[REVIEW]: DeepOF: a Python package for supervised and unsupervised pattern recognition in mice motion tracking data

[editorialbot]

Submitting author: @lucasmiranda42 (Lucas Miranda)
Repository: https://github.com/mlfpm/deepof
Branch with paper.md (empty if default branch): JOSS_paper
Version: JOSS
Editor: @emdupre
Reviewers: @cellistigs, @edeno
Archive: 10.5281/zenodo.8013401

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/972bafaea89bbce5f0246d5160e84afc"><img src="https://joss.theoj.org/papers/972bafaea89bbce5f0246d5160e84afc/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/972bafaea89bbce5f0246d5160e84afc/status.svg)](https://joss.theoj.org/papers/972bafaea89bbce5f0246d5160e84afc)

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

@cellistigs & @edeno, 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 @edeno

📝 Checklist for @cellistigs

[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=0.44 s (194.1 files/s, 174470.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            18            813             72          18288
Python                          19           2481           2533          10112
JavaScript                      15           2435           2505           9215
SVG                              1              0              0           2671
Jupyter Notebook                 6              0          23518            916
CSS                              4            182             35            762
Markdown                         2             43              0            165
reStructuredText                12             55            106             90
TeX                              1              4              0             67
TOML                             1              4              0             61
YAML                             2             14              8             39
DOS Batch                        1              8              1             26
Dockerfile                       1              0              0             21
JSON                             1              0              0             11
Bourne Shell                     1              3              0             10
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            86           6046          28785          42463
-------------------------------------------------------------------------------


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/s41593-018-0209-y is OK
- 10.1016/j.neuron.2020.09.017 is OK
- 10.1038/s42003-022-04080-7 is OK
- 10.1101/2020.04.19.049452 is OK
- 10.1101/2022.06.23.497350 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 585

[editorialbot]

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

[emdupre]

👋 Hi @cellistigs and @edeno, and thank you again for agreeing to review this submission !

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 DeepOF. 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 !

[edeno]

Review checklist for @edeno

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/mlfpm/deepof?
• 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 (@lucasmiranda42) 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?

[lucasmiranda42]

Hi all! And thank you very much for reviewing our package! 😃

Quick question: are we allowed to push to the paper branch while reviews are ongoing? We're pushing some refactoring to master, and I was wondering if I should push here too. Nothing major is changing (neither API nor anything depicted in the tutorials).

Best, and thanks a lot once again!
Lucas

[emdupre]

Hi @lucasmiranda42 ,

Yes, you can make changes to the paper branch during review, though we recommend minimizing these ! As we're still quite early in the process (i.e., @edeno and @cellistigs have not yet started opening issues on the software), it would be ok to make these refactoring changes now.

But as you suggest, please try to avoid large changes in functionality during the review, unless the reviewers specifically request these !

Thanks for checking !

Elizabeth

[cellistigs]

Review checklist for @cellistigs

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/mlfpm/deepof?
• 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 (@lucasmiranda42) 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?

[lucasmiranda42]

Wonderful! Everything has been pushed, and we also added the so far missing contributing guidelines. No further changes are expected unless requested by the reviewers :)

Best, and thank you!
Lucas

[emdupre]

👋 Hi @edeno and @cellistigs ! I just wanted to check-in and see how this review is going for you.

Please let me know if you are hitting any blockers that I can help to remove 👷‍♀️ And thank you again for volunteering to review this submission !

[edeno]

Hi @emdupre, intend to file some issues soon. Sorry for the delay.

[lucasmiranda42]

I closed all issues to mark that I took care of them, but of course feel free to reopen / open new ones if needed! 👍

[emdupre]

Thank you, @edeno ! We're still within the review window, but I'm glad you haven't hit any blockers.
Please let me know if that changes (for you and @cellistigs ) !

Otherwise, please do let us know when you've finished working through the review checklist. And thank you again !

[lucasmiranda42]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.1038/s41593-018-0209-y is OK
- 10.1016/j.neuron.2020.09.017 is OK
- 10.1038/s42003-022-04080-7 is OK
- 10.1101/2020.04.19.049452 is OK
- 10.1101/2022.06.23.497350 is OK
- 10.1016/j.conb.2022.102544 is OK
- 10.1109/cvpr46437.2021.00290 is OK
- 10.7554/eLife.63720 is OK
- 10.1038/s41467-021-25420-x is OK
- 10.1101/2023.03.16.532307 is OK
- 10.1101/2021.06.16.448685 is OK
- 10.1016/J.NEUBIOREV.2023.105243 is OK
- 10.1101/2022.11.04.515138 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[emdupre]

@editorialbot set JOSS as version

[editorialbot]

Done! version is now JOSS

[emdupre]

Apologies for the last minute switch ; I realized the tag and release names are different, so I've now corrected to the tag name ! This correctly matches the archive.

[emdupre]

Thank you, @lucasmiranda42 !

I'm now happy to recommend DeepOF for publication 🚀 I'll now generate the a finalized proof ; please read through and review it for any last minute corrections.
Congratulations on this work, and thank you to @cellistigs and @edeno for your time and expertise in reviewing this submission !

