to check-in and make sure you weren't encountering any issues in doing so. Please let me know, and thank you again for agreeing to review lys !

[kuadrat]

@editorialbot generate pdf

[editorialbot]

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

[lys-devel]

Thank you, @emdupre. I have merged the PR. I'm looking forward to the publication!

[emdupre]

Thank you for your engagement throughout the review process, @lys-devel ! I'm now happy to recommend lys to the EiC team for publication in JOSS 🎉

Thank you, too, to @pr4deepr, @kuadrat, and @ziatdinovmax for your reviews and input throughout this process ! JOSS runs thanks to volunteers like you, so thank you 💐

[emdupre]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.25080/majora-7b98e3ed-013 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1109/mcse.2011.35 is OK
- 10.7567/APEX.11.092601 is OK
- 10.1021/acs.nanolett.0c01006 is OK
- 10.1063/4.0000059 is OK
- 10.1021/acs.nanolett.2c03938 is OK
- 10.1126/sciadv.abg1322 is OK
- 10.1063/5.0106517 is OK
- 10.1093/jmicro/dfad021 is OK
- 10.1039/D2FD00062H is OK
- 10.21105/joss.02969 is OK
- 10.1017/S1431927622006328 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/csism-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#4838, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@lys-devel - I'm the track editor, working on the final steps for accepting and publishing your submission. I've suggested some changes in lys-devel/lys#22. Please merge this, or let me know what you disagree with. Also, I note your use of RRIDs, in the statement of need section. JOSS doesn't typically use RRIDs, and while I don't mind you using them, it would be useful if you would also use more widely-understood citations. Can you replace or add references for these items?

[emdupre]

Hi @danielskatz, thanks for the quick follow-up !

Just to flag that I had requested RRIDs for IGOR Pro and MATLAB as the previous citations had only listed the associated companies. So, this was on me, not @lys-devel. I traditionally find RRIDs clearer in this case, but will defer to you as the expert on these citations !

[danielskatz]

Let's use both then, as I don't think many people outside of the life sciences have ever heard of RRIDs, let alone know what to do with them. (https://f1000research.com/articles/9-1257/v2 might be useful in terms of guidance about how to cite software that's not clear otherwise)

[emdupre]

Thanks, @danielskatz !

@lys-devel , just to make the updates a bit easier, here is the relevant MATLAB citation in bibtex :

@software{MATLAB,
year = {2023},
author = {The MathWorks Inc.},
title = {MATLAB (R2023b)},
publisher = {The MathWorks Inc.},
address = {Natick, Massachusetts, United States},
url = {https://www.mathworks.com}
}

I've suggested citing the most recent version, but please amend if necessary.

For IGOR Pro, it seems the field-accepted standard is (WaveMetrics, Inc., Lake Oswego, OR, USA).

[lys-devel]

Hi @emdupre, @danielskatz!

Thank you for your kind suggestions. I have merged the PR #22 and have added citation for MATLAB and IGOR Pro.
Could you confirm these are suitable for JOSS?

[danielskatz]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.25080/majora-7b98e3ed-013 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1109/mcse.2011.35 is OK
- 10.7567/APEX.11.092601 is OK
- 10.1021/acs.nanolett.0c01006 is OK
- 10.1063/4.0000059 is OK
- 10.1021/acs.nanolett.2c03938 is OK
- 10.1126/sciadv.abg1322 is OK
- 10.1063/5.0106517 is OK
- 10.1093/jmicro/dfad021 is OK
- 10.1039/D2FD00062H is OK
- 10.21105/joss.02969 is OK
- 10.1017/S1431927622006328 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[danielskatz]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.25080/majora-7b98e3ed-013 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1109/mcse.2011.35 is OK
- 10.7567/APEX.11.092601 is OK
- 10.1021/acs.nanolett.0c01006 is OK
- 10.1063/4.0000059 is OK
- 10.1021/acs.nanolett.2c03938 is OK
- 10.1126/sciadv.abg1322 is OK
- 10.1063/5.0106517 is OK
- 10.1093/jmicro/dfad021 is OK
- 10.1039/D2FD00062H is OK
- 10.21105/joss.02969 is OK
- 10.1017/S1431927622006328 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/csism-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#4839, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

This looks good to me - I'm going to finish the processing now.

[danielskatz]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Nakamura
  given-names: Asuka
  orcid: "https://orcid.org/0000-0002-3010-9475"
doi: 10.5281/zenodo.10241638
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Nakamura
    given-names: Asuka
    orcid: "https://orcid.org/0000-0002-3010-9475"
  date-published: 2023-12-14
  doi: 10.21105/joss.05869
  issn: 2475-9066
  issue: 92
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5869
  title: "lys: interactive multi-dimensional data analysis and
    visualization platform"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05869"
  volume: 8
title: "lys: interactive multi-dimensional data analysis and
  visualization platform"

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]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05869 joss-papers#4840
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05869
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

Congratulations to @lys-devel (Asuka Nakamura) on your publication!!

And thanks to @kuadrat, @ziatdinovmax, and @pr4deepr for reviewing, and to @emdupre for editing!
JOSS depends on volunteers and we couldn't do this without you

[editorialbot]

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

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

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05869/status.svg)](https://doi.org/10.21105/joss.05869)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05869">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05869/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05869/status.svg
   :target: https://doi.org/10.21105/joss.05869

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[lys-devel]

Thank you again for your editorial effort, @danielskatz , @emdupre.
I also really appreciate fruitful comments from @pr4deepr, @kuadrat, and @ziatdinovmax! I will deal with remaining issues in the repository as soon as possible.