[REVIEW]: Developing and deploying an integrated workshop curriculum teaching computational skills for reproducible research

[whedon]

Submitting author: @pschloss (Patrick D Schloss)
Repository: https://github.com/UMCarpentries/intro-curriculum-r/
Version: v1.0.0
Editor: @magsol
Reviewer: @kdillmcfarland, @tracykteal
Archive: 10.5281/zenodo.5812479

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

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Markdown: [![status](https://jose.theoj.org/papers/4649d22db51c8150274f83f806792dc9/status.svg)](https://jose.theoj.org/papers/4649d22db51c8150274f83f806792dc9)

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

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

1. Make sure you're logged in to your GitHub account
2. 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 @magsol 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 @kdillmcfarland

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: v1.0.0
• Authorship: Has the submitting author (@pschloss) 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 @tracykteal

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: v1.0.0
• Authorship: Has the submitting author (@pschloss) 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)?

[whedon]

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

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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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:

@whedon generate pdf

[whedon]

PDF failed to compile for issue #144 with the following error:

 Can't find any papers to compile :-(

[whedon]

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

[whedon]

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

[kdillmcfarland]

This is the next review on my list! Slated to complete next week.

[kdillmcfarland]

I have completed my review and recommend this paper for publication without revision. I opened several GitHub issues to address minor changes and recommendations (see below). None of these are inhibitory to publication in JOSE.

• Improve Linux installation  UMCarpentries/intro-curriculum-r#147
• Expand index page introduction UMCarpentries/intro-curriculum-r#148
• Broken links UMCarpentries/intro-curriculum-r#149
• JOSE review UMCarpentries/intro-curriculum-r#150

[magsol]

Thanks Kimberly! @pschloss have you had a chance to review the feedback from Kimberly? It looks like this is about it.

@tracykteal how is your review going? Any chance of wrapping this up before the holidays?

[zenalapp]

Thanks so much for the review @kdillmcfarland! We have reviewed and implemented all of your suggested changes.

[magsol]

@tracykteal Hi Tracy! We're waiting on your review before we can move forward with this submission. Any chance of completing your review soon?

[magsol]

Hi @tracykteal! Haven't heard from you in several weeks now. Are you able to complete your review soon, or should we look for another reviewer? Please advise as soon as you can.

[tracykteal]

Thanks! I've gone through my review, and I'm very sorry for the delay. I also recommend this paper for publication without revision. This is an excellent lesson that creates a clear 2 day curriculum that is easy to use for instructors and learners, reducing the overhead of getting started.

This is a lesson based on Software Carpentry and developed by the UM Carpentries instance, so it makes sense to refer to it as 'Carpentries'. It's not officially Carpentries though, given that it's not in a Carpentries space, so some of the references to Carpentries infrastructure aren't relevant. I put in one PR to address.

• Suggesting changes to CoC guidelines language UMCarpentries/intro-curriculum-r#169

I also created an issue with some potential clarification language on the index page.

• Clarification on connection to Carpentries lessons UMCarpentries/intro-curriculum-r#170

The authors may have already had some conversations with Carpentries about naming and acknowledgement though, so if so, please just use whatever they've recommended!

[zenalapp]

Thanks, @tracykteal! We have merged your PR and updated the language about our connection to Carpentries lessons.

@magsol is there anything else we need to do?

[magsol]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #144 with the following error:

 Can't find any papers to compile :-(

[magsol]

@whedon generate pdf

[whedon]

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

[magsol]

@whedon check references

[whedon]

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

OK DOIs

- 10.21105/joss.01686 is OK
- 10.12688/f1000research.3-62.v2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[magsol]

@zenalapp This looks great! At this point I'd ask for you to create a tagged release (only if you don't already have one, or have made updates since your last one) and archive, and post both the release version number and the archive DOI here, and I can take it from there.

[kelly-sovacool]

@magsol I just released version 1.0.0 with DOI 10.5281/zenodo.5812479.

[magsol]

@whedon set 10.5281/zenodo.5812479 as archive

[whedon]

OK. 10.5281/zenodo.5812479 is the archive.

[magsol]

@whedon set v1.0.0 as version

[whedon]

OK. v1.0.0 is the version.

[magsol]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.21105/joss.01686 is OK
- 10.12688/f1000research.3-62.v2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/jose-papers#74

If the paper PDF and Crossref deposit XML look good in openjournals/jose-papers#74, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[labarba]

@pschloss – Could you try to fix the horizontal badness on URLs that appear in the References? Maybe using a \url inside the howpublished field of the .bib entry?

[zenalapp]

@labarba just merged the PR from @kelly-sovacool to fix this.

[labarba]

@whedon generate pdf

[whedon]

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

[labarba]

@whedon accept deposit=true

[whedon]

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

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.jose.00144 jose-papers#77
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/jose.00144
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...

[labarba]

Congratulations, @zenalapp and co-authors, your article is published in JOSE! 🚀

Huge thanks to our Editor: @magsol and the Reviewers: @kdillmcfarland, @tracykteal — we appreciate your contribution to this adventure in publishing 🙏

[whedon]

🎉🎉🎉 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.00144/status.svg)](https://doi.org/10.21105/jose.00144)

HTML:
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  <img src="https://jose.theoj.org/papers/10.21105/jose.00144/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://jose.theoj.org/papers/10.21105/jose.00144/status.svg
   :target: https://doi.org/10.21105/jose.00144

This is how it will look in your documentation:

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