[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/s41593-018-0209-y is OK
- 10.1016/j.neuron.2020.09.017 is OK
- 10.1038/s42003-022-04080-7 is OK
- 10.1101/2020.04.19.049452 is OK
- 10.1101/2022.06.23.497350 is OK
- 10.1016/j.conb.2022.102544 is OK
- 10.1109/cvpr46437.2021.00290 is OK
- 10.7554/eLife.63720 is OK
- 10.1038/s41467-021-25420-x is OK
- 10.1101/2023.03.16.532307 is OK
- 10.1101/2021.06.16.448685 is OK
- 10.1016/J.NEUBIOREV.2023.105243 is OK
- 10.1101/2022.11.04.515138 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/bcm-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#4296, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[lucasmiranda42]

I just finished reading and everything looks perfect. Thank you very much for your efforts!

[lucasmiranda42]

One small detail is that the DOI appears as not found when I click on it in the paper, but I reckon that's by design and will change upon acceptance, right? :)

[emdupre]

Yes exactly ; the DOI will not be finalized until publication 👍 But thank you for confirming your review of the proof !

[Kevin-Mattheus-Moerman]

@emdupre good job editing this one :) there seems to be no changes required.

@lucasmiranda42 I have check your repository, this review, the archive, and the paper and all seems in order. I'll now proceed to process this for acceptance in JOSS.

[Kevin-Mattheus-Moerman]

@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: Miranda
  given-names: Lucas
  orcid: "https://orcid.org/0000-0002-5484-6744"
- family-names: Bordes
  given-names: Joeri
  orcid: "https://orcid.org/0000-0003-2909-2976"
- family-names: Pütz
  given-names: Benno
  orcid: "https://orcid.org/0000-0002-2208-209X"
- family-names: Schmidt
  given-names: Mathias V
  orcid: "https://orcid.org/0000-0002-3788-2268"
- family-names: Müller-Myhsok
  given-names: Bertram
  orcid: "https://orcid.org/0000-0002-0719-101X"
contact:
- family-names: Müller-Myhsok
  given-names: Bertram
  orcid: "https://orcid.org/0000-0002-0719-101X"
doi: 10.5281/zenodo.8013401
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Miranda
    given-names: Lucas
    orcid: "https://orcid.org/0000-0002-5484-6744"
  - family-names: Bordes
    given-names: Joeri
    orcid: "https://orcid.org/0000-0003-2909-2976"
  - family-names: Pütz
    given-names: Benno
    orcid: "https://orcid.org/0000-0002-2208-209X"
  - family-names: Schmidt
    given-names: Mathias V
    orcid: "https://orcid.org/0000-0002-3788-2268"
  - family-names: Müller-Myhsok
    given-names: Bertram
    orcid: "https://orcid.org/0000-0002-0719-101X"
  date-published: 2023-06-12
  doi: 10.21105/joss.05394
  issn: 2475-9066
  issue: 86
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5394
  title: "DeepOF: a Python package for supervised and unsupervised
    pattern recognition in mice motion tracking data"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05394"
  volume: 8
title: "DeepOF: a Python package for supervised and unsupervised pattern
  recognition in mice motion tracking data"

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.05394 joss-papers#4298
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05394
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...

[lucasmiranda42]

Hi @Kevin-Mattheus-Moerman! And thank you for checking and accepting the paper!

I unfortunately see that the DOI does not resolve (nor does the paper show when clicking on the link that appears in the landing page). Is this normal at this point? Please let me know if there's anything we can do to troubleshoot.

Thank you!
Lucas

[Kevin-Mattheus-Moerman]

@lucasmiranda42 it usually takes a while. It does show up for me now. Perhaps refresh the page and try again?

[lucasmiranda42]

It worked after rebooting the browser. Apologies, and thank you once again!

[Kevin-Mattheus-Moerman]

Okay since we are all set I'll take this opportunity to congratulate @lucasmiranda42 on this JOSS publication! 🎉

I'd also like to thank @emdupre for the great job editing this work! And a special thanks to the reviewers: @cellistigs and @edeno!

[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.05394/status.svg)](https://doi.org/10.21105/joss.05394)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05394">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05394/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05394/status.svg
   :target: https://doi.org/10.21105/joss.05394

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

[lucasmiranda42]

Dear @emdupre, @Kevin-Mattheus-Moerman,

Thank you once again for your help during the revision process! I write because I'm including this paper as part of my doctoral thesis, and I've been asked to support it with an explicit permission from the publisher for the article to be included. Do you happen to know how to proceed in these cases?

Best, and thank you very much!
Lucas

[Kevin-Mattheus-Moerman]

@lucasmiranda42 JOSS papers are fully open access. Copyright of JOSS papers is retained by submitting authors and accepted papers are subject to a Creative Commons Attribution 4.0 International License. Hence you are permitted to use the paper in your doctoral thesis as you see fit. Hope this addresses your query.

https://joss.theoj.org/about