[REVIEW]: Computational models of human social behavior and neuroscience: An open educational course and Jupyter Book to advance computational training #146

whedon · 2021-10-19T22:42:09Z

Submitting author: @shawnrhoads (Shawn A. Rhoads)
Repository: https://github.com/shawnrhoads/gu-psyc-347
Version: v1.1.0
Editor: @emckiernan
Reviewer: @arokem, @djmannion
Archive: 10.5281/zenodo.5907205

⚠️ JOSE reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSE is currently operating in a "reduced service mode".

Status

Status badge code:

HTML: <a href="https://jose.theoj.org/papers/62fca31989cb19be1eb93970ac7554be"><img src="https://jose.theoj.org/papers/62fca31989cb19be1eb93970ac7554be/status.svg"></a>
Markdown: [![status](https://jose.theoj.org/papers/62fca31989cb19be1eb93970ac7554be/status.svg)](https://jose.theoj.org/papers/62fca31989cb19be1eb93970ac7554be)

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

@arokem & @djmannion, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/jose-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @emckiernan 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 ✨

Review checklist for @arokem

Conflict of interest

As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

I confirm that I read and will adhere to the JOSE code of conduct.

General checks

Repository: Is the source for this learning module available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
Version: v1.1.0
Authorship: Has the submitting author (@shawnrhoads) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

A statement of need: Do the authors clearly state the need for this module and who the target audience is?
Installation instructions: Is there a clearly stated list of dependencies?
Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

Authors: Does the paper.md file include a list of authors with their affiliations?
A statement of need: Does the paper clearly state the need for this module and who the target audience is?
Description: Does the paper describe the learning materials and sequence?
Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
Could someone else teach with this module, given the right expertise?
Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @djmannion

Conflict of interest

As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

I confirm that I read and will adhere to the JOSE code of conduct.

General checks

Repository: Is the source for this learning module available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
Version: v1.1.0
Authorship: Has the submitting author (@shawnrhoads) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

A statement of need: Do the authors clearly state the need for this module and who the target audience is?
Installation instructions: Is there a clearly stated list of dependencies?
Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

Authors: Does the paper.md file include a list of authors with their affiliations?
A statement of need: Does the paper clearly state the need for this module and who the target audience is?
Description: Does the paper describe the learning materials and sequence?
Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
Could someone else teach with this module, given the right expertise?
Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

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

whedon · 2021-10-19T22:42:12Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @arokem, @djmannion it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSE reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSE is currently operating in a "reduced service mode".

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/jose-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/jose-reviews:

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

whedon · 2021-10-19T22:42:21Z

Wordcount for paper.md is 1668

whedon · 2021-10-19T22:42:22Z

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

OK DOIs

- 10.1111/tops.12404 is OK
- 10.1177/1745691620970585 is OK
- 10.7554/eLife.49547 is OK
- 10.1093/scan/nsaa040 is OK
- 10.1093/scan/nsaa089 is OK
- 10.1016/j.tics.2017.03.011 is OK
- 10.1016/j.neuron.2021.04.001 is OK
- 10.1016/j.tics.2021.03.018 is OK
- 10.1371/journal.pone.0244974 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.3509134 is OK
- 10.1073/pnas.1603198113 is OK
- 10.3758/s13428-018-01193-y is OK
- 10.5281/zenodo.2561065 is OK
- 10.1016/j.neuron.2013.10.038 is OK
- 10.1002/9781119159193.ch17 is OK
- 10.1186/s13742-016-0121-x is OK
- 10.5281/zenodo.3909717 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-10-19T22:42:24Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.21 s (285.1 files/s, 223638.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           3            727           1282           5141
Jupyter Notebook                33              0          26552           4478
JavaScript                       2            655            503           3247
XML                              2              0              0           1651
Markdown                        11            234              0            820
TeX                              2             37              0            719
YAML                             5             14             26            158
HTML                             1              7              4             29
-------------------------------------------------------------------------------
SUM:                            59           1674          28367          16243
-------------------------------------------------------------------------------


Statistical information for the repository 'ca40fafda596e0be725e9ca8' was
gathered on 2021/10/19.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Shawn Rhoads                     7         26446          14891          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Shawn Rhoads              11555           43.7          0.0               15.27

whedon · 2021-10-19T22:42:28Z

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

emckiernan · 2021-10-19T22:44:34Z

Hi @arokem and @djmannion: Thank you for agreeing to review for JOSE! There are individual checklists for you both at the top of this issue. Please work your way through those, feel free to ask questions or post comments here, and also open issues in the submission repository as needed. I'm here to help, so please let me know if you need anything. Thanks!

djmannion · 2021-10-20T05:14:10Z

I confirm that I read and will adhere to the JOSE code of conduct.

