[REVIEW]: Pybehave: a hardware-agnostic, Python-based framework for developing behavioral neuroscience experiments #6515

editorialbot · 2024-03-21T16:26:18Z

Submitting author: @theonlydvr (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: @sappelhoff
Reviewers: @tuliofalmeida, @alustig3
Archive: 10.5281/zenodo.11244351

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e115eb80185bcfa240ca9689ee59c2cd"><img src="https://joss.theoj.org/papers/e115eb80185bcfa240ca9689ee59c2cd/status.svg"></a>
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

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-03-21T16:26:22Z

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editorialbot · 2024-03-21T16:26:37Z

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 · 2024-03-21T16:26:40Z

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 · 2024-03-21T16:26:44Z

Paper file info:

📄 Wordcount for paper.md is 932

✅ The paper includes a Statement of need section

editorialbot · 2024-03-21T16:26:46Z

License info:

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

editorialbot · 2024-03-21T16:27:46Z

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

sappelhoff · 2024-03-21T16:28:32Z

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 #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 · 2024-03-21T16:58:59Z

Review checklist for @alustig3

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/tne-lab/py-behav-box-v2?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
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?
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.
- Windows dependency tne-lab/py-behav-box-v2#77
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
- Contribution guidelines tne-lab/py-behav-box-v2#70

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?

tuliofalmeida · 2024-03-22T14:23:54Z

Review checklist for @tuliofalmeida

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/tne-lab/py-behav-box-v2?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
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?
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?

sappelhoff · 2024-04-02T08:05:31Z

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 · 2024-04-15T11:28:56Z

@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 · 2024-04-16T01:42:53Z

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

sappelhoff · 2024-04-29T10:15:10Z

@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 · 2024-04-29T12:23:53Z

@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 · 2024-04-29T13:30:52Z

@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 · 2024-04-30T19:40:00Z

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

tuliofalmeida · 2024-05-13T07:11:55Z

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 · 2024-05-13T18:50:19Z

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 · 2024-05-21T15:17:01Z

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

sappelhoff · 2024-05-21T15:51:05Z

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 · 2024-05-21T17:07:06Z

I recommend this paper for publication

Kevin-Mattheus-Moerman · 2024-06-05T07:15:34Z

@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:

Please spell out USA as United States of America in your affiliations.

theonlydvr · 2024-06-05T16:33:57Z

The spelling should be updated with the latest commit

Kevin-Mattheus-Moerman · 2024-06-05T19:00:33Z

@editorialbot generate pdf

editorialbot · 2024-06-05T19:02:13Z

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

Kevin-Mattheus-Moerman · 2024-06-05T20:50:33Z

@editorialbot accept

editorialbot · 2024-06-05T20:50:35Z

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

editorialbot · 2024-06-05T20:57:15Z

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 · 2024-06-05T20:57:19Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-06-05T20:57:19Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06515 joss-papers#5456
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06515
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

theonlydvr · 2024-06-06T00:55:52Z

Awesome! Everything looks good except it seems like my last name "Dastin-van Rijn" autogenerated to only have "Rijn" as the last name in the citation metadata. I've corrected this in the CITATION.cff in the original repository but I assume this has no effect on the actual merged paper. Apologies for the space in the last name...

sappelhoff · 2024-06-06T07:24:45Z

Thanks for letting us know @theonlydvr -- That's probably a task for an AEIC to sort out, as my influence on these things is limited. Is that correct @Kevin-Mattheus-Moerman?

Kevin-Mattheus-Moerman · 2024-06-06T08:21:14Z

@sappelhoff @theonlydvr yes we can take it from here. I'll ping @openjournals/dev to see if they can offer some guidance on this one.

xuanxu · 2024-06-06T10:13:49Z

The parts of the name can be described with more precision in the paper's metadata:
https://joss.readthedocs.io/en/latest/paper.html#names

Updating the paper.md file and then reaccepting should update the published strings.

theonlydvr · 2024-06-06T15:08:53Z

Thank you! I think I've fixed it with the latest commit (I just replaced the name with an explicit given and surname).

Kevin-Mattheus-Moerman · 2024-06-06T18:59:18Z

@editorialbot reaccept

editorialbot · 2024-06-06T18:59:20Z

Rebuilding paper!

editorialbot · 2024-06-06T19:01:31Z

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#5462

Kevin-Mattheus-Moerman · 2024-06-06T19:04:00Z

@theonlydvr Are you happy with the update?

theonlydvr · 2024-06-06T19:20:56Z

Looks great! Thank you!

Kevin-Mattheus-Moerman · 2024-06-09T07:10:07Z

@theonlydvr congratulations on this JOSS publication!

@sappelhoff thanks for editing!

And a special thank you to the reviewers: @tuliofalmeida, @alustig3 !!

editorialbot · 2024-06-09T07:10:08Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

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  <img src="https://joss.theoj.org/papers/10.21105/joss.06515/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06515/status.svg
   :target: https://doi.org/10.21105/joss.06515

This is how it will look in your documentation:

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editorialbot added C Python review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Mar 21, 2024

editorialbot assigned sappelhoff Mar 21, 2024

editorialbot mentioned this issue Mar 21, 2024

[PRE REVIEW]: Pybehave: a hardware-agnostic, Python-based framework for developing behavioral neuroscience experiments #6374

Closed

tuliofalmeida mentioned this issue Apr 2, 2024

Review Joss Paper Tulio tne-lab/py-behav-box-v2#68

Closed

sappelhoff mentioned this issue May 20, 2024

parameter updates from user within a session tne-lab/py-behav-box-v2#80

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editorialbot added accepted published Papers published in JOSS labels Jun 5, 2024

Kevin-Mattheus-Moerman closed this as completed Jun 9, 2024

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[REVIEW]: Pybehave: a hardware-agnostic, Python-based framework for developing behavioral neuroscience experiments #6515

[REVIEW]: Pybehave: a hardware-agnostic, Python-based framework for developing behavioral neuroscience experiments #6515

Comments

editorialbot commented Mar 21, 2024 • edited Loading

Status

Reviewer instructions & questions

Checklists

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sappelhoff commented Mar 21, 2024

alustig3 commented Mar 21, 2024 • edited Loading

Review checklist for @alustig3

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

tuliofalmeida commented Mar 22, 2024 • edited Loading

Review checklist for @tuliofalmeida

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

sappelhoff commented Apr 2, 2024

sappelhoff commented Apr 15, 2024

alustig3 commented Apr 16, 2024

sappelhoff commented Apr 29, 2024

tuliofalmeida commented Apr 29, 2024 • edited Loading

theonlydvr commented Apr 29, 2024

alustig3 commented Apr 30, 2024

tuliofalmeida commented May 13, 2024

sappelhoff commented May 13, 2024

theonlydvr commented May 21, 2024 • edited Loading

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alustig3 commented May 21, 2024

Kevin-Mattheus-Moerman commented Jun 5, 2024 • edited Loading

theonlydvr commented Jun 5, 2024

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theonlydvr commented Jun 6, 2024

sappelhoff commented Jun 6, 2024

Kevin-Mattheus-Moerman commented Jun 6, 2024

xuanxu commented Jun 6, 2024

theonlydvr commented Jun 6, 2024

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edited

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tuliofalmeida commented Apr 29, 2024 •

edited

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theonlydvr commented May 21, 2024 •

edited

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Kevin-Mattheus-Moerman commented Jun 5, 2024 •

edited

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