[REVIEW]: stimupy: A Python stimulus creation package for vision science

[editorialbot]

Submitting author: @LynnSchmittwilken (Lynn Schmittwilken)
Repository: https://github.com/computational-psychology/stimupy
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @emdupre
Reviewers: @alexander-pastukhov, @JonathanReardon
Archive: 10.17605/OSF.IO/Z439V

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/af54c793f6f4c02a4af6a8b5f6f57e9d"><img src="https://joss.theoj.org/papers/af54c793f6f4c02a4af6a8b5f6f57e9d/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/af54c793f6f4c02a4af6a8b5f6f57e9d/status.svg)](https://joss.theoj.org/papers/af54c793f6f4c02a4af6a8b5f6f57e9d)

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

@alexander-pastukhov & @JonathanReardon, 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 @alexander-pastukhov

📝 Checklist for @JonathanReardon

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.26 s (588.5 files/s, 148114.5 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                           70           3834           9676          12456
Markdown                         58           1543              0           9436
JSON                              9              0              0            812
YAML                              8             32             19            209
TeX                               1             17              0            203
TOML                              1              9              2             68
Bourne Again Shell                1              2              2              6
reStructuredText                  6             81            348              6
--------------------------------------------------------------------------------
SUM:                            154           5518          10047          23196
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1913

[editorialbot]

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

OK DOIs

- 10.1167/jov.22.14.3519 is OK
- 10.1163/156856897X00357 is OK
- 10.1117/12.348473 is OK
- 10.1117/12.387150 is OK
- 10.1109/CVPR.2009.5206848 is OK
- 10.1177/03010066211057347 is OK
- 10.1109/ICCV.2001.937655 is OK
- 10/gh57gf is OK
- 10.1146/annurev-vision-093019-115159 is OK
- 10.3758/s13428-018-01193-y is OK
- 10.1167/jov.22.3.36 is OK
- 10.1167/jov.22.8.5 is OK
- 10.1167/jov.22.14.4041 is OK
- 10.1167/jov.22.14.4160 is OK
- 10.1167/jov.21.9.2824 is OK
- 10.1167/8.12.8 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[emdupre]

Hi @alexander-pastukhov and @JonathanReardon 👋 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 stimupy. 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 !

[alexander-pastukhov]

Review checklist for @alexander-pastukhov

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/computational-psychology/stimupy?
• 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 (@LynnSchmittwilken) 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?

[JonathanReardon]

Review checklist for @JonathanReardon

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/computational-psychology/stimupy?
• 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 (@LynnSchmittwilken) 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?

[alexander-pastukhov]

@emdupre I am first-time reviewer for JOSS, so I am not sure how do I proceed. I like the concept behind the package and I can see how it would be widely used by the visual community (I probably would with a caveat that virtually all my stimuli are dynamic and the package appears to only be able to handle the static ones). Paper-wise, I have only couple of minor issues (but I am not sure where and how I post them).

But... Either the docs, or the package (or both) are half-backed. There is a limited number of examples in "Getting started" and a lot of them simply do not work (and errors are fairly variable, implying that this is not the same issue such as a single missing dependence). An important section of documentation
Topic Guides is completely empty. Couple of unit test files produce quite a few warnings (17 for test_overviews, 6 for test_waves), which I don't think was the plan. API docs seem to be complete but without topic guides it is not very usable for a novice. "Demos of parameters" section also seem to work but I would perhaps polish the error handling, so it looks less as a complete crash (which is good for experimental code but not so ideal in an interactive tool).

In short, is it a good package that will be useful for the community - yes, should it be accepted by JOSS once it is more polished and ready - absolutely, is it ready (at least the docs) - no.

[JonathanReardon]

@alexander-pastukhov I am having trouble importing the package after install, though I have left an issue about this. From what I can see so far, the developers have submitted this for publication too early. I'm happy to continue with the review (assuming I can eventually install it) but I think it's going to take too much work to address all that is missing during this review cycle.

[emdupre]

Thank you both for your quick (!) and considered feedback, @alexander-pastukhov and @JonathanReardon !

To cross-link the currently raised issues:

• Issue on page /reference/demos/components/angulars.html computational-psychology/stimupy#74
• removal of unnecessary information computational-psychology/stimupy#73
• problem installing computational-psychology/stimupy#72
• Issue on page /getting_started/installation.html computational-psychology/stimupy#71
• Issue on page /getting_started/first_stim.html computational-psychology/stimupy#70
• Issue on page /getting_started/stimulus.html computational-psychology/stimupy#69

I am able to install and import the package locally, and I can replicate the Stimuli - Bullseyes demo locally (with an additional ipywidgets dependency installation). So, it seems that the package is functional -- though with noted issues -- but the documentation, and in particular the Topic Guides, are sparsely populated.

The JOSS reviewing guidelines note that :

There should be sufficient documentation for you, the reviewer, to understand the core functionality of the software under review. A high-level overview of this documentation should be included in a README file (or equivalent).