Sorry, I can't seem to find the JOSE code of conduct - the link on the linked-to website (https://github.com/openjournals/jose/blob/master/CODE_OF_CONDUCT.md) gives a "Page not found" error.

arokem · 2021-10-20T16:21:32Z

To this question:

"Version: Does the release version given match the repository release (v1.0.0)?"

There are currently no releases on the GitHub repo, although there is a v1.0.0 tag that could easily be released through the GitHub interface, if that's needed.

shawnrhoads · 2021-10-20T16:29:14Z

To this question:

"Version: Does the release version given match the repository release (v1.0.0)?"

There are currently no releases on the GitHub repo, although there is a v1.0.0 tag that could easily be released through the GitHub interface, if that's needed.

@arokem, thanks for pointing this out! I just changed the repo settings to display the release version. Does it look right now? https://github.com/shawnrhoads/gu-psyc-347

emckiernan · 2021-10-20T16:41:24Z

Sorry, I can't seem to find the JOSE code of conduct - the link on the linked-to website (https://github.com/openjournals/jose/blob/master/CODE_OF_CONDUCT.md) gives a "Page not found" error.

@djmannion, thanks for flagging this! I get a 404 too, and I can't find the COC in the JOSE repo. I have a message in to the EIC, and will update you ASAP.

labarba · 2021-10-20T19:44:11Z

Where do you see the broken link to the CoC?

In the reviewer checklists, I see the text linking to https://jose.theoj.org/about#code_of_conduct which resolves properly for me.

emckiernan · 2021-10-20T19:52:09Z

Where do you see the broken link to the CoC?

In the reviewer checklists, I see the text linking to https://jose.theoj.org/about#code_of_conduct which resolves properly for me.

Hi @labarba: yes, that link does resolve correctly. But that page just describes that there is a CoC and then is supposed to link out to the CoC itself. The embedded link there, which points to https://github.com/openjournals/jose/blob/main/CODE_OF_CONDUCT.md, is what gives the 404.

labarba · 2021-10-20T20:00:59Z

Thanks for flagging this. We reorganized the Open Journals repositories this Summer, and a few things remain broken. Argh!

This repository is now just a placeholder and has no real content: https://github.com/openjournals/jose/

The JOSE content is now on a jose branch of the joss repo, and the COI is here: https://github.com/openjournals/joss/blob/jose/COI.md

We've made a note to fix this.

labarba · 2021-10-20T20:02:20Z

Argh! That is the COI, not COC — try again.

https://github.com/openjournals/joss/blob/jose/CODE_OF_CONDUCT.md

emckiernan · 2021-10-20T20:07:04Z

Thanks, @labarba! Got it now :)

@arokem and @djmannion: The link Lorena shared above will get you to the CoC. Please let me know if you have any other questions, thanks!

whedon · 2021-11-02T22:42:25Z

👋 @arokem, please update us on how your review is going (this is an automated reminder).

whedon · 2021-11-02T22:42:25Z

👋 @djmannion, please update us on how your review is going (this is an automated reminder).

arokem · 2021-11-03T02:34:12Z

Clearly, not going fast enough 😄

I am still working through this slowly. I hope to be able to work through everything in the next couple of weeks.

emckiernan · 2021-11-03T16:34:20Z

No worries, @arokem, thanks for letting us know!

djmannion · 2021-11-03T22:05:09Z

wave @djmannion, please update us on how your review is going (this is an automated reminder).

Working on it 😄

emckiernan · 2021-11-03T22:15:51Z

Super, thanks, @djmannion!

djmannion · 2021-11-04T23:35:48Z

A general comment about the documentation (which I take to mean the repository documentation, rather than the jupyter book), which affects my response to those criteria, is that it seems to be for students in the course rather than for others who might like to adapt/use the material.

