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[REVIEW]: pytransform3d: 3D Transformations for Python #1159

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whedon opened this Issue Jan 7, 2019 · 44 comments

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whedon commented Jan 7, 2019

Submitting author: @AlexanderFabisch (Alexander Fabisch)
Repository: https://github.com/rock-learning/pytransform3d
Version: 1.1
Editor: @brainstorm
Reviewer: @luizirber
Archive: 10.5281/zenodo.2553451

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/4402b4b5fa1ca270f9e22dc7cf0b3cfc"><img src="http://joss.theoj.org/papers/4402b4b5fa1ca270f9e22dc7cf0b3cfc/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/4402b4b5fa1ca270f9e22dc7cf0b3cfc/status.svg)](http://joss.theoj.org/papers/4402b4b5fa1ca270f9e22dc7cf0b3cfc)

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

@luizirber, 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 @brainstorm know.

Please try and complete your review in the next two weeks

Review checklist for @luizirber

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 (1.0)?
  • Authorship: Has the submitting author (@AlexanderFabisch) 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 7, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @luizirber 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 7, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Jan 7, 2019

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brainstorm commented Jan 19, 2019

👋 @luizirber Let me know if you need sth else from me ;)

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luizirber commented Jan 24, 2019

Hello @AlexanderFabisch! Great package =]

Some comments:

License

It almost matches https://opensource.org/licenses/BSD-3-Clause
but is missing the copyright line in the beginning and has some minor format
differences. I suggest copying the license from the link and saving to your LICENSE file (GitHub will also be able to pick it up and show in the landing repo page).

Also fix https://github.com/rock-learning/pytransform3d/blob/879e37069e16e372ad10762a5bb32bf5256fb0de/setup.py#L25
https://docs.python.org/3/distutils/setupscript.html#additional-meta-data

Installation

You can specify your dependencies on setup.py. It seems like you're almost there,
but the right key is install_requires, and not requires:
https://github.com/rock-learning/pytransform3d/blob/879e37069e16e372ad10762a5bb32bf5256fb0de/setup.py#L26

More info: https://packaging.python.org/discussions/install-requires-vs-requirements/

Community guidelines

You can also create a CONTRIBUTING file (GitHub recognizes it and render the content when a new issue or PR is opened):
https://github.blog/2012-09-17-contributing-guidelines/

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AlexanderFabisch commented Jan 25, 2019

Hi @luizirber,

thanks for the kind words and the review! I hope I addressed everything in this merge request.

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luizirber commented Jan 28, 2019

thanks @AlexanderFabisch! Last recommendation: tag a new release for the software and upload to PyPI =]

@brainstorm I checked all the boxes, good to go!

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brainstorm commented Jan 29, 2019

@whedon check references

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whedon commented Jan 29, 2019

Attempting to check references...
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whedon commented Jan 29, 2019


OK DOIs

- http://doi.org/10.3389/frobt.2018.00043 is OK
- http://doi.org/10.1109/MCSE.2011.37 is OK
- http://doi.org/10.1109/MCSE.2007.55 is OK

MISSING DOIs

- https://doi.org/10.21105/joss.00787 may be missing for title: rowan: A Python package for working with quaternions

INVALID DOIs

- None
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AlexanderFabisch commented Jan 29, 2019

thanks @AlexanderFabisch! Last recommendation: tag a new release for the software and upload to PyPI =]

Yep, 1.1 is available. Thanks!

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brainstorm commented Jan 29, 2019

Thanks a lot @luizirber and @AlexanderFabisch! @AlexanderFabisch, can you check out the MISSING DOI referenced by whedon?

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AlexanderFabisch commented Jan 29, 2019

@whedon check references

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whedon commented Jan 29, 2019

Attempting to check references...
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whedon commented Jan 29, 2019


OK DOIs

- http://doi.org/10.3389/frobt.2018.00043 is OK
- http://doi.org/10.1109/MCSE.2011.37 is OK
- http://doi.org/10.1109/MCSE.2007.55 is OK
- http://doi.org/10.21105/joss.00787 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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AlexanderFabisch commented Jan 29, 2019

OK, the bibtex entry had a dor. I changed it to doi. 😆

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brainstorm commented Jan 30, 2019

@whedon generate pdf

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whedon commented Jan 30, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Jan 30, 2019

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brainstorm commented Jan 30, 2019

LGTM, @AlexanderFabisch can you deposit the release to zenodo and come back with the DOI?

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AlexanderFabisch commented Jan 30, 2019

Yes, this is the DOI: 10.5281/zenodo.2553451

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brainstorm commented Jan 30, 2019

@whedon set 10.5281/zenodo.2553451 as archive

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whedon commented Jan 30, 2019

OK. 10.5281/zenodo.2553451 is the archive.

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brainstorm commented Jan 30, 2019

@whedon accept

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whedon commented Jan 30, 2019

Attempting dry run of processing paper acceptance...
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whedon commented Jan 30, 2019


OK DOIs

- http://doi.org/10.3389/frobt.2018.00043 is OK
- http://doi.org/10.1109/MCSE.2011.37 is OK
- http://doi.org/10.1109/MCSE.2007.55 is OK
- http://doi.org/10.21105/joss.00787 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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brainstorm commented Jan 30, 2019

@arfon I think we are ready for depositing here :)

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danielskatz commented Jan 30, 2019

Hi @brainstorm - We've moved to rotating editors-in-chief, and this week it's me. For the future, please notify @joss-eics when there's a paper ready to go, or to otherwise get the person on-duty...

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danielskatz commented Jan 30, 2019

@whedon accept

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whedon commented Jan 30, 2019

Attempting dry run of processing paper acceptance...
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brainstorm commented Jan 30, 2019

Absolutely, thanks for the heads-up @danielskatz!

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whedon commented Jan 30, 2019


OK DOIs

- http://doi.org/10.3389/frobt.2018.00043 is OK
- http://doi.org/10.1109/MCSE.2011.37 is OK
- http://doi.org/10.1109/MCSE.2007.55 is OK
- http://doi.org/10.21105/joss.00787 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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danielskatz commented Jan 30, 2019

👋 @arfon - this didn't seem to correctly generate a proof PR - any idea why not?

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arfon commented Jan 30, 2019

@whedon accept

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whedon commented Jan 30, 2019

Attempting dry run of processing paper acceptance...
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whedon commented Jan 30, 2019


OK DOIs

- http://doi.org/10.3389/frobt.2018.00043 is OK
- http://doi.org/10.1109/MCSE.2011.37 is OK
- http://doi.org/10.1109/MCSE.2007.55 is OK
- http://doi.org/10.21105/joss.00787 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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whedon commented Jan 30, 2019

Check final proof 👉 openjournals/joss-papers#464

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#464, 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 Jan 30, 2019

Check final proof 👉 openjournals/joss-papers#465

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#465, 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 Jan 31, 2019

Check final proof 👉 openjournals/joss-papers#468

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#468, 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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danielskatz commented Jan 31, 2019

@whedon accept deposit=true

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whedon commented Jan 31, 2019

Doing it live! Attempting automated processing of paper acceptance...
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whedon commented Jan 31, 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#470
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01159
  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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whedon commented Jan 31, 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.01159/status.svg)](https://doi.org/10.21105/joss.01159)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01159">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01159/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01159/status.svg
   :target: https://doi.org/10.21105/joss.01159

This is how it will look in your documentation:

DOI

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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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AlexanderFabisch commented Jan 31, 2019

Thanks again @luizirber for the review and @brainstorm for handling the process!

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