If you believe that there is sufficient documentation for you to understand the core functionality of the software and assess how it meets the functionality claims described in the JOSS paper, then I think we can proceed with the review. Please let me know.

@LynnSchmittwilken, please feel free to start addressing the current issues as raised by the reviewers ! You do not need to wait until a specific point to engage in this process.

[LynnSchmittwilken]

Thanks a lot for the considerate and honest review! We have started working on the issues that you raised, particularly with respect to the documentation.

[emdupre]

👋 Hi everyone,

🎉 Happy Monday ! I just wanted to follow-up @alexander-pastukhov and @JonathanReardon and confirm if you feel comfortable proceeding with the review.

Please let me know, and thank you again for your thoughtful comments to date !

[emdupre]

I also wanted to cross-link another, more recently raised issue from this review : computational-psychology/stimupy#75

[JorisVincent]

Hello all!

I'm one of the authors and maintainers of stimupy! 👋 Thanks for the very helpful feedback so far.

Updates from our side:

1. we've recently pushed some bugfixes, and simultaneously updated the documentation, as version 0.100.0. Specifically, the "Getting started" tutorial section should now work without errors, and the installation instructions have been cleaned up. This should close some of the issues raised, although happy to address them further if @alexander-pastukhov and/or @JonathanReardon feel like these pages are not yet clear enough. Our hope is that we this tutorial, the reviewers can get up and running to evaluate some more of the package.

2. We're also working on the topic guides, e.g. how stimupy is organized -- a few other pages should fill in by the end of this week. The purpose of those guides, broadly, is to explain some of the concepts and design decisions of the package. The scope of that is something we could definitely use the input from the reviewers on: what are elements of the package that are not easily understood from just the tutorial plus API reference / demos? For now, we have in mind to explain:

   • image resolution (pixels to visual degrees) and how to specify it
   • an explanation of how periodic stimuli (e.g., sinewave gratings) can be specified in stimupy
   • a brief description of the various directions/distances that underlie some of the stimuli, e.g. radial vs. horizontal vs. angular gratings.

3. In the meantime, we're working on the CI/CD aspect of publishing the package on PyPI. Once this is done, installation should simplify a lot as well, thus preventing some of the earlier raised issues.

4. We're addressing some of the remaining issues individually.

I hope this gives some perspective on how we're taking in the review from our side. If there are any questions or concerns, we're very happy to address those. Thanks again for the constructive and critical review, since we really want stimupy to become a great solution to common problems in vision science, for both experts and novices, all feedback is hugely valuable to us!

[emdupre]

👋 Happy Tuesday, everyone, and thank you for these updates, @JorisVincent !

@alexander-pastukhov and @JonathanReardon , please let me know if these edits address your initial concerns. And thank you again for your time and expertise !

[JonathanReardon]

Apologies for the delay @emdupre. Yes, it looks like there's been a lot of work on the project since I last checked, which is brilliant. Concerns are most certainly being addressed. Thanks @LynnSchmittwilken & @JorisVincent !

[alexander-pastukhov]

@emdupre Sorry, somehow lost the track of time. The authors addressed my initial concerns but I've raised two more issues regarding documentation. I feel that having topic guides on 1) how to use stimuli generated by the package in other software, and 2) how to create and deposit your own stimulus for later replication, are critical as they relate to the core use of the package (create and use stimulus for my research, then tell others how to replicate it).

[emdupre]

Thank you for the update, @alexander-pastukhov !

I'm cross-linking the two newly raised issues for clarity:

• Topic Guide: step-by-step tutorial for create and submitting stimulus for a paper computational-psychology/stimupy#78
• Topic Guide: using stimuli with PsychoPy, PTB, etc. computational-psychology/stimupy#79

[JorisVincent]

Hi all! 👋

@LynnSchmittwilken and I have been hard at work addressing the remaining issues, primarily related to documentation. Those are now merged in, and the latest documentation is live!
As we see it, this addresses the latest issues raised by @alexander-pastukhov -- but of course we're happy to provide more detail.

Please let us know if there is anything else that we should address!

[emdupre]

Thank you for confirming, @JorisVincent ! It's great to see these issues addressed.

@JonathanReardon and @alexander-pastukhov , could you please revisit your reviewer checklists and confirm if you feel that stimupy now meets JOSS publication standards, given these revisions ?

If you have any remaining concerns, of course, please let me know !

[alexander-pastukhov]

@emdupre The authors did a brilliant job, as now the already excellent package is very thoroughly documented, Nothing else on my side.

[alexander-pastukhov]

@emdupre Done my checklist as well, I think it is ready for publication.

[JorisVincent]

@emdupre Hm, this seems to be an issue on OSF's side. The OSF registration is marked as public, but not showing up as such (yet). We have contacted OSF about this, and hope to hear back from them soon.

