[REVIEW]: Pybehave: a hardware-agnostic, Python-based framework for developing behavioral neuroscience experiments

[editorialbot]

Submitting author: !--author-handle-->@theonlydvr<!--end-author-handle-- (Evan Dastin-van Rijn) Repository: https://github.com/tne-lab/py-behav-box-v2 Branch with paper.md (empty if default branch): Version: v1.0.19 Editor: !--editor-->@sappelhoff<!--end-editor-- Reviewers: @tuliofalmeida, @alustig3 Archive: 10.5281/zenodo.11244351

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/e115eb80185bcfa240ca9689ee59c2cd/status.svg)](https://joss.theoj.org/papers/e115eb80185bcfa240ca9689ee59c2cd)

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

@tuliofalmeida & @alustig3, 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 @sappelhoff 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 @alustig3

📝 Checklist for @tuliofalmeida

[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:

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

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[editorialbot]

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

OK DOIs

- 10.7554/eLife.67846 is OK
- 10.1016/j.jneumeth.2019.05.002 is OK
- 10.3758/s13428-014-0458-y is OK
- 10.3758/s13428-018-01193-y is OK
- 10.1163/156856897X00357 is OK
- 10.1016/j.neuron.2016.12.041 is OK
- 10.1590/1516-4446-2020-1675 is OK
- 10.1101/2023.02.03.527033 is OK
- 10.1016/j.biopsych.2023.02.774 is OK
- 10.1016/j.biopsych.2023.02.702 is OK
- 10.3389/fninf.2015.00007 is OK
- 10.3758/BRM.42.4.1059 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.08 s (1522.6 files/s, 185489.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          83           1208            717           5464
Markdown                        21           1333              0           2453
SVG                             15             15             12           1125
C/C++ Header                     1            597           1837            229
TeX                              1             12              0            216
TOML                             1              8              0             48
YAML                             3             11             13             48
DOS Batch                        1              0              0              4
-------------------------------------------------------------------------------
SUM:                           126           3184           2579           9587
-------------------------------------------------------------------------------

Commit count by author:

   225  theonlydvr
     9  JoelNielsen7
     3  fjkdasilva
     2  jazlinumn
     1  bucci026

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 932

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[sappelhoff]

Hello again! 👋


@tuliofalmeida, @alustig3

FYI @theonlydvr

This is the review thread for the paper. All of our higher-level communications will happen here from now on, review comments and discussion can happen in the repository of the project (details below).

📓 Please read the "Reviewer instructions & questions" in the comment from our editorialbot (above).

✅ All reviewers get their own checklist with the JOSS requirements - you generate them as per the details in the editorialbot comment. As you go over the submission, please check any items that you feel have been satisfied.

💻 The JOSS review is different from most other journals: The reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention the link to https://github.com/openjournals/joss-reviews/issues/6515 so that a link is created to this thread. That will also help me to keep track!

❓ Please also feel free to comment and ask questions on this thread if you are unsure about something!

🎯 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.

[alustig3]

Review checklist for @alustig3

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the https://github.com/tne-lab/py-behav-box-v2?
• [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@theonlydvr) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] 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.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] 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

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
  • https://github.com/tne-lab/py-behav-box-v2/issues/81
  • https://github.com/tne-lab/py-behav-box-v2/issues/83
  • https://github.com/tne-lab/py-behav-box-v2/pull/84
  • https://github.com/tne-lab/py-behav-box-v2/issues/88

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • https://github.com/tne-lab/py-behav-box-v2/issues/77
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • https://github.com/tne-lab/py-behav-box-v2/pull/73
  • https://github.com/tne-lab/py-behav-box-v2/issues/74
  • https://github.com/tne-lab/py-behav-box-v2/issues/75
  • https://github.com/tne-lab/py-behav-box-v2/issues/79
  • https://github.com/tne-lab/py-behav-box-v2/issues/80
  • https://github.com/tne-lab/py-behav-box-v2/pull/85
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] 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
  • https://github.com/tne-lab/py-behav-box-v2/issues/70

Software paper

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] 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?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

[tuliofalmeida]

Review checklist for @tuliofalmeida

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the https://github.com/tne-lab/py-behav-box-v2?
• [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@theonlydvr) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] 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.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] 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

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] 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?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

[sappelhoff]

Hi @tuliofalmeida @alustig3 -- just to check in with you: What are your respective timelines for completing the present review? Are there any blockers that I can help remove?