For example, it looks like the repository README.md is copied to become the index page of the jupyter book. That means that it has things like the course logistics that are relevant for students, but not for non-students considering using the material - and that any changes to the README.md to address such topics (e.g., how to build the book) would be not appropriate to show to students.

Might it be better to separate the material for those different audiences? For example, have the repository documentation (README.md) be about the need for the module from an educator perspective, how someone can adapt and build it for their own course, etc., and have all the student-targeted material in docs?

arokem · 2021-11-05T21:48:54Z

For this point:

Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?

I think that you could add a bit in the paper about your experience . This is also a +1 to @djmannion's comment above that the document could be improved to make this more accessible to other instructors. You might consider adding a section about how to use the materials from the instructor point of view.

This point:

Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?

Also does not currently clearly come through.

arokem · 2021-11-05T21:49:51Z

Other than these two points, I have read through the materials and the paper and added a couple of issues on the project repo, but have no other comments/suggestions. So, once these issues are all addressed, I would be happy to recommend this paper be accepted.

shawnrhoads · 2022-01-26T16:57:18Z

On Zenodo, there is an option that says the following:

Optional. Did your publisher already assign a DOI to your upload? If not, leave the field empty and we will register a new DOI for you. A DOI allows others to easily and unambiguously cite your upload. Please note that it is NOT possible to edit a Zenodo DOI once it has been registered by us, while it is always possible to edit a custom DOI.

Should I provide a DOI from JOSE or have one assigned by Zenodo?

labarba · 2022-01-26T17:22:04Z

Have Zenodo assign a DOI. This is for the archive of your materials. The JOSE DOI is for the citable paper only.

shawnrhoads · 2022-01-26T17:35:32Z

Sounds good! Here it is: https://doi.org/10.5281/zenodo.5907205

emckiernan · 2022-01-26T21:18:36Z

@whedon set v1.1.0 as version

whedon · 2022-01-26T21:18:41Z

OK. v1.1.0 is the version.

emckiernan · 2022-01-26T21:20:56Z

@whedon set https://doi.org/10.5281/zenodo.5907205 as archive

whedon · 2022-01-26T21:21:00Z

OK. 10.5281/zenodo.5907205 is the archive.

emckiernan · 2022-01-26T21:21:14Z

@whedon generate pdf

whedon · 2022-01-26T21:21:35Z

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

emckiernan · 2022-01-26T21:23:45Z

@whedon check references

whedon · 2022-01-26T21:23:56Z

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

OK DOIs

- 10.1111/tops.12404 is OK
- 10.1177/1745691620970585 is OK
- 10.7554/eLife.49547 is OK
- 10.1093/scan/nsaa040 is OK
- 10.1093/scan/nsaa089 is OK
- 10.1016/j.tics.2017.03.011 is OK
- 10.1016/j.neuron.2021.04.001 is OK
- 10.1016/j.tics.2021.03.018 is OK
- 10.1371/journal.pone.0244974 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.3509134 is OK
- 10.1073/pnas.1603198113 is OK
- 10.3758/s13428-018-01193-y is OK
- 10.5281/zenodo.2561065 is OK
- 10.1016/j.neuron.2013.10.038 is OK
- 10.1002/9781119159193.ch17 is OK
- 10.1186/s13742-016-0121-x is OK
- 10.5281/zenodo.3909717 is OK

MISSING DOIs

- None

INVALID DOIs

- None

emckiernan · 2022-01-26T21:26:29Z

@labarba Hi Lorena, thanks for the assist :) I think everything is good to go here! I've set the version and archive DOI, checked the proofs and refs, etc. Is there anything else for me to do?

labarba · 2022-01-26T21:31:52Z

👋 If everything is ready to go, you as handling editor run @whedon recommend-accept — and I think that would automatically do the check on references and generate the pdf ... try it! 😁

emckiernan · 2022-01-26T21:33:03Z

@whedon recommend-accept

whedon · 2022-01-26T21:33:06Z

Attempting dry run of processing paper acceptance...

