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 🎉.

⭐️ 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:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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

@whedon commands

Attempting PDF compilation. Reticulating splines etc...

👉 Check article proof 📄 👈

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

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

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.

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

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

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

@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!

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

@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!

@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! 😸

@maelle will do, thanks!

Submitted a presub inquiry see #300.

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

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

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

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.

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

👋 @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.

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:in parse_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:in load'
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:in open'
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:in load_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:in new'
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:in prepare'
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:in invoke_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:in start'
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:in load'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

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

@danielskatz Ah ok, I’ll take a look.

@whedon generate pdf

👉 Check article proof 📄 👈

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

thanks - I'll proofread this soon.

👋 @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.

@whedon assign @danielskatz as editor

👋 @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...

@whedon accept

No archive DOI set. Exiting...

👋 @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.

Also, please merge the changes in ropensci/Rclean#202

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

@whedon set v1.1.8 as version

OK. v1.1.8 is the version.

@whedon set 10.5281/zenodo.3665732 as archive

OK. 10.5281/zenodo.3665732 is the archive.

@whedon accept

Attempting dry run of processing paper acceptance...

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

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

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

👋 @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?