[REVIEW]: TLViz: Visualising and analysing tensor decomposition models with Python

[editorialbot]

Submitting author: @MarieRoald (Marie Roald)
Repository: https://github.com/tensorly/viz
Branch with paper.md (empty if default branch): paper
Version: v0.1.6
Editor: @faroit
Reviewers: @sara-02, @yiitozer
Archive: 10.5281/zenodo.7274925

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/43044545885a3e47b35c6775530a67c0"><img src="https://joss.theoj.org/papers/43044545885a3e47b35c6775530a67c0/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/43044545885a3e47b35c6775530a67c0/status.svg)](https://joss.theoj.org/papers/43044545885a3e47b35c6775530a67c0)

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

@sara-02 & @yiitozer, 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 @faroit 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 @yiitozer

📝 Checklist for @sara-02

[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=0.11 s (597.5 files/s, 125159.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          36           2009           3530           4488
SVG                              3              0             53           2572
TeX                              2             34              0            340
reStructuredText                16            132            128            193
YAML                             4             15             10            132
Markdown                         1             24              0             81
DOS Batch                        1              8              1             27
TOML                             1              5              0             13
INI                              1              1              0             10
make                             1              4              6             10
-------------------------------------------------------------------------------
SUM:                            66           2232           3728           7866
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1198

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.1007/978-1-84800-046-9_8 is OK
- 10.1137/07070111X is OK
- 10.1016/S0169-7439(97)00032-4 is OK
- 10.1016/j.neuroimage.2004.02.026 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1016/S0169-7439(00)00071-X is OK
- 10.21105/joss.03021 is OK
- 10.5334/jors.148 is OK
- 10.48550/arXiv.2111.15662 is OK

MISSING DOIs

- Errored finding suggestions for "TensorLy: Tensor Learning in Python", please try later

INVALID DOIs

- None

[faroit]

👏 @MarieRoald @@sara-02 @yiitozer - this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread contains links to the JOSS reviewer guidelines.

The JOSS review is different from other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. The reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews/issues/4754 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@faroit) if you have any questions/concerns.

[yiitozer]

Review checklist for @yiitozer

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/tensorly/viz?
• 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 (@MarieRoald) 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?

[sara-02]

Review checklist for @sara-02

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/tensorly/viz?
• 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 (@MarieRoald) 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?

[faroit]

@sara-02 @yiitozer can you update us on the status on your reviews?

We aim for reviews to be completed within about 2-4 weeks (we are one week overdue here). Please let me know if any of you require some more time or help with your review.

[yiitozer]

@faroit, sorry I have been quite busy in the last weeks. I can finish my review until next Wednesday. Would this be OK?

[faroit]

@editorialbot remind @yiitozer in one weeks

[editorialbot]

Reminder set for @yiitozer in one weeks

[faroit]

@sara-02 can you update us on the status on your review?

[sara-02]

Sure will update it by tomorrow, sorry for the delay

[editorialbot]

👋 @yiitozer, please update us on how your review is going (this is an automated reminder).

[yiitozer]

@faroit I am done with my review: I recommend the toolbox / paper for publication!

[MarieRoald]

@sara-02: Thank you so much for your comments! For the paper, I have updated the text to have capitalization and a full stop for each list element.

[sara-02]

Since the PRs related to my issue have already been raised by the team, I think @faroit this is ready for publication. Good to go from my side.

[faroit]

@sara-02 @yiitozer thanks a lot for your excellent reviews.

[faroit]

@editorialbot generate pdf

[editorialbot]

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

[faroit]

The submission looks good now and we can move forward 👏 I just did check the paper again for grammar and spellings and created a minor pull request that you can merge in if you like.

@MarieRoald when the paper is ready, please then please make a new release of the main repo that includes all of the changes that have resulted from the review. Please report the version number here.

Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive. For the archive version, please make sure that:

• The title of the archive is the same as the JOSS paper title
• The authors of the archive are the same as the JOSS paper authors

[MarieRoald]

Great! Thanks @faroit! We have created a new release (v0.1.6) and DOI: 10.5281/zenodo.7274925

[faroit]

@editorialbot set v0.1.6 as version

[editorialbot]

Done! version is now v0.1.6

[faroit]

@editorialbot set 10.5281/zenodo.7274925 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7274925

[faroit]

@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

- 10.1007/978-1-84800-046-9_8 is OK
- 10.1137/07070111X is OK
- 10.1016/S0169-7439(97)00032-4 is OK
- 10.1016/j.neuroimage.2004.02.026 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1016/S0169-7439(00)00071-X is OK
- 10.21105/joss.03021 is OK
- 10.5334/jors.148 is OK
- 10.48550/arXiv.2111.15662 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/dsais-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#3680, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[faroit]

@openjournals/dsais-eics is there an estimate for when the paper can be checked and published?

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet 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.04754 joss-papers#3755
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04754
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...

[arfon]

Hi all, apologies for the delay getting to this paper!

@sara-02, @yiitozer – many thanks for your reviews here and to @faroit for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@MarieRoald – your paper is now accepted and published in JOSS ⚡🚀💥

[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.04754/status.svg)](https://doi.org/10.21105/joss.04754)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04754">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04754/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04754/status.svg
   :target: https://doi.org/10.21105/joss.04754

This is how it will look in your documentation:

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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:

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[MarieRoald]

🎉 Thank you to @faroit for editing, and thanks a lot to @yiitozer and @sara-02! Your helpful comments improved the paper and code 😃✨

[faroit]

@MarieRoald congratulations to the accepted paper 🥳. I am very happy how this review process turned out.

Thanks to @yiitozer and @sara-02 for your excellent and timely reviews!