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[REVIEW]: Capytaine: a Python-based linear potential flow solver #1341

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whedon opened this Issue Mar 20, 2019 · 39 comments

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whedon commented Mar 20, 2019

Submitting author: @mancellin (Matthieu Ancellin)
Repository: https://github.com/mancellin/capytaine
Version: v1.0.1
Editor: @leouieda
Reviewer: @mikaem, @harpolea
Archive: 10.5281/zenodo.2633744

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/cd95bd8d080b463cbc39642ed283f234"><img src="http://joss.theoj.org/papers/cd95bd8d080b463cbc39642ed283f234/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/cd95bd8d080b463cbc39642ed283f234/status.svg)](http://joss.theoj.org/papers/cd95bd8d080b463cbc39642ed283f234)

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

@mikaem & @harpolea, 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 @leouieda know.

Please try and complete your review in the next two weeks

Review checklist for @mikaem

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: v1.0.1
  • Authorship: Has the submitting author (@mancellin) 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 @harpolea

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: v1.0.1
  • Authorship: Has the submitting author (@mancellin) 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 Mar 20, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @mikaem, 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 Mar 20, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Mar 20, 2019

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mikaem commented Mar 22, 2019

@leouieda This is a strong submission and I'm ready to sign off as it is. My only real issue, that I don't consider a blocker, is that the authors should put a little more effort into the installation. I think they would benefit greatly from using both conda-forge and pypi, and from making this code available on mac and windows, not just linux. I could build it myself on mac using conda-forge compilers, using instructions from here.

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leouieda commented Mar 22, 2019

@mikaem thank you for your quick reply 👍 Would you mind opening an issue on the software repository to address these issues? I agree that it's a non-blocker if you managed to get installed but our goal is to help improve the software through the review.

@mancellin would you like to try to fix these issues while we wait for @harpolea? I agree with @mikaem that using conda-forge is a better choice than using your own conda channel. I have a lot of experience with it and can help set things up as well. I also agree that uploading to PyPI is a good thing as conda-forge often uses PyPI to get the source code for building packages.

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mikaem commented Mar 25, 2019

@leouieda just opened an issue with a suggestion for recipe. @mancellin needs to take it from there.

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mancellin commented Mar 25, 2019

Yes, I agree that the distribution of the package should be improved.

I had not considered conda-forge, I will try it. Thank you @mikaem for the links and the recipe!

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mancellin commented Mar 26, 2019

Mac and Linux packages are now available on conda-forge.
I still have some issues building a Windows package. I'll try to keep myself informed on the conda(-forge) Fortran toolchain for Windows.

It is also on PyPI, although only as a source package.

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leouieda commented Mar 29, 2019

@mancellin thank you for keeping us updated 👍

👋 @harpolea just checking in: I see that there are some checklist items remaining for you. Please let me know when you have a chance to go through those remaining items.

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harpolea commented Apr 1, 2019

@leouieda and @mancellin I'm really sorry for the delay - I was travelling last week and had far less time/wifi availability than I had anticipated. I have completed most of the checks I had intended to do, but just wanted to do a couple more things before I sign off on my review. I shall have a look at them this evening and should be finished by the end of the day.

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leouieda commented Apr 1, 2019

Thanks for the update, @harpolea 👍 I'm sure we're can all sympathize with your situation 🙂

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harpolea commented Apr 1, 2019

Sorry again for the delay - I've finished up with the checks I had intended to do and recommend this for acceptance @leouieda

This is a really nice package - the documentation in particular is very thorough and was great for a new user like myself!

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leouieda commented Apr 8, 2019

@harpolea thank you for your review!

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leouieda commented Apr 8, 2019

@whedon check references

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whedon commented Apr 8, 2019

Attempting to check references...
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whedon commented Apr 8, 2019


OK DOIs

- 10.5802/smai-jcm.36 is OK
- 10.1115/OMAE2018-77924 is OK
- 10.1504/IJCSE.2009.029165 is OK
- 10.5334/jors.148 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1016/j.apor.2018.10.007 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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leouieda commented Apr 8, 2019

@whedon generate pdf

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whedon commented Apr 8, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Apr 8, 2019

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leouieda commented Apr 8, 2019

@mancellin I have given the paper a final check and I'm happy to accept it for publication in JOSS 🎉 🎉

There a few steps that we need to take before publication. Please make a new release with any changes that came about after submission (if required) and archive a copy of the source code on Zenodo or figshare. Once that is done, please post the DOI of the archive here.

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mancellin commented Apr 9, 2019

Thank you @leouieda, @harpolea and @mikaem!

I've read the paper once more and found a small typo in the bibliography. I have pushed a correction.

The DOI of the latest archive is 10.5281/zenodo.2633744

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leouieda commented Apr 9, 2019

@whedon generate pdf

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whedon commented Apr 9, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Apr 9, 2019

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leouieda commented Apr 9, 2019

@mancellin thanks for catching that!

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leouieda commented Apr 9, 2019

@whedon set v1.0.1 as version

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whedon commented Apr 9, 2019

OK. v1.0.1 is the version.

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leouieda commented Apr 9, 2019

@whedon set 10.5281/zenodo.2633744 as archive

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whedon commented Apr 9, 2019

OK. 10.5281/zenodo.2633744 is the archive.

@leouieda leouieda added the accepted label Apr 9, 2019

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leouieda commented Apr 9, 2019

👋 @openjournals/joss-eics this submission is ready to be accepted

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labarba commented Apr 10, 2019

@whedon accept

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whedon commented Apr 10, 2019

Attempting dry run of processing paper acceptance...
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whedon commented Apr 10, 2019

Check final proof 👉 openjournals/joss-papers#613

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#613, 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 Apr 10, 2019


OK DOIs

- 10.5802/smai-jcm.36 is OK
- 10.1115/OMAE2018-77924 is OK
- 10.1504/IJCSE.2009.029165 is OK
- 10.5334/jors.148 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1016/j.apor.2018.10.007 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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labarba commented Apr 10, 2019

@whedon accept deposit=true

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whedon commented Apr 10, 2019

Doing it live! Attempting automated processing of paper acceptance...
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whedon commented Apr 10, 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#614
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01341
  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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labarba commented Apr 10, 2019

Congratulations, @mancellin, your JOSS paper is published!

Many thanks to our editor: @leouieda, and the reviewers: @mikaem, @harpolea — your contribution is greatly appreciated 🙏

@labarba labarba closed this Apr 10, 2019

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whedon commented Apr 10, 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.01341/status.svg)](https://doi.org/10.21105/joss.01341)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01341">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01341/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01341/status.svg
   :target: https://doi.org/10.21105/joss.01341

This is how it will look in your documentation:

DOI

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