Joss-reviews: [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

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:

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

• [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)?

[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 :tada:.

:star: Important :star:

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:

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For a list of things I can do to help you, just type:

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[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! :smile_cat:

[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 https://github.com/ropensci/software-review/issues/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.

[maelle]

The package is under review at rOpenSci https://github.com/ropensci/software-review/issues/327 cc handling editor @annakrystalli

[danielskatz]

Ok, thanks - it makes sense to keep it here then - please update this thread when it is accepted

[danielskatz]

@maelle & @MKLau - Has the rOpenSci package now been accepted? I see that the status is 6/approved, but am not sure if there's another step after that.

[MKLau]

Hi @danielskatz ,

It has been accepted. I’m currently finishing the transfer to ROpenSci org and revisions of the manuscript.

[maelle]

Yes it has been accepted. Cc @annakrystalli

[danielskatz]

@MKLau - please let us know when the paper is complete, so we can proceed to accept this in JOSS. We don't need to wait for the transfer to rOpenSci, but we do need the final paper.

[MKLau]

Hi @danielskatz , just finished sorting out a couple of issues with Travis and Zenodo tracking.

The manuscript is now good to go for review, you can find it here.

[danielskatz]

@MKLau - we need the paper to be a .md file here, with a .bib file, as shown in https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography We will then build it with @whedon generate pdf (you can do this too to check)

[danielskatz]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #1312 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1312/joss/paper.md): mapping values are not allowed in this context at line 74 column 72 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:inparse_stream'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:325:in parse' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:252:inload'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:473:in block in load_file' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:inopen'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon.rb:125:inload_yaml'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon.rb:85:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/processor.rb:36:innew'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:55:inprepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:ininvoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:instart'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

[danielskatz]

@MKLau - please fix the problems in the .md and/or .bib files, perhaps updating them based on recent changes made for the rOpenSci process

[MKLau]

@danielskatz Ah ok, I’ll take a look.

[MKLau]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[MKLau]

@danielskatz , looks like it should be good to go now.

[danielskatz]

thanks - I'll proofread this soon.

[danielskatz]

👋 @labarba - I now notice that you are listed as the editor - if you want to handle this from this point onward, please feel free. If not, let me know and I'll switch it to me and finish it.

[danielskatz]

@whedon assign @danielskatz as editor

[danielskatz]

👋 @cboettig, @benmarwick - as this is an rOpenSci paper, we don't need an independent JOSS review of the software, so your help will not be called on - also, sorry for what might have been too many notifications...

[danielskatz]

@whedon accept

[whedon]

No archive DOI set. Exiting...

[danielskatz]

👋 @MKLau - At this point could you:

• [ ] Make a tagged release of your software, and list the version tag of the archived version here.
• [ ] Archive the reviewed software in Zenodo or a similar service (e.g. figshare, an institutional repository)
• [ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata, this includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it); you may also add the authors' ORCID.
• [ ] Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

[danielskatz]

Also, please merge the changes in https://github.com/ropensci/Rclean/pull/202

[MKLau]

Thanks @danielskatz for the edits.

I've reviewed and accepted your pull request and tagged as v1.1.8.

Here's the DOI and link to Zenodo.

10.5281/zenodo.3665732

[danielskatz]

@whedon set v1.1.8 as version

[whedon]

OK. v1.1.8 is the version.

[danielskatz]

@whedon set 10.5281/zenodo.3665732 as archive

[whedon]

OK. 10.5281/zenodo.3665732 is the archive.

[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 :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]

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

@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 :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]

@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:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1308
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01312
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...

[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]

: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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