[REVIEW]: Rclean: A Tool for Writing Cleaner, More Transparent Code

whedon commented 5 years ago

Submitting author: @MKLau (Matthew Lau) Repository: https://github.com/ropensci/Rclean Version: v1.1.8 Editor: @danielskatz Reviewer: @danielskatz Archive: 10.5281/zenodo.3665732

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/334d80d5508056dc6e7e17c6fd3ed5a6"><img src="http://joss.theoj.org/papers/334d80d5508056dc6e7e17c6fd3ed5a6/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/334d80d5508056dc6e7e17c6fd3ed5a6/status.svg)](http://joss.theoj.org/papers/334d80d5508056dc6e7e17c6fd3ed5a6)

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

@danielskatz, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
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 @danielskatz know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @danielskatz

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS 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 JOSS 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: v1.1.8
[ ] Authorship: Has the submitting author (@MKLau) 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)?

danielskatz commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1038/533452a is OK
- 10.1145/2602649.2602651 is OK
- 10.1073/pnas.1708290115 is OK
- 10.1038/sdata.2017.114 is OK
- 10.1038/s41567-018-0342-2 is OK
- 10.1126/science.1213847 is OK
- 10.1109/MCSE.2018.042781334 is OK
- 10.1371/journal.pcbi.1004140 is OK

MISSING DOIs

- https://doi.org/10.21105/joss.00550 may be missing for title: The drake R package: a pipeline toolkit for reproducibility and high-performance computing

INVALID DOIs

- None

whedon commented 4 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1305

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1305, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz commented 4 years ago

There are also some changes needed in the bib file - please merge https://github.com/ropensci/Rclean/pull/203

danielskatz commented 4 years ago

👋 @openjournals/dev - note the second author's name has gotten parsed incorrectly in the XML - should I accept this and then ask you to fix this manually? Or can we do something before that?

arfon commented 4 years ago

@danielskatz - let's accept and then I'll fix afterwards.

MKLau commented 4 years ago

@danielskatz @arfon

If the multiple middle initials is a problem, he can be cited as Thomas Pasquier, as in this paper.

danielskatz commented 4 years ago

It's not a problem, we can handle it. However, we are waiting on

There are also some changes needed in the bib file - please merge ropensci/Rclean#203

MKLau commented 4 years ago

@danielskatz Great, pull request accepted. Thanks for those fixes.

danielskatz commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1038/533452a is OK
- 10.1145/2602649.2602651 is OK
- 10.1073/pnas.1708290115 is OK
- 10.1038/sdata.2017.114 is OK
- 10.1038/s41567-018-0342-2 is OK
- 10.1126/science.1213847 is OK
- 10.1109/MCSE.2018.042781334 is OK
- 10.1371/journal.pcbi.1004140 is OK

MISSING DOIs

- https://doi.org/10.21105/joss.00550 may be missing for title: The drake R package: a pipeline toolkit for reproducibility and high-performance computing

INVALID DOIs

- None

whedon commented 4 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1306

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1306, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1038/533452a is OK
- 10.1145/2602649.2602651 is OK
- 10.1073/pnas.1708290115 is OK
- 10.1038/sdata.2017.114 is OK
- 10.1038/s41567-018-0342-2 is OK
- 10.1126/science.1213847 is OK
- 10.1109/MCSE.2018.042781334 is OK
- 10.1371/journal.pcbi.1004140 is OK

MISSING DOIs

- https://doi.org/10.21105/joss.00550 may be missing for title: The drake R package: a pipeline toolkit for reproducibility and high-performance computing

INVALID DOIs

- None

whedon commented 4 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1307

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1307, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz commented 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago

Doing it live! Attempting automated processing of paper acceptance...

whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 4 years ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1308
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01312
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

danielskatz commented 4 years ago

👋 @arfon - over to you to fix the 2nd author in the metadata (xml file), then to close this

danielskatz commented 4 years ago

Thanks to @labarba for starting this process!

And congratulations to @MKLau and co-authors for this publication and the accompanying rOpenSci acceptance!

arfon commented 4 years ago

👋 @arfon - over to you to fix the 2nd author in the metadata (xml file), then to close this

Done.

whedon commented 4 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01312/status.svg)](https://doi.org/10.21105/joss.01312)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01312">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01312/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01312/status.svg
   :target: https://doi.org/10.21105/joss.01312

This is how it will look in your documentation:

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