[emdupre]

@editorialbot set 10.17605/OSF.IO/Z439V as archive

[editorialbot]

Done! archive is now 10.17605/OSF.IO/Z439V

[emdupre]

@editorialbot generate pdf

[editorialbot]

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

[emdupre]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1167/jov.22.14.3519 is OK
- 10.1163/156856897X00357 is OK
- 10.1117/12.348473 is OK
- 10.1117/12.387150 is OK
- 10.1109/CVPR.2009.5206848 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.3233/978-1-61499-649-1-87 is OK
- 10.3758/s13428-022-01900-w is OK
- 10.1177/03010066211057347 is OK
- 10.1109/ICCV.2001.937655 is OK
- 10.1167/jov.20.7.28 is OK
- 10.1146/annurev-vision-093019-115159 is OK
- 10.3758/s13428-018-01193-y is OK
- 10.1167/jov.22.3.36 is OK
- 10.1167/jov.22.8.5 is OK
- 10.1167/jov.22.14.4041 is OK
- 10.1167/jov.22.3.20 is OK
- 10.1167/jov.22.14.4160 is OK
- 10.1167/jov.21.9.2824 is OK
- 10.1167/8.12.8 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[emdupre]

Thank you, @JorisVincent ! Confirming that I am now able to access the archive and have confirmed its metadata.

[emdupre]

I'm now happy to recommend stimupy for publication 🚀

Congratulations @LynnSchmittwilken, and thank you to @alexander-pastukhov and @JonathanReardon 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

- 10.1167/jov.22.14.3519 is OK
- 10.1163/156856897X00357 is OK
- 10.1117/12.348473 is OK
- 10.1117/12.387150 is OK
- 10.1109/CVPR.2009.5206848 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.3233/978-1-61499-649-1-87 is OK
- 10.3758/s13428-022-01900-w is OK
- 10.1177/03010066211057347 is OK
- 10.1109/ICCV.2001.937655 is OK
- 10.1167/jov.20.7.28 is OK
- 10.1146/annurev-vision-093019-115159 is OK
- 10.3758/s13428-018-01193-y is OK
- 10.1167/jov.22.3.36 is OK
- 10.1167/jov.22.8.5 is OK
- 10.1167/jov.22.14.4041 is OK
- 10.1167/jov.22.3.20 is OK
- 10.1167/jov.22.14.4160 is OK
- 10.1167/jov.21.9.2824 is OK
- 10.1167/8.12.8 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/sbcs-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#4294, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[LynnSchmittwilken]

Dear @emdupre ,
the final proof looks good, so we are happy to proceed.

We also want to use this chance to thank you as well as @alexander-pastukhov and @JonathanReardon for the pleasant and very constructive review and all your feedback!

[oliviaguest]

@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

- 10.1167/jov.22.14.3519 is OK
- 10.1163/156856897X00357 is OK
- 10.1117/12.348473 is OK
- 10.1117/12.387150 is OK
- 10.1109/CVPR.2009.5206848 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.3233/978-1-61499-649-1-87 is OK
- 10.3758/s13428-022-01900-w is OK
- 10.1177/03010066211057347 is OK
- 10.1109/ICCV.2001.937655 is OK
- 10.1167/jov.20.7.28 is OK
- 10.1146/annurev-vision-093019-115159 is OK
- 10.3758/s13428-018-01193-y is OK
- 10.1167/jov.22.3.36 is OK
- 10.1167/jov.22.8.5 is OK
- 10.1167/jov.22.14.4041 is OK
- 10.1167/jov.22.3.20 is OK
- 10.1167/jov.22.14.4160 is OK
- 10.1167/jov.21.9.2824 is OK
- 10.1167/8.12.8 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/sbcs-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#4304, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[oliviaguest]

@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: Schmittwilken
  given-names: Lynn
  orcid: "https://orcid.org/0000-0003-3621-9576"
- family-names: Maertens
  given-names: Marianne
- family-names: Vincent
  given-names: Joris
  orcid: "https://orcid.org/0000-0001-6882-5584"
contact:
- family-names: Schmittwilken
  given-names: Lynn
  orcid: "https://orcid.org/0000-0003-3621-9576"
doi: 10.17605/OSF.IO/Z439V
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Schmittwilken
    given-names: Lynn
    orcid: "https://orcid.org/0000-0003-3621-9576"
  - family-names: Maertens
    given-names: Marianne
  - family-names: Vincent
    given-names: Joris
    orcid: "https://orcid.org/0000-0001-6882-5584"
  date-published: 2023-06-13
  doi: 10.21105/joss.05321
  issn: 2475-9066
  issue: 86
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5321
  title: "stimupy: A Python package for creating stimuli in vision
    science"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05321"
  volume: 8
title: "`stimupy`: A Python package for creating stimuli in vision
  science"

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.05321 joss-papers#4306
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05321
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...

[oliviaguest]

Congratulations to @LynnSchmittwilken! 🍾 And a big thanks to @emdupre and the reviewers: @alexander-pastukhov, @JonathanReardon! 👏

[editorialbot]

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

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  <img src="https://joss.theoj.org/papers/10.21105/joss.05321/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05321/status.svg
   :target: https://doi.org/10.21105/joss.05321

This is how it will look in your documentation:

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