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[REVIEW]: Rclean: A Tool for Writing Cleaner, More Transparent Code #1312

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whedon opened this issue Mar 10, 2019 · 39 comments
Open

[REVIEW]: Rclean: A Tool for Writing Cleaner, More Transparent Code #1312

whedon opened this issue Mar 10, 2019 · 39 comments
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@whedon whedon commented Mar 10, 2019

Submitting author: @MKLau (Matthew Lau)
Repository: https://github.com/provtools/rclean
Version: v1.0.1
Editor: @labarba
Reviewer: @cboettig, @benmarwick
Archive: Pending

Status

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

@cboettig & @benmarwick, 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 @labarba know.

Please try and complete your review in the next two weeks

Review checklist for @cboettig

Conflict of interest

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: Does the release version given match the GitHub release (v1.0.1)?
  • 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)?

Review checklist for @benmarwick

Conflict of interest

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: Does the release version given match the GitHub release (v1.0.1)?
  • 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)?
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@whedon whedon commented Mar 10, 2019

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:

watching

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

notifications

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

@whedon commands
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@whedon whedon commented Mar 10, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Mar 10, 2019

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@labarba labarba commented Mar 10, 2019

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

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@labarba labarba commented Mar 10, 2019

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

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@MKLau MKLau commented Mar 15, 2019

@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?

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@labarba labarba commented Mar 15, 2019

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.

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@MKLau MKLau commented Mar 15, 2019

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

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@labarba labarba commented Mar 15, 2019

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

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@MKLau MKLau commented Mar 15, 2019

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

@labarba labarba added the paused label Mar 16, 2019
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@labarba labarba commented Mar 16, 2019

@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!

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@labarba labarba commented May 11, 2019

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

@arfon arfon added paused and removed paused labels May 11, 2019
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@MKLau MKLau commented May 13, 2019

@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!

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@maelle maelle commented May 13, 2019

@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! 😸

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@MKLau MKLau commented May 14, 2019

@maelle will do, thanks!

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@MKLau MKLau commented May 14, 2019

Submitted a presub inquiry see #300.

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@danielskatz danielskatz commented Jun 18, 2019

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

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@MKLau MKLau commented Jun 28, 2019

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.

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@MKLau MKLau commented Jul 15, 2019

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!

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@labarba labarba commented Jul 15, 2019

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.

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@cboettig cboettig commented Jul 15, 2019

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

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@danielskatz danielskatz commented Oct 29, 2019

👋 @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.

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@maelle maelle commented Oct 29, 2019

The package is under review at rOpenSci ropensci/software-review#327 cc handling editor @annakrystalli

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@danielskatz danielskatz commented Oct 29, 2019

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

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@danielskatz danielskatz commented Feb 10, 2020

@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.

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@MKLau MKLau commented Feb 10, 2020

Hi @danielskatz ,

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

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@maelle maelle commented Feb 11, 2020

Yes it has been accepted. Cc @annakrystalli

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@danielskatz danielskatz commented Feb 11, 2020

@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.

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@MKLau MKLau commented Feb 12, 2020

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.

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@danielskatz danielskatz commented Feb 13, 2020

@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)

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@danielskatz danielskatz commented Feb 13, 2020

@whedon generate pdf

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@whedon whedon commented Feb 13, 2020

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 `

'

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@danielskatz danielskatz commented Feb 13, 2020

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

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@MKLau MKLau commented Feb 13, 2020

@danielskatz Ah ok, I’ll take a look.

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@MKLau MKLau commented Feb 13, 2020

@whedon generate pdf

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@whedon whedon commented Feb 13, 2020

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@MKLau MKLau commented Feb 13, 2020

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

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@danielskatz danielskatz commented Feb 13, 2020

thanks - I'll proofread this soon.

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@danielskatz danielskatz commented Feb 13, 2020

👋 @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 danielskatz removed the paused label Feb 13, 2020
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