[sappelhoff]

@tuliofalmeida I see that you have nearly completed your review, thanks for that. Please let me know if there are any questions that I can help with in the meantime. Once you have fully completed your review, I'd appreciate if you could post your final "verdict" as a comment in this thread.

@alustig3 I have reached out to you via email, using the email you provide on your website -- hoping to hear from you soon!

[alustig3]

@sappelhoff I am making progress and aim to finish within a week.

[sappelhoff]

@alustig3 @tuliofalmeida could I get a brief status update of your reviews, please?

@theonlydvr could you provide an update from your side as well, please? Are there any questions about the review process, or anything we should discuss/clarify?

[tuliofalmeida]

@alustig3 @tuliofalmeida could I get a brief status update of your reviews, please?

@theonlydvr could you provide an update from your side as well, please? Are there any questions about the review process, or anything we should discuss/clarify?

I'm finishing! The authors made the updates in the package (very quickly) but I didn't had time to check it yet. I'm planning to finish this week.

[theonlydvr]

@alustig3 @tuliofalmeida could I get a brief status update of your reviews, please?

@theonlydvr could you provide an update from your side as well, please? Are there any questions about the review process, or anything we should discuss/clarify?

Review process has been going well! Feedback has been very helpful and useful for addressing some of the weak points in the documentation and setup process.

[alustig3]

@sappelhoff I have completed my review checklist. @theonlydvr is addressing a few remaining GitHub issues and pull requests that I created.

[tuliofalmeida]

Hey @sappelhoff I finished my part of the review. The idea was to test it with a lab friend that do experiments but doesn't code. @theonlydvr did a good job, my main point is to improve the documentation and tutorial for people that are not comfortable with coding and he's doing it.

[sappelhoff]

Thanks for the note @tuliofalmeida!

@alustig3 @tuliofalmeida, I can see you both checked your reviewer lists fully. I'd appreciate it, if you could briefly make a statement whether you would recommend this paper for publication, or whether there are items that need to be dealt with before. For example, in @alustig3's reviewer list, I see some linked PRs/issues that have not yet been merged/closed, and @tuliofalmeida mentions:

... and he's doing it.

... which suggest to me, that there are still some things to be done.

In any way, thanks already for the work until here, it seems like we are nearing the completion of this review process.

[theonlydvr]

All of @alustig3's remaining issues/PRs should now be addressed

[sappelhoff]

Thanks @theonlydvr.

And thanks a lot @tuliofalmeida and @alustig3 for your reviews. 🚀

Maybe I am being pedantic, but I would like to see your explicit recommendation to publish this paper. Something along the lines: "I recommend this paper for publication".

If I don't hear back within one week, I will go ahead and take your previous comments and your respectively finished reviewers lists as implicit recommendation for publication, and will start with the final steps.

[alustig3]

I recommend this paper for publication

[tuliofalmeida]

I also recommend this paper for publication

[sappelhoff]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• [x] Double check authors and affiliations (including ORCIDs)
• [x] 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.
• [x] Archive the release on Zenodo/figshare/etc and post the DOI here.
• [x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• [x] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

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

[sappelhoff]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.7554/eLife.67846 is OK
- 10.1016/j.jneumeth.2019.05.002 is OK
- 10.3758/s13428-014-0458-y is OK
- 10.3758/s13428-018-01193-y is OK
- 10.1163/156856897X00357 is OK
- 10.1016/j.neuron.2016.12.041 is OK
- 10.1590/1516-4446-2020-1675 is OK
- 10.1101/2023.02.03.527033 is OK
- 10.1016/j.biopsych.2023.02.774 is OK
- 10.1016/j.biopsych.2023.02.702 is OK
- 10.3389/fninf.2015.00007 is OK
- 10.3758/BRM.42.4.1059 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[sappelhoff]

@theonlydvr I have generated the final steps that you and I need to go through, see: https://github.com/openjournals/joss-reviews/issues/6515#issuecomment-2124051446

Could you please take care of your items (upper list), and let me know once you are finished?

[theonlydvr]

Authors and affiliations have been checked. Version number is 1.0.19 on both the Github and pypi releases. DOI was created with Zenodo and all information is consistent with the JOSS submission: https://doi.org/10.5281/zenodo.11244351

[sappelhoff]

@editorialbot set 10.5281/zenodo.11244351 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.11244351

[sappelhoff]

@editorialbot set v1.0.19 as version

[editorialbot]

Done! version is now v1.0.19

[sappelhoff]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[sappelhoff]

@theonlydvr I have completed my final checks of this submission. Before I can instruct the bot to "recommend-accept", I would like to clarify the following two points:

• [x] The software version in the archive (as can be seen in pyproject.toml) is 1.0.18, and not 1.0.19, as I expected. Did something go wrong during the release / archiving?

