[REVIEW]: Multi-view-AE: A Python package for multi-view autoencoder models

[editorialbot]

Submitting author: @alawryaguila (Ana Lawry Aguila)
Repository: https://github.com/alawryaguila/multi-view-AE
Branch with paper.md (empty if default branch): joss
Version: v1.0.0
Editor: @arfon
Reviewers: @abhi-glitchhg, @Saran-nns
Archive: 10.5281/zenodo.7871099

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/72168d9c6ae651a4ac6a779bb17ca3c4"><img src="https://joss.theoj.org/papers/72168d9c6ae651a4ac6a779bb17ca3c4/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/72168d9c6ae651a4ac6a779bb17ca3c4/status.svg)](https://joss.theoj.org/papers/72168d9c6ae651a4ac6a779bb17ca3c4)

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

@abhi-glitchhg & @Saran-nns, 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 @arfon 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 @Saran-nns

📝 Checklist for @abhi-glitchhg

[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:

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.09 s (921.5 files/s, 77814.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          33            824            951           3062
YAML                            35            233             64            675
TeX                              1             28              0            227
reStructuredText                 8            221            304            187
Markdown                         3             32              0            115
TOML                             1              4              0             27
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            83           1354           1327           4328
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1551

[editorialbot]

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

OK DOIs

- 10.1016/B978-0-12-815480-9.00013-X is OK
- 10.1016/S0003-2670(00)85460-4 is OK
- 10.1109/ACCESS.2020.2992063 is OK
- 10.1109/ACCESS.2020.3048309 is OK
- 10.1016/j.knosys.2019.01.017 is OK
- 10.1080/01691864.2022.2035253 is OK
- 10.48550/ARXIV.1911.03393 is OK
- 10.48550/ARXIV.1611.01891 is OK
- 10.1080/09544120050135443 is OK
- 10.1016/j.neuroimage.2010.07.034 is OK
- 10.1016/j.crmeth.2021.100071 is OK
- 10.1007/s00034-020-01522-7 is OK
- 10.1016/j.crmeth.2021.100071 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[arfon]

@abhi-glitchhg, @Saran-nns – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

@editorialbot generate my checklist

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.

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 https://github.com/openjournals/joss-reviews/issues/5093 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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[Saran-nns]

Review checklist for @Saran-nns

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/alawryaguila/multi-view-AE?
• 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 (@alawryaguila) 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?

[arfon]

Great to see your review up and running here @Saran-nns. @abhi-glitchhg – anything I can do to help you get started here?

[abhi-glitchhg]

Review checklist for @abhi-glitchhg

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/alawryaguila/multi-view-AE?
• 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 (@alawryaguila) 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?

[Saran-nns]

@editorialbot generate pdf

[editorialbot]

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

[Saran-nns]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/B978-0-12-815480-9.00013-X is OK
- 10.1016/S0003-2670(00)85460-4 is OK
- 10.1109/ACCESS.2020.2992063 is OK
- 10.1109/ACCESS.2020.3048309 is OK
- 10.1016/j.knosys.2019.01.017 is OK
- 10.1080/01691864.2022.2035253 is OK
- 10.48550/ARXIV.1911.03393 is OK
- 10.48550/ARXIV.1611.01891 is OK
- 10.1080/09544120050135443 is OK
- 10.1016/j.neuroimage.2010.07.034 is OK
- 10.1016/j.crmeth.2021.100071 is OK
- 10.1007/s00034-020-01522-7 is OK
- 10.1016/j.crmeth.2021.100071 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[Saran-nns]

@alawryaguila awesome work. thanks for addressing the issues and for answering my concerns @arfon my checklist is complete and i am happy to recommend accept.

[alawryaguila]

@Saran-nns thank you for taking the time to review our library and for your helpful comments!

[arfon]

👋 @abhi-glitchhg – how are you getting on with your review?

[arfon]

A quick update here – I just emailed @abhi-glitchhg to see when they might be able to complete their review by.

[alawryaguila]

A quick update here – I just emailed @abhi-glitchhg to see when they might be able to complete their review by.

Hi @arfon, I was just wondering if there was any update on this? Please let me know if there's anything you need from our end!

[arfon]

Sorry for the delays here @alawryaguila. I've just pinged @abhi-glitchhg again to ask for an ETA from them on completing their review. If they don't get back to us in the next week we will need to find a different reviewer.

[alawryaguila]

Sorry for the delays here @alawryaguila. I've just pinged @abhi-glitchhg again to ask for an ETA from them on completing their review. If they don't get back to us in the next week we will need to find a different reviewer.

No worries, thank you for the update @arfon.

[arfon]

I just heard back from @abhi-glitchhg via email that they should be able to pick up their review again later this week 🎉

[alawryaguila]

I just heard back from @abhi-glitchhg via email that they should be able to pick up their review again later this week 🎉

Great news! 🎉

[abhi-glitchhg]

Hey @alawryaguila , Sorry for the delay.

The installation instructions are missing from the website. Having an installation guide page in the documentation website would be more user-friendly. Thoughts?

Also how about adding the project to Pypi (This is not a blocker, just a suggestion)

[alawryaguila]

Hey @alawryaguila , Sorry for the delay.

