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

[whedon]

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

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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

@danielskatz, 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 @danielskatz know.

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

Review checklist for @danielskatz

Conflict of interest

• 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

• 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)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @cboettig, it looks like you're currently assigned as the reviewer for this paper 🎉.

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[labarba]

👋 @cboettig, @benmarwick — We'll carry out the review here. Thanks for your contribution to JOSS!

[labarba]

@benmarwick asked in the Pre-review issue whether submitting to Ropensci had been considered. Comments, @MKLau?

[MKLau]

@labarba @benmarwick
No we hadn't thought to submit to Ropensci but I am familiar with the work there and would be interested in submitting there.

Per "Has there been any discussion about whether this pkg might be suitable for @ropensci onboarding? Perhaps @noamross or @maelle could advise if this pkg is suitable? It it passes that, then it's auto-submitted here, if I understand correctly."

The on-boarding process sounds very useful. Also, I am familiar with Noam Ross's work and would think that he would be suitable to review.

I'm not quite sure that I fully understand the suggestion though. Would we do a submission to ROpenSci in addition to (e.g. for on-boarding) or in-lieu of submitting to JOSS?

[labarba]

We have an agreement with ROpenSci where if your package goes through their review, it gets fast-tracked to a publication in JOSS with minor editorial checks.

[MKLau]

OK, if we go that route, what are the next steps given that we've already started the review here?

[labarba]

We can just pause the review, and wait until you ping us back!

[MKLau]

Ah, ok. That seems good. I'll look at their review process and let your know. Thanks!

[labarba]

@cboettig, @benmarwick — Thank you for agreeing to review this JOSS submission. The review is now paused, while the author investigates going the ROpenSci route. Stay tuned!

[labarba]

@MKLau 👋 — did you look into ROpenSci? What do you want to do about this submission?

[MKLau]

@labarba Yes, I'm almost done with a couple of pre-submission edits based on the ROpenSci guidelines. Shooting to submit before the end of this month. Thanks!

[maelle]

@MKLau before submission to rOpenSci you can open a pre-submission inquiry so that the editors might assess whether your package is in scope. Thank you! 😸

[MKLau]

@maelle will do, thanks!

[MKLau]

Submitted a presub inquiry see #300.

[danielskatz]

👋 @MKLau - what's happened in this in the last month?

[MKLau]

Hi Daniel, sorry for the slow reply I've been traveling and just saw this post. Not much happened last month, but shouldn't be more than a week to get things finished for submission. There are a few more functions that need some tests and the vignette needs to be added: https://github.com/ProvTools/Rclean/projects/4.

@danielskatz

[MKLau]

Hi @danielskatz @labarba @benmarwick, the package review should be good to start. I made an inquiry over in pre-submission thread ropensci/software-review#300 to see what the best way would be to proceed. One of you might have a thought as well. Should I just re-open the closed pre-submission thread and re-label it? Or, should I start a new issue?

Thanks!

@MKLau

[labarba]

I don't know how you submit to rOpenSci, but that's what you need to do next. Once your software is reviewed there, it will be fast-tracked in JOSS.

[cboettig]

@labarba @MKLau To submit to rOpenSci, simply open an issue in https://github.com/ropensci/software-review/ as described in the README there.

[danielskatz]

👋 @MKLau - is there any news here? After 4 months, if not, I suggest we mark this as withdrawn and let you resubmit later when you are ready - I will do this in a few days if I don't hear back from you.

[whedon]

Check final proof 👉 openjournals/joss-papers#1305

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#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]

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

[danielskatz]

👋 @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]

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

[MKLau]

@danielskatz @arfon

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

[danielskatz]

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-archive/Rclean#203

[MKLau]

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

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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]

Check final proof 👉 openjournals/joss-papers#1306

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#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]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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]

Check final proof 👉 openjournals/joss-papers#1307

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#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]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

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

Any issues? notify your editorial technical team...

[danielskatz]

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

[danielskatz]

Thanks to @labarba for starting this process!

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

[arfon]

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

Done.

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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