[REVIEW]: A course on the implicit finite volume method for CFD using Python

[whedon]

Submitting author: @ctdegroot (Christopher DeGroot)
Repository: https://bitbucket.org/cdegroot/cfdcourse/
Branch with paper.md (empty if default branch):
Version: v1.0
Editor: @IanHawke
Reviewers: @sconde, @zingale
Archive: Pending

Status

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Markdown: [![status](http://jose.theoj.org/papers/2f41f8e108eac1c0bf482f1fa9968008/status.svg)](http://jose.theoj.org/papers/2f41f8e108eac1c0bf482f1fa9968008)

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) 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

@sconde & @zingale, 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://jose.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @IanHawke know.

Review checklist for @sconde

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: Does the release version given match the repository release (v1.0)?
• Authorship: Has the submitting author (@ctdegroot) 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 @zingale

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: Does the release version given match the repository release (v1.0)?
• Authorship: Has the submitting author (@ctdegroot) 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. @sconde, @zingale it looks like you're currently assigned to review this paper 🎉.

⭐ 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:

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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]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[sconde]

@IanHawke The repository hosted on bitbucket does not have issue tracking enabled

[IanHawke]

@ctdegroot : I don't know why bitbucket don't automatically switch on issue tracking, but there we go. Could you switch on an issue tracker (if needed, instructions are at https://confluence.atlassian.com/bitbucket/enable-an-issue-tracker-223216498.html)? A public one would be easiest, but at least both referees will need access to it if you choose the private one.

[labarba]

We're working on a new site for JOSE and will then have a joint documentation site with JOSS where this will be made clear, but (like JOSS) we do want our submissions to have an open issue tracker. See the updated JOSS submission requirements.

[ctdegroot]

@IanHawke I didn't notice that, but the issue tracker has been enabled now.

[zingale]

https://bitbucket.org/cdegroot/cfdcourse/issues/1/missing-community-guidelines

[zingale]

https://bitbucket.org/cdegroot/cfdcourse/issues/2/markdown-links-dont-render-in-tip-boxes

https://bitbucket.org/cdegroot/cfdcourse/issues/3/comments-on-descriptions-in-chapter-1

[zingale]

https://bitbucket.org/cdegroot/cfdcourse/issues/4/comments-on-descriptions-in-chapter-2

[ctdegroot]

Thanks for the feedback so far. I will be away for a couple of weeks on holidays, but I will address these soon after I return.

[IanHawke]

@whedon remind @ctdegroot in 3 weeks

[whedon]

Reminder set for @ctdegroot in 3 weeks

[whedon]

👋 @ctdegroot, please update us on how things are progressing here.

[labarba]

@ctdegroot — Can we have a status update from you on the revision?

[ctdegroot]

@labarba My apologies for the delay. I will be able to work on the issues raised so far during the upcoming week.

[ctdegroot]

Sorry to everyone for the delay in addressing the comments. I've done everything except fixing the rendering of some of the HTML code. This worked properly in a previous version of Jupyter, but broke at some point. I'll work on a fix. In the meantime, is there anything else I should be addressing with regard to the remaining un-checked boxes?

[ctdegroot]

It took a while to figure out how to fix the rendering of Markdown inside of HTML blocks. All solved now, so there are no open issues at this point.

[labarba]

Hi @IanHawke @sconde @zingale 👋
I'm now coming back to tend to our neglected little project in publishing. SIGH. Being General Chair of JupyterCon, with the pivot online, was a huge lift and I had months of piled up work. This here submission has been languishing for a long time. Could you all come in here and have a look?

@ctdegroot — apologies for dropping the ball completely here. It looks like you made a lot of changes to address reviewer comments. Just to check: you're OK with reviewers coming in to have a new look?

[labarba]

@whedon generate pdf

[whedon]

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

[ctdegroot]

No worries on the delay @labarba. It happens to the best of us :)

I do believe that I have made all of the requested changes by the reviewers. Interestingly, I am offering the associated course in the current semester for the second go-around.

