Joss-reviews: [REVIEW]: bikedata

[whedon]

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:

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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:

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: http://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @karthik know.

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

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: Does the release version given match the GitHub release (v0.0.4)?
• [x] Authorship: Has the submitting author (@mpadge) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [x] 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

• [x] Authors: Does the paper.md file include a list of authors with their affiliations?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

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 :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 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:

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

1. 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]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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]

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

[arfon]

@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]

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

[karthik]

@arfon Here is the issue: https://github.com/ropensci/onboarding/issues/116

[mpadge]

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

[arfon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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]

@mpadge - please merge this PR which fixes up the YAML metadata in your paper: https://github.com/ropensci/bikedata/pull/50

[mpadge]

@arfon that's done now

[arfon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[arfon]

@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]

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]

@whedon set 10.5281/zenodo.1089207 as archive

[whedon]

OK. 10.5281/zenodo.1089207 is the archive.

[arfon]

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

[mpadge]

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