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[REVIEW]: BladeX: Python Blade Deformation #1203

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whedon opened this Issue Jan 26, 2019 · 62 comments

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whedon commented Jan 26, 2019

Submitting author: @mtezzele (Marco Tezzele)
Repository: https://github.com/mathLab/BladeX
Version: v0.1
Editor: @labarba
Reviewer: @benoitpaillard, @Juanlu001
Archive: 10.5281/zenodo.2556690

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/5b0ef70a351c1a51daf3a9354cd7b3fa"><img src="http://joss.theoj.org/papers/5b0ef70a351c1a51daf3a9354cd7b3fa/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/5b0ef70a351c1a51daf3a9354cd7b3fa/status.svg)](http://joss.theoj.org/papers/5b0ef70a351c1a51daf3a9354cd7b3fa)

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

@benoitpaillard & @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/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @labarba know.

Please try and complete your review in the next two weeks

Review checklist for @benoitpaillard

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: Does the release version given match the GitHub release (v0.1)?
  • Authorship: Has the submitting author (@mtezzele) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience 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 code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: Does the release version given match the GitHub release (v0.1)?
  • Authorship: Has the submitting author (@mtezzele) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
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whedon commented Jan 26, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @benoitpaillard, 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/joss-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/joss-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 commented Jan 26, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Jan 26, 2019

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labarba commented Jan 26, 2019

@benoitpaillard, @Juanlu001 — this is where the action happens. You can read about the JOSS Review Process in our docs. Each of you has a review checklist at the top of this issue 👆 and you should feel free to ask questions here, and open issues in the submission repository as needed.

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labarba commented Jan 27, 2019

@whedon check references

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whedon commented Jan 27, 2019

Attempting to check references...
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whedon commented Jan 27, 2019


OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None
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labarba commented Jan 27, 2019

@mtezzele — I notice that you cited the software repository in your paper. The paper format will have a link to the repository (and software archive, made after review is complete) on the front page, so it's not necessary to add it to the References list. You also cite a submitted paper: would you be able to post a pre-print of the manuscript, for example in engrXiv or arXiv or a similar service? (Then you can add the DOI or pre-print identifier in your References list.)

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Juanlu001 commented Jan 28, 2019

I did a first pass on the repository and left two minor suggestions, mathLab/BladeX#42 and mathLab/BladeX#43 (none of them blockers). I will finish my review during the coming days.

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mtezzele commented Jan 28, 2019

@Juanlu001 fixed! Thank you for the suggestions.

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mtezzele commented Jan 28, 2019

@whedon generate pdf

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whedon commented Jan 28, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Jan 28, 2019

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mtezzele commented Jan 28, 2019

@labarba I added the Preprint record to the bibitem but it does not appear in the pdf (mathLab/BladeX#45). Can you please tell me how to do it?

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Juanlu001 commented Jan 28, 2019

@whedon commands

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whedon commented Jan 28, 2019

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Ask Whedon to check the references for missing DOIs
@whedon check references

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Juanlu001 commented Jan 28, 2019

I find the software very well written and its documentation excellent, it was a pleasing surprise to see an engineering tool with such up to date coding practices. Congratulations @mtezzele and @mahgadalla!

@labarba is there anything else I have to do apart from crossing off all the elements of the list?

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labarba commented Jan 28, 2019

@Juanlu001 — If you have checked off all the review items, and the authors have made any improvements to your satisfaction, all I need is a statement from you here that you recommend publication.

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labarba commented Jan 28, 2019

@whedon generate pdf

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whedon commented Jan 28, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Jan 28, 2019

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labarba commented Jan 28, 2019

@mtezzele — I believe you should use the note field to provide the URL to the preprint. Also, the entry type should probably be @unpublished or @misc.

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Juanlu001 commented Jan 28, 2019

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mtezzele commented Jan 28, 2019

@whedon generate pdf

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whedon commented Jan 28, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Jan 28, 2019

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mtezzele commented Jan 28, 2019

@whedon generate pdf

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mtezzele commented Jan 28, 2019

@labarba Finally we did it! Thank you very much!

