[REVIEW]: Ethome: machine learning for animal behavior

[editorialbot]

Submitting author: @benlansdell (Benjamin Lansdell)
Repository: https://github.com/benlansdell/ethome
Branch with paper.md (empty if default branch):
Version: v0.6.3
Editor: @adi3
Reviewers: @imcatta, @neuromusic, @KonradDanielewski
Archive: 10.5281/zenodo.10680136

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/0472dab158806827a83da79e602e16e4"><img src="https://joss.theoj.org/papers/0472dab158806827a83da79e602e16e4/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/0472dab158806827a83da79e602e16e4/status.svg)](https://joss.theoj.org/papers/0472dab158806827a83da79e602e16e4)

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

@imcatta & @neuromusic, 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 @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 ✨

Checklists

📝 Checklist for @imcatta

📝 Checklist for @KonradDanielewski

[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=0.12 s (732.9 files/s, 197646.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      26           1013           1272           4908
HTML                            11           3327              8           4705
Python                          23            863            836           3036
Markdown                        14            996              0           1356
TeX                              1              0              0            168
Ruby                             1             28             12            106
YAML                             4             10             10            104
XML                              1              0              0             53
Jupyter Notebook                 1              0            225             51
make                             1             11             21             42
JSON                             2              0              0             24
TOML                             1              0              0              6
-------------------------------------------------------------------------------
SUM:                            86           6248           2384          14559
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.7554/eLife.63377 is OK
- 10.48550/ARXIV.2011.13917 is OK
- 10.1101/2020.05.14.095430 is OK
- 10.1101/2020.04.19.049452 is OK
- 10.5281/zenodo.6669074 is OK
- 10.1038/s41386-020-0776-y is OK
- 10.1016/j.conb.2019.10.008 is OK
- 10.7554/eLife.63720 is OK
- 10.1038/s41467-021-25420-x is OK
- 10.1101/2022.11.04.515138 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 931

[editorialbot]

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

[imcatta]

Review checklist for @imcatta

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/benlansdell/ethome?
• 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 (@benlansdell) 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?

[adi3]

Folks, apologies for the delay in pre-review phase but we'll pick up speed during this review. Thanks for your patience!

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

👋🏼 @imcatta, @neuromusic - you both should generate your checklists with the JOSS requirements by running @editorialbot generate my checklist. As you go over the submission, please check the items that you feel have been satisfied and let the author know where further work needs to be done.

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 #5623 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 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!!

[neuromusic]

@editorialbot commands

[editorialbot]

Hello @neuromusic, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

[neuromusic]

Thanks @adi3!! I'm going to be unavailable through August 1st, but will be able to start my review then.

[adi3]

@neuromusic that will work out just fine, thank you!

[Kevin-Mattheus-Moerman]

@neuromusic to get started, the command you were looking for was: @editorialbot generate my checklist

[imcatta]

Hi @benlansdell! I've completed my review. Here are my comments.

The package is interesting and useful. While running through the code, I had the feeling that it is well structured and of good quality. I also appreciated that the package is made available through PiPY and that there is a pipeline for automated testing. However, I think there is still room for improvement in the documentation. Here are my specific comments.

General checks

• The project includes some sample data from animals, but no evidence is provided that this data was collected in accordance with the JOSS Policy.

Functionality

• There are two methods to get example data: get_sample_nwb__paths(), which returns NWB data, and get_sample_data_paths(), which returns DLC and BORIS. I suggest renaming the latter to something that recalls DLC and BORIS for consistency.

Documentation

• I struggled a little in following the code presented in the README.
  • dataset.features.add('cnn1d_prob') If I run this on the nwb example dataset, as suggested above, it tells me that DataFrame doesn't have necessary columns to compute this set of features.. Also, I can’t find which columns are needed. Please consider stating in the documentation what columns are needed and how to get those in the sample dataset.
  • cross_val_score(..., dataset.ml.labels, ...). No labels are present in the nwb example dataset, so this is not working with the dataset proposed above.
  • Please add package requirements (e.g. Python versions supported) to the README.
  • “For this, you must have labeled your body parts in a certain way (refer to How To)”. Please add the link to the How to section.
  • Please add a link to the web documentation in the README.
• It is stated that “dataset.features.add('cnn1d_prob')Uses a pretrained CNN to output probabilities of 3 behaviors (attack, mount, social investigation).”. More information on this is needed. How was this CNN built? Also, I found out that the repository contains 5 pre-trained models, but no information on that is provided.
• Some users may not be fully confident with the DLC, SLEAP, NWB, BORIS and NWB file formats. Please explain the different data input formats supported in more detail.
• Guidelines for report issues or problems with the software and seek support are missing.
• In How To guide, section “3a In-built support for resident-intruder setup”, more information on what is MARS and context should be provided.

[benlansdell]

Thanks for the review @imcatta. For some of these points, I'll create issues in the package repo and let you know when I've addressed them.

[adi3]

@imcatta thanks for the review so far! @benlansdell looking forward to seeing your changes and getting the first reviewer's checklist complete. @neuromusic should be back soon and will begin the second review sometime this week.

