[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

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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:

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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 commented 5 years ago

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:.

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whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

labarba commented 5 years ago

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

labarba commented 5 years ago

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

MKLau commented 5 years ago

@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 commented 5 years ago

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 commented 5 years ago

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

labarba commented 5 years ago

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

MKLau commented 5 years ago

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

labarba commented 5 years ago

@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 commented 5 years ago

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

MKLau commented 5 years ago

@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 commented 5 years ago

@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 commented 5 years ago

@maelle will do, thanks!

MKLau commented 5 years ago

Submitted a presub inquiry see #300.

danielskatz commented 5 years ago

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

MKLau commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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

danielskatz commented 5 years ago

👋 @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 commented 5 years ago

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

danielskatz commented 5 years ago

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

danielskatz commented 4 years ago

@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 commented 4 years ago

Hi @danielskatz ,

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

maelle commented 4 years ago

Yes it has been accepted. Cc @annakrystalli

danielskatz commented 4 years ago

@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 commented 4 years ago

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 commented 4 years ago

@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 commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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 commented 4 years ago

@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 commented 4 years ago

@danielskatz Ah ok, I’ll take a look.

MKLau commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

MKLau commented 4 years ago

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

danielskatz commented 4 years ago

thanks - I'll proofread this soon.

danielskatz commented 4 years ago

👋 @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 commented 4 years ago

@whedon assign @danielskatz as editor

danielskatz commented 4 years ago

👋 @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 commented 4 years ago

@whedon accept

whedon commented 4 years ago

No archive DOI set. Exiting...

danielskatz commented 4 years ago

👋 @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 commented 4 years ago

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

MKLau commented 4 years ago

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 commented 4 years ago

@whedon set v1.1.8 as version

whedon commented 4 years ago

OK. v1.1.8 is the version.

danielskatz commented 4 years ago

@whedon set 10.5281/zenodo.3665732 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3665732 is the archive.

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