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

whedon commented 5 years ago

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

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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:

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Review checklist for @weymouth

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSE 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: v1.0
[x] Authorship: Has the submitting author (@labarba) 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?
[ ] 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 @Juanlu001

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSE 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: v1.0
[x] 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?
[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 commented 5 years ago

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 :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 😿

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whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

kyleniemeyer commented 5 years ago

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

astrojuanlu commented 5 years ago

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 commented 5 years ago

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

weymouth commented 5 years ago

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

The write-up doesn't make the development "story" clear.
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?
I don't see the version number. (Which I only mention because of the checklist.)

mesnardo commented 5 years ago

Hi @weymouth,

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

(@Juanlu001, looking forward to your review.)

kyleniemeyer commented 5 years ago

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

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

mesnardo commented 5 years ago

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

labarba commented 5 years ago

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 commented 5 years ago

Sorry for the super long delay. On it!

astrojuanlu commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

👋 @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 commented 5 years ago

Looks good to me!

astrojuanlu commented 5 years ago

And to me! :+1:

labarba commented 5 years ago

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

@kyleniemeyer — we await your final checks for publication.

kyleniemeyer commented 5 years ago

@labarba will do those shortly

kyleniemeyer commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

kyleniemeyer commented 5 years ago

@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 commented 5 years ago

@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 commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

kyleniemeyer commented 5 years ago

@mesnardo looks like those DOIs were not actually added properly (used a bibdesk URL field rather than DOI field); I fixed in PR barbagroup/AeroPython#46

That should be the final edit necessary; please merge and then deposit for a DOI.

labarba commented 5 years ago

…and sneaked in an en-dash, I see 😁

PR merged. Thanks!

kyleniemeyer commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

kyleniemeyer commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

kyleniemeyer commented 5 years ago

@labarba @mesnardo I'm not sure why the reference checking isn't working, but this looks good to go to me. Could you archive and provide me with the DOI?

labarba commented 5 years ago

@whedon set v1.0 as version

whedon commented 5 years ago

OK. v1.0 is the version.

labarba commented 5 years ago

👋 @weymouth, @Juanlu001 — We have now released v1.0 and updated the version number here, so you can tick off that item in your checklist. Many thanks!

labarba commented 5 years ago

@whedon set 10.6084/m9.figshare.1004727.v4 as archive

whedon commented 5 years ago

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

kyleniemeyer commented 5 years ago

@whedon accept

whedon commented 5 years ago

Attempting dry run of processing paper acceptance...

whedon commented 5 years ago

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:incollect!' 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:infind_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:inrun' 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:indispatch' 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 commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

kyleniemeyer commented 5 years ago

@whedon accept

whedon commented 5 years ago

Attempting dry run of processing paper acceptance...

whedon commented 5 years ago

Check final proof :point_right: https://github.com/openjournals/jose-papers/pull/33

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/jose-papers/pull/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

openjournals / jose-reviews