whedon · 2022-01-26T21:33:16Z

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

OK DOIs

- 10.1111/tops.12404 is OK
- 10.1177/1745691620970585 is OK
- 10.7554/eLife.49547 is OK
- 10.1093/scan/nsaa040 is OK
- 10.1093/scan/nsaa089 is OK
- 10.1016/j.tics.2017.03.011 is OK
- 10.1016/j.neuron.2021.04.001 is OK
- 10.1016/j.tics.2021.03.018 is OK
- 10.1371/journal.pone.0244974 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.3509134 is OK
- 10.1073/pnas.1603198113 is OK
- 10.3758/s13428-018-01193-y is OK
- 10.5281/zenodo.2561065 is OK
- 10.1016/j.neuron.2013.10.038 is OK
- 10.1002/9781119159193.ch17 is OK
- 10.1186/s13742-016-0121-x is OK
- 10.5281/zenodo.3909717 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2022-01-26T21:33:28Z

👋 @openjournals/jose-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/jose-papers#79

If the paper PDF and Crossref deposit XML look good in openjournals/jose-papers#79, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

emckiernan · 2022-01-26T21:35:01Z

@whedon accept deposit=true

whedon · 2022-01-26T21:35:04Z

I'm sorry @emckiernan, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

emckiernan · 2022-01-26T21:35:46Z

Haha, oops! Guess that last one is yours, @labarba!

labarba · 2022-01-26T22:06:40Z

@whedon accept deposit=true

whedon · 2022-01-26T22:06:43Z

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

whedon · 2022-01-26T22:07:12Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.jose.00146 jose-papers#80
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/jose.00146
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

shawnrhoads · 2022-01-26T22:13:02Z

Amazing! Thank you again to @arokem and @djmannion for your thoughtful reviews, and to @emckiernan and @labarba for supporting this incredible initiative!

I signed up to be a potential reviewer a few months back and will hope to contribute sometime in the future! 😄

labarba · 2022-01-26T22:13:07Z

Congratulations, @shawnrhoads, your JOSE paper is published! 🚀

Huge thanks to our Editor: @emckiernan, and the Reviewers: @arokem, @djmannion — your contributions make this adventure in scholarly publication possible, and we are grateful for it 🙏

whedon · 2022-01-26T22:13:35Z

🎉🎉🎉 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://jose.theoj.org/papers/10.21105/jose.00146/status.svg)](https://doi.org/10.21105/jose.00146)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jose.00146">
  <img src="https://jose.theoj.org/papers/10.21105/jose.00146/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://jose.theoj.org/papers/10.21105/jose.00146/status.svg
   :target: https://doi.org/10.21105/jose.00146

This is how it will look in your documentation:

We need your help!

Journal of Open Source Education is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: http://jose.theoj.org/reviewer-signup.html
Making a small donation to support our running costs here: https://numfocus.org/donate-to-jose

whedon added review TeX labels Oct 19, 2021

whedon assigned emckiernan Oct 19, 2021

whedon mentioned this issue Oct 19, 2021

[PRE REVIEW]: Computational models of human social behavior and neuroscience: An open educational course and Jupyter Book to advance computational training #136

Closed

whedon assigned arokem and djmannion Oct 20, 2021

whedon added the recommend-accept Papers recommended for acceptance in JOSE. label Jan 26, 2022

whedon added accepted published Papers published in JOSE labels Jan 26, 2022

labarba closed this as completed Jan 26, 2022

[REVIEW]: Computational models of human social behavior and neuroscience: An open educational course and Jupyter Book to advance computational training #146

[REVIEW]: Computational models of human social behavior and neuroscience: An open educational course and Jupyter Book to advance computational training #146

Comments

whedon commented Oct 19, 2021 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @arokem

Conflict of interest

Code of Conduct

General checks

Documentation

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

JOSE paper

Review checklist for @djmannion

Conflict of interest

Code of Conduct

General checks

Documentation

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

JOSE paper

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shawnrhoads commented Jan 26, 2022

labarba commented Jan 26, 2022

whedon commented Jan 26, 2022

whedon commented Oct 19, 2021 •

edited

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whedon commented Oct 19, 2021 •

edited by labarba

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shawnrhoads commented Oct 20, 2021 •

edited

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shawnrhoads commented Jan 26, 2022 •

edited

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