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benoitpaillard commented Feb 3, 2019

Hi all, sorry for the late completion.

The really only issue I'd mention is the dependency to pythonocc which is still a mess to compile, but don't get me wrong, I'm using it in my projects as well ! I just wish it could be compiled more easily.

Appart from that, finally a code that does 3D blades, but also robust naca and general airfoil generators !! Congrats guys, great tool.

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labarba commented Feb 3, 2019

@mtezzele — Some final editorial comments:

¶1.
obtain designs which allow >> that allow
prototipation environment >> prototyping environment
By a practical standpoint, the propeller blade >> From a practical standpoint, a propeller blade
the shape of a certain number of sectional profile shapes >> the shape of a certain number of sectional profiles
a morphing tool that expand >> expands
In particular we followed >> In particular, we followed [add comma]

¶2.
In the BladeX Python package we implemented >> package, we… [add comma]
simulation driven design >> simulation-driven design [add hyphen]

¶3.
naval propulsion”, >>naval propulsion,” [comma inside quote]
can be found in (Tezzele, Demo, Mola, & Rozza, 2018) >> this is an in-text citation (meaning, the citation is part of the sentence), so you need to suppress the parenthesis; see Citation Syntax

¶4.
the resulted iges and stl le formats >> the resulting
(same in caption of Figure 1)

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mahgadalla commented Feb 4, 2019

@whedon generate pdf

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whedon commented Feb 4, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Feb 4, 2019

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mahgadalla commented Feb 4, 2019

@labarba thanks a lot! the editorial comments are now fixed. Please let us know if the in-text citation looks ok now, also if the first citation should be regarded as in-text as well?

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labarba commented Feb 4, 2019

Yes, I missed that one. Whenever the citation is part of the sentence, treat as in-text.

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mahgadalla commented Feb 4, 2019

@whedon generate pdf

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whedon commented Feb 4, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Feb 4, 2019

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mahgadalla commented Feb 4, 2019

@labarba ok done!
Are there any further comments to consider?

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labarba commented Feb 4, 2019

At this point, we ask you that you make a full archive of the repository in Zenodo or a similar service, and post the archive DOI on this thread. Thanks!

@labarba labarba added the accepted label Feb 4, 2019

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mahgadalla commented Feb 4, 2019

@labarba here's the Zenodo archive DOI:
10.5281/zenodo.2556690

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labarba commented Feb 4, 2019

Could you edit the title on Zenodo to match the paper?

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mahgadalla commented Feb 4, 2019

@labarba Sure! Edited now. (Y)

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labarba commented Feb 4, 2019

@whedon set 10.5281/zenodo.2556690 as archive

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whedon commented Feb 4, 2019

OK. 10.5281/zenodo.2556690 is the archive.

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labarba commented Feb 4, 2019

@whedon accept

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whedon commented Feb 4, 2019

Attempting dry run of processing paper acceptance...
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whedon commented Feb 4, 2019

Check final proof 👉 openjournals/joss-papers#474

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#474, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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whedon commented Feb 4, 2019


OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None
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labarba commented Feb 4, 2019

@whedon accept deposit=true

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whedon commented Feb 4, 2019

Doing it live! Attempting automated processing of paper acceptance...
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whedon commented Feb 4, 2019

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#475
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01203
  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...

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mtezzele commented Feb 4, 2019

@labarba @Juanlu001 @benoitpaillard thank you all for your time and effort in this review.
It has been a pleasure.

@labarba labarba closed this Feb 4, 2019

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whedon commented Feb 4, 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](http://joss.theoj.org/papers/10.21105/joss.01203/status.svg)](https://doi.org/10.21105/joss.01203)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01203">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01203/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01203/status.svg
   :target: https://doi.org/10.21105/joss.01203

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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labarba commented Feb 4, 2019

My sincere thanks to our reviewers, @benoitpaillard, @Juanlu001 — this adventure in new-wave publishing would not be possible without you.

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