The installation instructions are missing from the website. Having an installation guide page in the documentation website would be more user-friendly. Thoughts?

Also how about adding the project to Pypi (This is not a blocker, just a suggestion)

Thank you for your comments @abhi-glitchhg, we have now added the installation instructions to the readthedocs link. Great suggestion about adding the project to Pypi. We had originally considered adding to Pypi prior to submission, so we will make sure to do this over the next few weeks.

[editorialbot]

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

OK DOIs

- 10.1016/B978-0-12-815480-9.00013-X is OK
- 10.1016/S0003-2670(00)85460-4 is OK
- 10.1109/ACCESS.2020.2992063 is OK
- 10.1109/ACCESS.2020.3048309 is OK
- 10.1016/j.knosys.2019.01.017 is OK
- 10.1080/01691864.2022.2035253 is OK
- 10.48550/ARXIV.1911.03393 is OK
- 10.48550/ARXIV.1611.01891 is OK
- 10.1080/09544120050135443 is OK
- 10.1016/j.neuroimage.2010.07.034 is OK
- 10.1016/j.crmeth.2021.100071 is OK
- 10.1007/s00034-020-01522-7 is OK
- 10.1016/j.crmeth.2021.100071 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

⚠️ Error preparing paper acceptance.

[arfon]

@alawryaguila – apologies for the delayed response here. Looks like there are some errors with the metadata – can you please merge this PR to fix? alawryaguila/multi-view-AE#35

[alawryaguila]

@alawryaguila – apologies for the delayed response here. Looks like there are some errors with the metadata – can you please merge this PR to fix? alawryaguila/multi-view-AE#35

Hi @arfon I have now merged, hopefully that fixes the issue :)

[arfon]

@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/B978-0-12-815480-9.00013-X is OK
- 10.1016/S0003-2670(00)85460-4 is OK
- 10.1109/ACCESS.2020.2992063 is OK
- 10.1109/ACCESS.2020.3048309 is OK
- 10.1016/j.knosys.2019.01.017 is OK
- 10.1080/01691864.2022.2035253 is OK
- 10.48550/ARXIV.1911.03393 is OK
- 10.48550/ARXIV.1611.01891 is OK
- 10.1080/09544120050135443 is OK
- 10.1016/j.neuroimage.2010.07.034 is OK
- 10.1016/j.crmeth.2021.100071 is OK
- 10.1007/s00034-020-01522-7 is OK
- 10.1016/j.crmeth.2021.100071 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

ID ref-Minoura2021 already defined

[arfon]

@alawryaguila – this also needs merging too please: alawryaguila/multi-view-AE#36

[arfon]

@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/B978-0-12-815480-9.00013-X is OK
- 10.1016/S0003-2670(00)85460-4 is OK
- 10.1109/ACCESS.2020.2992063 is OK
- 10.1109/ACCESS.2020.3048309 is OK
- 10.1016/j.knosys.2019.01.017 is OK
- 10.1080/01691864.2022.2035253 is OK
- 10.48550/ARXIV.1911.03393 is OK
- 10.48550/ARXIV.1611.01891 is OK
- 10.1080/09544120050135443 is OK
- 10.1016/j.neuroimage.2010.07.034 is OK
- 10.1016/j.crmeth.2021.100071 is OK
- 10.1007/s00034-020-01522-7 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#4236, 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]

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: Aguila
  given-names: Ana Lawry
  orcid: "https://orcid.org/0000-0003-0727-3274"
- family-names: Jayme
  given-names: Alejandra
- family-names: Montaña-Brown
  given-names: Nina
  orcid: "https://orcid.org/0000-0001-5685-971X"
- family-names: Heuveline
  given-names: Vincent
- family-names: Altmann
  given-names: Andre
  orcid: "https://orcid.org/0000-0002-9265-2393"
contact:
- family-names: Aguila
  given-names: Ana Lawry
  orcid: "https://orcid.org/0000-0003-0727-3274"
doi: 10.5281/zenodo.7871099
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Aguila
    given-names: Ana Lawry
    orcid: "https://orcid.org/0000-0003-0727-3274"
  - family-names: Jayme
    given-names: Alejandra
  - family-names: Montaña-Brown
    given-names: Nina
    orcid: "https://orcid.org/0000-0001-5685-971X"
  - family-names: Heuveline
    given-names: Vincent
  - family-names: Altmann
    given-names: Andre
    orcid: "https://orcid.org/0000-0002-9265-2393"
  date-published: 2023-05-16
  doi: 10.21105/joss.05093
  issn: 2475-9066
  issue: 85
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5093
  title: "Multi-view-AE: A Python package for multi-view autoencoder
    models"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05093"
  volume: 8
title: "Multi-view-AE: A Python package for multi-view autoencoder
  models"

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]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[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.05093 joss-papers#4237
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05093
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...

[Saran-nns]

congrats @alawryaguila and team

[alawryaguila]

congrats @alawryaguila and team

Thank you @Saran-nns !

[arfon]

@abhi-glitchhg, @Saran-nns – many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@alawryaguila – 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.05093/status.svg)](https://doi.org/10.21105/joss.05093)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05093">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05093/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05093/status.svg
   :target: https://doi.org/10.21105/joss.05093

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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[gkthiruvathukal]

Thank you, @arfon.