• [x] I see that very few of the authors on your author list have an associated ORCID. However, a quick check shows me that some of these authors do in fact have an ORCID (for example https://orcid.org/0000-0002-1669-8752, if I am not mistaken). Could you please add all ORCIDs that are available, unless the respective authors explicitly don't want to list them?

• (not strictly a "to do") @theonlydvr I could not find you in our reviewer database - we'd be very grateful if you considered signing up to pay it forward 🙂 you can do that here: https://reviewers.joss.theoj.org/join (same goes for @alustig3: if you'd like to continue reviewing for JOSS, please consider signing up as a reviewer, so that editors can find and match you to papers that may be in your area of expertise; @tuliofalmeidais already signed up)

[theonlydvr]

So it looks like the release grabbed the commit that preceded me updating the version number in the toml file but has all the correct code and content. It should be correct otherwise but I can make a new release and send the information over if necessary. Most of the authors are technical staff and trainees who helped with development and testing so they don't have ORCID IDs yet. I did add two new ORCID IDs for the ones that do though.

I have also now added myself to the reviewer database 🙂

[sappelhoff]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[sappelhoff]

Wonderful, thanks @theonlydvr!

[sappelhoff]

@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.67846 is OK
- 10.1016/j.jneumeth.2019.05.002 is OK
- 10.3758/s13428-014-0458-y is OK
- 10.3758/s13428-018-01193-y is OK
- 10.1163/156856897X00357 is OK
- 10.1016/j.neuron.2016.12.041 is OK
- 10.1590/1516-4446-2020-1675 is OK
- 10.1101/2023.02.03.527033 is OK
- 10.1016/j.biopsych.2023.02.774 is OK
- 10.1016/j.biopsych.2023.02.702 is OK
- 10.3389/fninf.2015.00007 is OK
- 10.3758/BRM.42.4.1059 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

:wave: @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5440, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@theonlydvr as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. I only have the below point that requires your attention:

• [x] Please spell out USA as United States of America in your affiliations.

[theonlydvr]

The spelling should be updated with the latest commit

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[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: Rijn given-names: Evan M. Dastin-van orcid: "https://orcid.org/0000-0002-1428-0723" - family-names: Nielsen given-names: Joel - family-names: Sachse given-names: Elizabeth M. orcid: "https://orcid.org/0000-0002-1669-8752" - family-names: Li given-names: Christina - family-names: Mensinger given-names: Megan E. - family-names: Simpson given-names: Stefanie G. - family-names: Buccini given-names: Michelle C. - family-names: Iacobucci given-names: Francesca A. - family-names: Titus given-names: David J. orcid: "https://orcid.org/0000-0001-7819-734X" - family-names: Widge given-names: Alik S. orcid: "https://orcid.org/0000-0001-8510-341X" contact: - family-names: Rijn given-names: Evan M. Dastin-van orcid: "https://orcid.org/0000-0002-1428-0723" doi: 10.5281/zenodo.11244351 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Rijn given-names: Evan M. Dastin-van orcid: "https://orcid.org/0000-0002-1428-0723" - family-names: Nielsen given-names: Joel - family-names: Sachse given-names: Elizabeth M. orcid: "https://orcid.org/0000-0002-1669-8752" - family-names: Li given-names: Christina - family-names: Mensinger given-names: Megan E. - family-names: Simpson given-names: Stefanie G. - family-names: Buccini given-names: Michelle C. - family-names: Iacobucci given-names: Francesca A. - family-names: Titus given-names: David J. orcid: "https://orcid.org/0000-0001-7819-734X" - family-names: Widge given-names: Alik S. orcid: "https://orcid.org/0000-0001-8510-341X" date-published: 2024-06-05 doi: 10.21105/joss.06515 issn: 2475-9066 issue: 98 journal: Journal of Open Source Software publisher: name: Open Journals start: 6515 title: "Pybehave: a hardware agnostic, Python-based framework for controlling behavioral neuroscience experiments" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06515" volume: 9 title: "Pybehave: a hardware agnostic, Python-based framework for controlling behavioral neuroscience experiments" ```

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 👈 🐘🐘🐘