[REVIEW]: gmr: Gaussian Mixture Regression

[whedon]

Submitting author: @AlexanderFabisch (Alexander Fabisch)
Repository: https://github.com/AlexanderFabisch/gmr
Version: v1.6.1
Editor: @mikldk
Reviewers: @inakleinbottle, @soodoku
Archive: 10.5281/zenodo.4449631

⚠️ JOSS reduced service mode ⚠️

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Status

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Markdown: [![status](https://joss.theoj.org/papers/6068dbe557a76dd12fb89137bb28293c/status.svg)](https://joss.theoj.org/papers/6068dbe557a76dd12fb89137bb28293c)

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

@soodoku & @inakleinbottle, 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 @mikldk 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 @soodoku

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 (@AlexanderFabisch) 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: 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?
• 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: 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)?
• 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 @inakleinbottle

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 (@AlexanderFabisch) 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: 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?
• 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: 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)?
• 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. @vs74, @inakleinbottle 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

[mikldk]

@whedon generate pdf

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.17 s (141.8 files/s, 18649.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          19            539            677           1522
Markdown                         1             23              0            128
TeX                              1              5              0             61
reStructuredText                 1             57             45             51
SVG                              1              0              0             34
YAML                             1              0              0             14
-------------------------------------------------------------------------------
SUM:                            24            624            722           1810
-------------------------------------------------------------------------------


Statistical information for the repository '8cd147d612e0c232f7c8054f' was
gathered on 2021/02/22.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Alexander Fabisch              106          3381            642           99.48
Joao Felipe Santos               2            10             11            0.52

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Alexander Fabisch          2730           80.7         36.9                5.60
Joao Felipe Santos            8           80.0         69.1                0.00

[whedon]

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

OK DOIs

- 10.1109/TSMCB.2006.886952 is OK
- 10.1016/j.neunet.2015.05.005 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[whedon]

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

[mikldk]

@vs74, @inakleinbottle: Thanks for agreeing to review. Please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If possible create issues (and cross-reference) in the submission's repository to avoid too specific discussions in this review thread.

If you have any questions or concerns please let me know.

[inakleinbottle]

@mikldk The invitation to collaborate on the repository got lost in my inbox amongst many (many) notifications. I only just found it and it has expired. Can this be reissued?

[danielskatz]

@whedon re-invite @inakleinbottle as reviewer

[whedon]

OK, the reviewer has been re-invited.

@inakleinbottle please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[mikldk]

@vs74, @inakleinbottle, can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

[inakleinbottle]

I've been busy this week, but I have managed to have a look at the paper and the package. Hoping to give a review this weekend.

[vasudev-sharma]

I've some comments to make and will open an issue in the target repo and reference them here. I'll make these comments over the weekends.

[inakleinbottle]

I submitted a new issue for my review: AlexanderFabisch/gmr#25

[whedon]

👋 @vs74, please update us on how your review is going (this is an automated reminder).

[whedon]

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

[AlexanderFabisch]

@whedon generate pdf

[whedon]

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

[inakleinbottle]

I am now satisfied that the criteria have been met.

[mikldk]

@vs74, can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

[mikldk]

@vs74, can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

[mikldk]

@vs74, can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1109/TSMCB.2006.886952 is OK
- 10.1016/j.neunet.2015.05.005 is OK
- 10.1007/978-3-540-30301-5_60 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2355

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2355, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[mikldk]

@whedon generate pdf

[whedon]

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

[Kevin-Mattheus-Moerman]

@AlexanderFabisch I'll be helping to get your paper ready for publication in JOSS. Below are some remaining issues.

• Please amend the Zenodo archive meta-data to match that of the paper. In particular the author list is not the same.
• Can you confirm sklearn is correct in ..while sklearn has..., or should this be skikit-learn. If it is a different package can you cite it?
• Both multimodal and multi-modal occur in the text, please choose one and correct throughout to be consistent.

[AlexanderFabisch]

@Kevin-Mattheus-Moerman Thanks. I addressed these points:

* [ ]  Please amend the Zenodo archive meta-data to match that of the paper. In particular the author list is not the same.

OK, I give up, for the corresponding Zenodo release the author lists are the same now.

* [ ]   Can you confirm `sklearn` is correct in `..while sklearn has...`, or should this be skikit-learn. If it is a different package can you cite it?

I replaced sklearn by scikit-learn.

* [ ]  Both `multimodal` and `multi-modal` occur in the text, please choose one and correct throughout to be consistent.

I use "multimodal" consistently now.

Should I make a new Zenodo release with these additional changes?

[AlexanderFabisch]

@whedon generate pdf

[whedon]

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

[Kevin-Mattheus-Moerman]

@whedon accept

[whedon]

To recommend a paper to be accepted use @whedon recommend-accept

[Kevin-Mattheus-Moerman]

@AlexanderFabisch apologies, one more change. Can you add a city and country to your affiliation?

There is no need to update the Zenodo archive.

[AlexanderFabisch]

@whedon generate pdf

[whedon]

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

[AlexanderFabisch]

@AlexanderFabisch apologies, one more change. Can you add a city and country to your affiliation?

Yes, I added both to the name of my affiliation if that is correct.

[Kevin-Mattheus-Moerman]

@whedon generate pdf

[whedon]

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

[Kevin-Mattheus-Moerman]

@AlexanderFabisch looks like we are all set. One recommendation I have is to also add your ORCID profile to the author listed on Zenodo. However we can proceed here with acceptance. Thanks for making those changes.

[Kevin-Mattheus-Moerman]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.03054 joss-papers#2363
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03054
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...

[Kevin-Mattheus-Moerman]

@AlexanderFabisch congratulations on your published paper!

@inakleinbottle, @soodoku thanks for reviewing this work! Also thank you @mikldk for editing this work!

[whedon]

🎉🎉🎉 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.03054/status.svg)](https://doi.org/10.21105/joss.03054)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03054">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03054/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03054/status.svg
   :target: https://doi.org/10.21105/joss.03054

This is how it will look in your documentation:

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[AlexanderFabisch]

One recommendation I have is to also add your ORCID profile to the author listed on Zenodo.

The ORCID profile already should have been linked on Zenodo.

@AlexanderFabisch congratulations on your published paper!

Thanks!

Also thanks to you @inakleinbottle, @soodoku, and @mikldk for reviewing and editing!