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[REVIEW]: Aero Python: classical aerodynamics of potential flow using Python #45

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whedon opened this issue Jan 31, 2019 · 68 comments
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@whedon whedon commented Jan 31, 2019

Submitting author: @labarba (Lorena A. Barba)
Repository: https://github.com/barbagroup/AeroPython
Version: v1.0
Editor: @kyleniemeyer
Reviewer: @weymouth, @Juanlu001
Archive: 10.6084/m9.figshare.1004727.v4

Status

status

Status badge code:

HTML: <a href="http://jose.theoj.org/papers/b679b34c976beec0bc64807bf087a468"><img src="http://jose.theoj.org/papers/b679b34c976beec0bc64807bf087a468/status.svg"></a>
Markdown: [![status](http://jose.theoj.org/papers/b679b34c976beec0bc64807bf087a468/status.svg)](http://jose.theoj.org/papers/b679b34c976beec0bc64807bf087a468)

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

@weymouth & @Juanlu001, 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 @kyleniemeyer know.

Review checklist for @weymouth

Conflict of interest

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
  • Authorship: Has the submitting author (@labarba) 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 @Juanlu001

Conflict of interest

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
  • Authorship: Has the submitting author (@labarba) 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
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@whedon whedon commented Jan 31, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @weymouth, it looks like you're currently assigned as the reviewer for 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:

  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
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@whedon whedon commented Jan 31, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Jan 31, 2019

@kyleniemeyer
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@kyleniemeyer kyleniemeyer commented Jan 31, 2019

👋 @weymouth @Juanlu001 @labarba the actual review will take place here; please note the separate review checklists above

@astrojuanlu
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@astrojuanlu astrojuanlu commented Mar 20, 2019

Hi all - sorry this is taking me so long. I will try to start the review next week, or the following one at most.

@labarba
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@labarba labarba commented Mar 21, 2019

Looking forward to your review comments, @weymouth and @Juanlu001 !

@weymouth
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@weymouth weymouth commented Apr 1, 2019

I think this is a great repository and a model for other similar projects. The only things I notice are

  1. The write-up doesn't make the development "story" clear.
  2. The usage of the code in the repository is well explained. Would it be helpful to explain how this ties in with the other parts of the class? For example, is this supposed to be the first time students see any of these concepts? Is it important how they use this material later on in their education?
  3. I don't see the version number. (Which I only mention because of the checklist.)
@mesnardo
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@mesnardo mesnardo commented Apr 4, 2019

Hi @weymouth,

Thank you for your review of AeroPython! We'll work on your suggestions.

(@Juanlu001, looking forward to your review.)

@kyleniemeyer
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@kyleniemeyer kyleniemeyer commented Apr 16, 2019

Hi @Juanlu001, just wanted to check in on the status of your review.

@mesnardo have you made changes according to @weymouth's suggestions?

@mesnardo
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@mesnardo mesnardo commented Apr 16, 2019

@kyleniemeyer We are waiting for the review of @Juanlu001 before making the suggested modifications.

@labarba
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@labarba labarba commented Apr 20, 2019

Hi @Juanlu001 — we're eager to get your review of the AeroPython module, to make a revision and get it to publication-ready status. Would you be able to get to this soon?

@astrojuanlu
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@astrojuanlu astrojuanlu commented Apr 21, 2019

Sorry for the super long delay. On it!

@astrojuanlu
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@astrojuanlu astrojuanlu commented Apr 21, 2019

It was quick because I already knew the course from the time it was released :)

Non-blocking comments:

  • There is no version number, so I left that unchecked
  • There is a statement of need in the paper but not in the repository itself - I understand that there are two checkboxes for this reason, so I left the first unchecked as well
  • Perhaps this is a bit presumptuous on my side, but I would add a little footnote somewhere stating somethink like "not to be confused with another Python course for aeronautical engineers in Spanish language, with the same name but different content" (refs: https://github.com/AeroPython/Curso_AeroPython/, https://twitter.com/LorenaABarba/status/464041427169583104)
@mesnardo
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@mesnardo mesnardo commented May 1, 2019

Thank you @weymouth and @Juanlu001 for your feedback!

Modifications based on your suggestions are available in the branch jose_revision ; their is an open PR (#44) to merge these commits in the master branch.

  • We added a version number to the GitHub repository; the GitHub release will be done once the revision is finished.
  • We added a note at the bottom of the README to mention the other AeroPython repository.
  • We modified the write-up to mention how AeroPython can be used as a full-semester course.
@labarba
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@labarba labarba commented May 1, 2019

Regarding the Statement of Need, the JOSE editors decided it would only be required in the paper (not the documentation), but unfortunately the checklists haven't been updated yet!

@labarba
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@labarba labarba commented May 12, 2019

👋 @weymouth, @Juanlu001 — I think we're ready with this revision. Would you take a final look? The editor will need your recommendation to accept.

@weymouth
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@weymouth weymouth commented May 12, 2019

Looks good to me!

@astrojuanlu
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@astrojuanlu astrojuanlu commented May 13, 2019

And to me! 👍

@labarba
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@labarba labarba commented May 13, 2019

Thank you, @weymouth and @Juanlu001 — we appreciate your time reviewing this submission!

@kyleniemeyer — we await your final checks for publication.

