[REVIEW]: ClusterValidityIndices.jl: Batch and Incremental Metrics for Unsupervised Learning

[whedon]

Submitting author: @AP6YC (Sasha Petrenko)
Repository: https://github.com/AP6YC/ClusterValidityIndices.jl
Branch with paper.md (empty if default branch):
Version: v0.6.3
Editor: @adi3
Reviewers: @rMassimiliano, @malmaud
Archive: 10.5281/zenodo.7332045

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/49689a7f5baf94f5d403a18a73b2d99e"><img src="https://joss.theoj.org/papers/49689a7f5baf94f5d403a18a73b2d99e/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/49689a7f5baf94f5d403a18a73b2d99e/status.svg)](https://joss.theoj.org/papers/49689a7f5baf94f5d403a18a73b2d99e)

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

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

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @adi3 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 ✨

Review checklist for @rMassimiliano

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 (@AP6YC) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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?

Review checklist for @malmaud

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 (@AP6YC) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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?

[whedon]

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

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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

@whedon commands

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

@whedon generate pdf

[whedon]

Wordcount for paper.md is 484

[whedon]

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

OK DOIs

- 10.1109/ACCESS.2020.2969849 is OK
- 10.1016/j.neunet.2012.09.017 is OK
- 10.1037/0033-295X.87.1.1 is OK
- 10.1016/j.neunet.2019.09.012 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.05 s (699.3 files/s, 67480.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           22            295            321           1881
Markdown                         7            224              0            637
YAML                             6              9             46            167
TeX                              1              4              0             54
TOML                             2              4              0             25
-------------------------------------------------------------------------------
SUM:                            38            536            367           2764
-------------------------------------------------------------------------------


Statistical information for the repository '4114c6579085a37680f54bd4' was
gathered on 2021/07/23.
No commited files with the specified extensions were found.

[whedon]

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

[adi3]

👋🏼 @AP6YC this is the review thread for the paper. All of our communications will happen here from now on.

👋🏼 @rMassimiliano @malmaudBoth - you both have checklists at the top of this thread with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

Here is a little more context for first-time reviewers :) - The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #3527 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 Whedon (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 (@adi3) if you have any questions/concerns. Thank you for all your help!!

[whedon]

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

[whedon]

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

[adi3]

@malmaud @rMassimiliano - seems you are yet to accept the invite to be part of the JOSS org which will allow you to proceed through your checklist. Could you please let me know if I can help you sort out any trouble you're facing? Thanks!

[malmaud]

Sorry, the invitation link has expired. Can you resend it?

[rMassimiliano]

Hi @adi3, my invitation expired too. Sorry for the inconvenience.

[rMassimiliano]

Hi @adi3 I started the review process and I will follow up with specific comments in the next days. However I still can't accept the review invitation and complete the check-list. Can you help me with that?

[adi3]

@rMassimiliano @malmaud - let me try re-adding both of you as reviewer, see if that sends you a renewed link. Can you please confirm? If not, then I'll escalate the issue to the EiC

[adi3]

@whedon add @malmaud as reviewer

[whedon]

OK, @malmaud is now a reviewer

[adi3]

@whedon add @rMassimiliano as reviewer

[adi3]

@AP6YC well done, and thanks for your effort!
@rMassimiliano - do the latest releases by the author satisfy your conditions? Would be awesome if you could update your reviewer checklist accordingly!

[rMassimiliano]

@AP6YC good job! I think the updated documentation and examples will be beneficial for new users.

@adi3 my checklist is now complete. I find Release 0.6.0 satisfactory.

[adi3]

@rMassimiliano - thank you for your patience and thoroughness with this review!

@AP6YC - we're almost there, congrats! As with your other submission, please make a tagged release of the project and archive it. Then report the version number and archive DOI here. Once I have that, I will send this for publication.

[adi3]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1145/3449639.3459341 is OK
- 10.1109/ACCESS.2020.2969849 is OK
- 10.1016/j.neunet.2012.09.017 is OK
- 10.1037/0033-295X.87.1.1 is OK
- 10.1016/j.neunet.2019.09.012 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.patcog.2012.07.021 is INVALID because of 'https://doi.org/' prefix

[adi3]

@AP6YC also please look into and fix that invalid DOI shown above in your references

[AP6YC]

@adi3 I fixed the DOI issue and have created an archived release; checking the DOI now:

[AP6YC]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/j.patcog.2012.07.021 is OK
- 10.1145/3449639.3459341 is OK
- 10.1109/ACCESS.2020.2969849 is OK
- 10.1016/j.neunet.2012.09.017 is OK
- 10.1037/0033-295X.87.1.1 is OK
- 10.1016/j.neunet.2019.09.012 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[AP6YC]

@adi3 Below is the information that you requested:

• DOI: 10.5281/zenodo.7327501
• Archive link: https://zenodo.org/record/7327501
• Version: v0.6.2

EDIT: I have recently identified an important bug that I would like to patch in a hotfix before submitting. A new version, DOI, and archive link is on the way.

EDIT 2: Here is the updated information with the aforementioned fix:

• DOI: 10.5281/zenodo.7332045
• Archive link: https://zenodo.org/record/7332045
• Version: v0.6.3

[adi3]

@editorialbot check references

[adi3]

@editorialbot set <10.5281/zenodo.7332045> as archive

[editorialbot]

Done! Archive is now <10.5281/zenodo.7332045>

[editorialbot]

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

OK DOIs

- 10.1016/j.patcog.2012.07.021 is OK
- 10.1145/3449639.3459341 is OK
- 10.1109/ACCESS.2020.2969849 is OK
- 10.1016/j.neunet.2012.09.017 is OK
- 10.1037/0033-295X.87.1.1 is OK
- 10.1016/j.neunet.2019.09.012 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[adi3]

@editorialbot set v0.6.3 as version

[editorialbot]

Done! version is now v0.6.3

[adi3]

@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

- 10.1016/j.patcog.2012.07.021 is OK
- 10.1145/3449639.3459341 is OK
- 10.1109/ACCESS.2020.2969849 is OK
- 10.1016/j.neunet.2012.09.017 is OK
- 10.1037/0033-295X.87.1.1 is OK
- 10.1016/j.neunet.2019.09.012 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#3738, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[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.03527 joss-papers#3756
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03527
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]

@rMassimiliano, @malmaud – many thanks for your reviews here and to @adi3 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 ✨

@AP6YC – 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.03527/status.svg)](https://doi.org/10.21105/joss.03527)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03527">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03527/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03527/status.svg
   :target: https://doi.org/10.21105/joss.03527

This is how it will look in your documentation:

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