[REVIEW]: bikedata #471

whedon · 2017-11-27T15:03:57Z

Submitting author: @mpadge (Mark Padgham)
Repository: https://github.com/ropensci/bikedata
Version: v0.0.4
Editor: @karthik
Reviewer: @arfon
Archive: 10.5281/zenodo.1089207

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/232cd77b73dbef4accd36ddfb20f96ae"><img src="http://joss.theoj.org/papers/232cd77b73dbef4accd36ddfb20f96ae/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/232cd77b73dbef4accd36ddfb20f96ae/status.svg)](http://joss.theoj.org/papers/232cd77b73dbef4accd36ddfb20f96ae)

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

@arfon, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: http://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @karthik know.

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: Does the release version given match the GitHub release (v0.0.4)?
Authorship: Has the submitting author (@mpadge) 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)?

The text was updated successfully, but these errors were encountered:

whedon · 2017-11-27T15:03:59Z

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @arfon 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 as 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:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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

whedon · 2017-11-27T15:04:00Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2017-11-27T15:04:09Z

PDF failed to compile for issue #471 with the following error: 

 /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in `parse': (tmp/471/paper.md): could not find expected ':' while scanning a simple key at line 16 column 7 (Psych::SyntaxError)
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in `parse_stream'
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:327:in `parse'
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:254:in `load'
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:475:in `block in load_file'
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:in `open'
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:in `load_file'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-33e05183aa0d/lib/whedon.rb:73:in `initialize'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-33e05183aa0d/lib/whedon/processor.rb:26:in `new'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-33e05183aa0d/lib/whedon/processor.rb:26:in `set_paper'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-33e05183aa0d/bin/whedon:37:in `prepare'
	from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:in `run'
	from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in `invoke_command'
	from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:in `dispatch'
	from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in `start'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-33e05183aa0d/bin/whedon:75:in `<top (required)>'
	from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in `load'
	from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in `<main>'

arfon · 2017-11-27T15:05:18Z

@karthik - could you link to the rOpenSci review here please?

arfon · 2017-11-27T15:07:55Z

@mpadge - our paper processing system expects there to be references associated with each paper. Is it possible for you to cite an related/existing work?

mpadge · 2017-11-27T17:15:00Z

@arfon yep, of course. I'll put in a paper.bib tomorrow (Tues 28/11). Great that this is progressing!

karthik · 2017-11-27T18:47:10Z

@arfon Here is the issue: ropensci/software-review#116

mpadge · 2017-11-28T09:26:07Z

paper.bib now inserted and referenced in paper.md. Let me know if there are any other requirements.

arfon · 2017-11-30T13:35:36Z

@whedon generate pdf

whedon · 2017-11-30T13:35:38Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2017-11-30T13:35:40Z

PDF failed to compile for issue #471 with the following error: 

 /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in `parse': (tmp/471/paper.md): could not find expected ':' while scanning a simple key at line 16 column 7 (Psych::SyntaxError)
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in `parse_stream'
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:327:in `parse'
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:254:in `load'
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:475:in `block in load_file'
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:in `open'
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:in `load_file'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-33e05183aa0d/lib/whedon.rb:73:in `initialize'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-33e05183aa0d/lib/whedon/processor.rb:26:in `new'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-33e05183aa0d/lib/whedon/processor.rb:26:in `set_paper'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-33e05183aa0d/bin/whedon:37:in `prepare'
	from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:in `run'
	from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in `invoke_command'
	from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:in `dispatch'
	from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in `start'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-33e05183aa0d/bin/whedon:75:in `<top (required)>'
	from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in `load'
	from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in `<main>'

arfon · 2017-11-30T13:47:41Z

@mpadge - please merge this PR which fixes up the YAML metadata in your paper: ropensci/bikedata#50

mpadge · 2017-12-04T13:00:20Z

@arfon that's done now

arfon · 2017-12-04T19:20:31Z

@whedon generate pdf

whedon · 2017-12-04T19:20:34Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2017-12-04T19:20:54Z

https://github.com/openjournals/joss-papers/blob/joss.00471/joss.00471/10.21105.joss.00471.pdf

arfon · 2017-12-04T19:53:09Z

@mpadge - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

mpadge · 2017-12-05T11:21:22Z

~~Zenodo DOI is here, with doi.org/10.5281/zenodo.844466.~~ No, wait, I'll do a new release - zenodo thinks the latest version failed, so didn't publish it. Okay @arfon zenodo link for latest v0.1.0.099, at doi.org/10.5281/zenodo.1089207.

arfon · 2017-12-05T14:36:54Z

@whedon set 10.5281/zenodo.1089207 as archive

whedon · 2017-12-05T14:36:57Z

OK. 10.5281/zenodo.1089207 is the archive.

arfon · 2017-12-05T14:43:41Z

@mpadge - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00471 ⚡️ 🚀 💥

mpadge · 2017-12-05T15:30:02Z

Awesome, thanks @arfon and @whedon. Hey @whedon, do you respond to praise? Love your work!

whedon assigned karthik Nov 27, 2017

whedon added the review label Nov 27, 2017

whedon mentioned this issue Nov 27, 2017

[PRE REVIEW]: bikedata #375

Closed

openjournals deleted a comment from whedon Nov 27, 2017

arfon closed this as completed Dec 5, 2017

arfon added the accepted label Dec 5, 2017

arfon added the rOpenSci Submissions associated with rOpenSci label Feb 6, 2020

whedon added published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. labels Mar 2, 2020

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[REVIEW]: bikedata #471

[REVIEW]: bikedata #471

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[REVIEW]: bikedata #471

[REVIEW]: bikedata #471

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Status

Reviewer instructions & questions

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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