@kyleniemeyer
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@kyleniemeyer kyleniemeyer commented May 13, 2019

@labarba will do those shortly

@kyleniemeyer
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@kyleniemeyer kyleniemeyer commented May 13, 2019

@whedon generate pdf

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@whedon whedon commented May 13, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented May 13, 2019

@kyleniemeyer
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@kyleniemeyer kyleniemeyer commented May 13, 2019

@labarba @mesnardo a few minor comments on the paper itself:

  • Could you add full affiliation details (city, state, country)?
  • I believe the final bullet in the list of lessons should start with "Assignment 3"
  • I just submitted a small fix to the paper near the end; multiple references in the same square brackets should be separated by semicolons: barbagroup/AeroPython#45
  • the Catrambone reference is missing the DOI: 10.1037/0096-3445.127.4.355
  • the Margulieux reference is missing the DOI: 10.1080/08993408.2016.1144429

Once you make those fixes, please archive the repo and provide the DOI. Almost done!

@mesnardo
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@mesnardo mesnardo commented May 14, 2019

@labarba @mesnardo a few minor comments on the paper itself:

  • Could you add full affiliation details (city, state, country)?

Done in 35cf51d.

  • I believe the final bullet in the list of lessons should start with "Assignment 3"

Done in 8209e1a.

  • I just submitted a small fix to the paper near the end; multiple references in the same square brackets should be separated by semicolons: barbagroup/AeroPython#45

Thank you.

  • the Catrambone reference is missing the DOI: 10.1037/0096-3445.127.4.355
  • the Margulieux reference is missing the DOI: 10.1080/08993408.2016.1144429

Added mission DOIs in 64b97fc.

Once you make those fixes, please archive the repo and provide the DOI. Almost done!

@kyleniemeyer
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@kyleniemeyer kyleniemeyer commented May 14, 2019

@whedon generate pdf

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@whedon whedon commented May 17, 2019

OK. 10.6084/m9.figshare.1004727.v4 is the archive.

@kyleniemeyer
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@kyleniemeyer kyleniemeyer commented May 17, 2019

@whedon accept

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@whedon whedon commented May 17, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented May 17, 2019

PDF failed to compile for issue #45 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/45 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:57:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:73:in compile' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:116:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

@kyleniemeyer
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@kyleniemeyer kyleniemeyer commented May 17, 2019

@whedon generate pdf

@whedon
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@whedon whedon commented May 17, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon
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@whedon whedon commented May 17, 2019

@kyleniemeyer
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@kyleniemeyer kyleniemeyer commented May 17, 2019

@whedon accept

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@whedon whedon commented May 17, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented May 17, 2019

Check final proof 👉 openjournals/jose-papers#33

If the paper PDF and Crossref deposit XML look good in openjournals/jose-papers#33, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
@kyleniemeyer
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@kyleniemeyer kyleniemeyer commented May 17, 2019

@whedon accept deposit=true

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@whedon whedon commented May 17, 2019

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

@labarba
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@labarba labarba commented May 17, 2019

Yikes!

@kyleniemeyer
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@kyleniemeyer kyleniemeyer commented May 17, 2019

@labarba hmm, I think I am supposed to have that power...

@labarba
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@labarba labarba commented May 17, 2019

On JOSS, yes. But here, we never set up an EiC team.

@kyleniemeyer
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@kyleniemeyer kyleniemeyer commented May 17, 2019

@labarba Ah. Well, we can figure that out offline. In the meantime, JOSE EiC, I'd like to recommend this submission be accepted 😄

@labarba
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@labarba labarba commented May 17, 2019

I was just fiddling to create a new team (which I did), but can't find how to give it Admin powers. Gah.

@labarba
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@labarba labarba commented May 17, 2019

I'll just go ahead and publish this.

@labarba
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@labarba labarba commented May 17, 2019

@whedon accept deposit=true

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@whedon whedon commented May 17, 2019

Doing it live! Attempting automated processing of paper acceptance...
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@whedon whedon commented May 17, 2019

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/jose-papers#34
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/jose.00045
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

@kyleniemeyer
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@kyleniemeyer kyleniemeyer commented May 17, 2019

Congrats to @labarba and @mesnardo on your submissions's publication in JOSE! Thanks to @weymouth and @Juanlu001 for reviewing!

@whedon
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@whedon whedon commented May 17, 2019

🎉🎉🎉 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.00045/status.svg)](https://doi.org/10.21105/jose.00045)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jose.00045">
  <img src="https://jose.theoj.org/papers/10.21105/jose.00045/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://jose.theoj.org/papers/10.21105/jose.00045/status.svg
   :target: https://doi.org/10.21105/jose.00045

This is how it will look in your documentation:

DOI

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@mesnardo
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@mesnardo mesnardo commented May 17, 2019

Yay! Many thanks to @kyleniemeyer, @Juanlu001, and @weymouth for all the suggestions and modifications provided!

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@whedon whedon commented May 17, 2019


OK DOIs

- 10.1080/08993408.2016.1144429 is OK
- 10.1037/0096-3445.127.4.355 is OK
- 10.1037/edu0000018 is OK
- 10.1016/j.learninstruc.2006.02.005 is OK
- 10.1007/978-3-642-84010-4_1 is OK
- 10.21105/jose.00021 is OK

MISSING DOIs

- None

INVALID DOIs

- None
2 similar comments
@whedon
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@whedon whedon commented May 17, 2019


OK DOIs

- 10.1080/08993408.2016.1144429 is OK
- 10.1037/0096-3445.127.4.355 is OK
- 10.1037/edu0000018 is OK
- 10.1016/j.learninstruc.2006.02.005 is OK
- 10.1007/978-3-642-84010-4_1 is OK
- 10.21105/jose.00021 is OK

MISSING DOIs

- None

INVALID DOIs

- None
@whedon
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@whedon whedon commented May 18, 2019


OK DOIs

- 10.1080/08993408.2016.1144429 is OK
- 10.1037/0096-3445.127.4.355 is OK
- 10.1037/edu0000018 is OK
- 10.1016/j.learninstruc.2006.02.005 is OK
- 10.1007/978-3-642-84010-4_1 is OK
- 10.21105/jose.00021 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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