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

Open whedon opened this issue 5 years ago • 42 comments

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

status

Status badge code:

HTML: <a href="http://jose.theoj.org/papers/2f41f8e108eac1c0bf482f1fa9968008"><img src="http://jose.theoj.org/papers/2f41f8e108eac1c0bf482f1fa9968008/status.svg"></a>
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

Code of Conduct

General checks

  • [x] Repository: Is the source for this learning module available at the repository url?
  • [x] 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)
  • [x] Version: Does the release version given match the repository release (v1.0)?
  • [x] Authorship: Has the submitting author (@ctdegroot) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

  • [x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
  • [x] Installation instructions: Is there a clearly stated list of dependencies?
  • [x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
  • [x] 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!)

  • [x] 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.)
  • [x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
  • [x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
  • [x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
  • [x] 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

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

Review checklist for @zingale

Conflict of interest

Code of Conduct

General checks

  • [x] Repository: Is the source for this learning module available at the repository url?
  • [x] 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)
  • [x] Version: Does the release version given match the repository release (v1.0)?
  • [x] Authorship: Has the submitting author (@ctdegroot) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

  • [x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
  • [x] Installation instructions: Is there a clearly stated list of dependencies?
  • [x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
  • [x] 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!)

  • [x] 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.)
  • [x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
  • [x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
  • [x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
  • [x] 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

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

whedon avatar Aug 11 '19 07:08 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 :tada:.

:star: Important :star:

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:

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

watching

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

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 avatar Aug 11 '19 07:08 whedon

Attempting PDF compilation. Reticulating splines etc...

whedon avatar Aug 11 '19 07:08 whedon

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

sconde avatar Aug 16 '19 00:08 sconde

@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.

IanHawke avatar Aug 16 '19 08:08 IanHawke

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.

labarba avatar Aug 16 '19 08:08 labarba

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

ctdegroot avatar Aug 16 '19 14:08 ctdegroot

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

zingale avatar Aug 18 '19 16:08 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 avatar Aug 20 '19 16:08 zingale

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

zingale avatar Aug 20 '19 16:08 zingale

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.

ctdegroot avatar Aug 21 '19 19:08 ctdegroot

@whedon remind @ctdegroot in 3 weeks

IanHawke avatar Aug 22 '19 13:08 IanHawke

Reminder set for @ctdegroot in 3 weeks

whedon avatar Aug 22 '19 13:08 whedon

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

whedon avatar Sep 12 '19 13:09 whedon

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

labarba avatar Oct 20 '19 12:10 labarba

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

ctdegroot avatar Oct 20 '19 17:10 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 avatar Mar 12 '20 02:03 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.

ctdegroot avatar Mar 12 '20 02:03 ctdegroot

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 avatar Feb 20 '21 17:02 labarba

@whedon generate pdf

labarba avatar Feb 20 '21 17:02 labarba

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

whedon avatar Feb 20 '21 17:02 whedon

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.

ctdegroot avatar Feb 23 '21 19:02 ctdegroot

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.

labarba avatar Feb 23 '21 20:02 labarba

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

Bitbucket issue

sconde avatar Mar 10 '21 19:03 sconde

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

sconde avatar Mar 10 '21 19:03 sconde

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?

labarba avatar May 10 '21 17:05 labarba

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 https://github.com/openjournals/jose-reviews/issues/67#issuecomment-837013741, 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/mzingalettps://zingale.github.io github: https://github.com/zingale http://github.com/zingale

zingale avatar May 12 '21 17:05 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!

zingale avatar May 17 '21 14:05 zingale

@whedon generate pdf

labarba avatar May 23 '21 12:05 labarba

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

whedon avatar May 23 '21 12:05 whedon