[adi3]

@neuromusic - could you kick off your review please? :)

[Kevin-Mattheus-Moerman]

@neuromusic thanks for agreeing to help with this review. If you are still able to help, please get started at your earliest convenience to avoid a delay with this submission. Thanks!

[Kevin-Mattheus-Moerman]

@benlansdell could you provide an update to say if you have dealt with the issues raised by @imcatta? Thanks

[Kevin-Mattheus-Moerman]

@benlansdell please respond to the above ☝️

To avoid delays it would be great if you could respond to queries in a timely manor. If instead you are no longer interested in pursuing a JOSS publication please do let us know.

[Kevin-Mattheus-Moerman]

@adi3 please can you pick this one up again. It looks like we may need to find an alternative reviewer, since @neuromusic has not responded.

[adi3]

@Kevin-Mattheus-Moerman for sure! I think we need to first wait for @benlansdell to resolve outstanding issues mentioned by the reviewer to ensure there is motivation to take this publication forward.

[benlansdell]

@adi3 and @Kevin-Mattheus-Moerman I am still motivated to take the publication forward at JOSS! Let me address these issues this week. Thanks for keeping this moving.

[editorialbot]

Done! archive is now 10.5281/zenodo.10680136

[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

- 10.7554/eLife.63377 is OK
- 10.48550/ARXIV.2011.13917 is OK
- 10.1101/2020.05.14.095430 is OK
- 10.1101/2020.04.19.049452 is OK
- 10.5281/zenodo.6669074 is OK
- 10.1038/s41386-020-0776-y is OK
- 10.1016/j.conb.2019.10.008 is OK
- 10.7554/eLife.63720 is OK
- 10.1038/s41467-021-25420-x 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#5051, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[benlansdell]

@adi3 This looks good to me! Is editorial bot's message for me? Do I tell it to accept, or do you?

[Kevin-Mattheus-Moerman]

@benlansdell at this point the AEiC on this track, me, steps in to process the final steps needed for acceptance.

[Kevin-Mattheus-Moerman]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• Read the text of the paper and offer comments/corrections (as either a list or a pull request)
• Check that the archive title, author list, version tag, and the license are correct
• Set archive DOI with @editorialbot set <DOI here> as archive
• Set version with @editorialbot set <version here> as version
• Double check rendering of paper with @editorialbot generate pdf
• Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• Recommend acceptance with @editorialbot recommend-accept

[Kevin-Mattheus-Moerman]

@adi3 next time you can call @editorialbot create post-review checklist to create the above. This will help us to ensure that the archive title, license etc. matches and all the final checks are done. I'll take it from here though.

[Kevin-Mattheus-Moerman]

@benlansdell I have checked the paper, your repository, this review, and the archive link. Most seems in order. However the below points require your attention:

• Ensure the archive link title matches the paper title.
• Ensure the archive listed license matches the software license.
• Ensure the archive listed author set matches the paper author set.
• In your paper affiliations, please spell out United States of America
• Add the following DOI's:

• 10.1038/s41592-022-01443-0
• 10.1038/s41592-022-01426-1

[benlansdell]

@Kevin-Mattheus-Moerman I've corrected the title, license and author list in the Zenodo archive so it matches the paper data, along with the DOIs and affiliation. Let me know if there's anything else.

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.7554/eLife.63377 is OK
- 10.48550/ARXIV.2011.13917 is OK
- 10.1101/2020.05.14.095430 is OK
- 10.1101/2020.04.19.049452 is OK
- 10.5281/zenodo.6669074 is OK
- 10.1038/s41386-020-0776-y is OK
- 10.1016/j.conb.2019.10.008 is OK
- 10.1038/s41592-022-01443-0 is OK
- 10.7554/eLife.63720 is OK
- 10.1038/s41467-021-25420-x is OK
- 10.1101/2022.11.04.515138 is OK
- 10.1038/s41592-022-01426-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@benlansdell all looks good now. Apologies for the delay. I'll now process this for acceptance.

[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: Lansdell
  given-names: Benjamin
  orcid: "https://orcid.org/0000-0003-1444-1950"
- family-names: Shirinifard
  given-names: Abbas
doi: 10.5281/zenodo.10680136
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Lansdell
    given-names: Benjamin
    orcid: "https://orcid.org/0000-0003-1444-1950"
  - family-names: Shirinifard
    given-names: Abbas
  date-published: 2024-03-08
  doi: 10.21105/joss.05623
  issn: 2475-9066
  issue: 95
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5623
  title: "Ethome: tools for machine learning of animal behavior"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05623"
  volume: 9
title: "Ethome: tools for machine learning of animal behavior"

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]

🐘🐘🐘 👉 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.05623 joss-papers#5107
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05623
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...

[benlansdell]

@Kevin-Mattheus-Moerman No worries about the delay. Thanks all for the reviews and editorial assistance!

[Kevin-Mattheus-Moerman]

@benlansdell you are welcome. Congratulations on this paper!

Thanks for editing @adi3

And a special thank you to the reviewers: @imcatta, @neuromusic, @KonradDanielewski !

[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.05623/status.svg)](https://doi.org/10.21105/joss.05623)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05623">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05623/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05623/status.svg
   :target: https://doi.org/10.21105/joss.05623

This is how it will look in your documentation:

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