[labarba]

I just heard back from @sconde via email, and he's ready to take another look. @zingale also got back to me and will pop in here soon.

[sconde]

• Version: Does the release version given match the repository release (v1.0)?

Bitbucket issue

[sconde]

The quality of the submission is very good and recommend to be published following the resolution of the remaining opened issues.

[labarba]

Hi @zingale 👋 — I see that you have a bunch of checks marked off on your review checklist, but several remain. The other reviewer recommended accepting. Can you give it a second look?

[zingale]

yes, I will look very soon. Finishing grading now.

…

On Mon, May 10, 2021 at 1:32 PM Lorena A. Barba ***@***.***> wrote: Hi @zingale <https://github.com/zingale> 👋 — I see that you have a bunch of checks marked off on your review checklist, but several remain. The other reviewer recommended accepting. Can you give it a second look? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#67 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB3USJM4AGTJBWNGQYYMBBDTNAKCNANCNFSM4IK3GKFA> .

-- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: ***@***.*** *web*: h <http://www.astro.sunysb.edu/mzingale>ttps://zingale.github.io github: https://github.com/zingale <http://github.com/zingale>

[zingale]

I'm happy with the current state and I believe I've checked off everything. Thank you for looking at my issues and nice work overall!

[labarba]

@whedon generate pdf

[whedon]

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

[labarba]

Hi @ctdegroot — it looks like we're nearly ready to publish this, yay! 🚀
Thank you so much for your enormous patience.

Could you now up the version, issue a tagged release in your repo, and make a Zenodo deposit? Report the version number here, as well as the Zenodo DOI, so we can run the commands to update that metadata for the submission.

[labarba]

@ctdegroot : one other thing... After reading the paper, I felt that beyond your anecdotal narrative of teaching a course with these materials, it would be nice to add a paragraph explaining how another instructor might adopt these materials and reuse them to teach their own class, or even how a self-learner might use them. Could you give this a think?

[labarba]

@ctdegroot — we are close to the finish line with your JOSE submission. Have a look at the requests above; should take less than half an hour to complete?

[ctdegroot]

@labarba Sorry for my slow reply here! I am on parental leave, which is why this slipped through the cracks. I will have time to wrap up these few items really soon. Hopefully this week.

[labarba]

@ctdegroot — lemme know how it goes, and we can take this through the finish line!

[labarba]

@ctdegroot — hi 👋
Have you been able to look into the final snags to getting your JOSE publication accepted? It got so close!

[labarba]

hi @ctdegroot — We're so close to the finish line here! Would you be able to come in and give it the final push? I think we're waiting on a little addition to the paper (a paragraph explaining how another instructor might adopt these materials and reuse them to teach their own class), and then the final archiving steps:

• cutting a version on the target repo (and report the version number here
• making an archive on Zenodo (and report the archive DOI here)

[labarba]

@ctdegroot — We are ready to publish your JOSE paper, but we need your last tasks, above! Let us know what you plan to do.

[ctdegroot]

@labarba Sorry, this came back to me at a really bad time, with a newborn at home and taking several months off work. I know there’s not a lot left to do, but given the lag time I want to review carefully the comments and make sure I properly take them into account rather than rush to tick the boxes - since the reviewers clearly took their time to give a quality review. That said, things are looking more positively that I can finish things off within a week or two from now.

[labarba]

Great to hear from you, @ctdegroot — and congratulations on the new 👶
Ping here when you are ready to proceed with the publication. Cheers!

[labarba]

@ctdegroot hi! 👋 — could you give us an update on the final steps? Let's get this through the finish line! We can also set a reminder here with @whedon.

[labarba]

hi @ctdegroot — I added a paused label on this one so it doesn't pop up on our weekly audit of in-progress submissions. Please get back to us when you are able to move it to the finish line.