Joss-reviews: [PRE REVIEW]: bit: a git-based tool for the management of code and data

[whedon]

Submitting author: @jorgeboucas (Jorge Boucas)
Repository: https://github.com/mpg-age-bioinformatics/bit
Version: 0.1.1
Editor: @acabunoc
Reviewer: @dvalters

Author instructions

Thanks for submitting your paper to JOSS @jorgeboucas. The JOSS editor (shown at the top of this issue) will work with you on this issue to find a reviewer for your submission before creating the main review issue.

@jorgeboucas if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

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

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 #534 with the following error: 

 /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in `parse': (tmp/534/paper.md): did not find expected key while parsing a block mapping at line 2 column 1 (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-8307502c3aee/lib/whedon.rb:73:in `initialize'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/lib/whedon/processor.rb:26:in `new'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/lib/whedon/processor.rb:26:in `set_paper'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/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-8307502c3aee/bin/whedon:99: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]

@acabunoc - would you be willing to edit this submission for JOSS?

[acabunoc]

@arfon happy to edit! I'll take a look later this week

[acabunoc]

@whedon assign @acabunoc as editor

[whedon]

OK, the editor is @acabunoc

[jorgeboucas]

@acabunoc thanks! I am here in case I am needed.

[acabunoc]

Hey @jorgeboucas! I took a quick look and I think we're good to start a review! Do you have any suggested reviewers? I like to have a few per submission 😄

pinging @dvalters or @jsta -- would either of you be up for reviewing this? Raise a ✋ to let me know!

[dvalters]

@acabunoc sure ✋

[jorgeboucas]

maybe @paulklemm would like to join the party?

[paulklemm]

Sure I will help.

[jorgeboucas]

Hi @acabunoc, will 3 do it?
@jsta we are taking your 🎉 as a show of hands ✋ - 😃

[jsta]

Unfortunately I am not available for this review. Best of luck tho!

[acabunoc]

What a showing! Thanks @paulklemm & @dvalters 😄
Here are the reviewer guidelines: http://joss.theoj.org/about#reviewer_guidelines

I'll take a quick look at your paper.md before we start the review

[acabunoc]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #534 with the following error: 

 /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in `parse': (tmp/534/paper.md): did not find expected key while parsing a block mapping at line 2 column 1 (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-8307502c3aee/lib/whedon.rb:73:in `initialize'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/lib/whedon/processor.rb:26:in `new'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/lib/whedon/processor.rb:26:in `set_paper'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/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-8307502c3aee/bin/whedon:99: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>'

[acabunoc]

@jorgeboucas could you merge this PR? I _think_ it will fix the error @whedon's running into

[acabunoc]

@whedon assign @paulklemm as reviewer

[whedon]

OK, the reviewer is @paulklemm

[acabunoc]

@whedon assign @dvalters as reviewer

[whedon]

OK, the reviewer is @dvalters

[jorgeboucas]

@acabunoc merged. Thanks!

[jorgeboucas]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #534 with the following error: 

 /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/lib/whedon.rb:86:in `check_fields': Paper YAML header is missing expected fields: bibliography (RuntimeError)
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/lib/whedon.rb:74:in `initialize'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/lib/whedon/processor.rb:26:in `new'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/lib/whedon/processor.rb:26:in `set_paper'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/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-8307502c3aee/bin/whedon:99: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>'

[jorgeboucas]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

https://github.com/openjournals/joss-papers/blob/joss.00534/joss.00534/10.21105.joss.00534.pdf

[jorgeboucas]

@acabunoc paper.md functional now.

[acabunoc]

@whedon start review magic-word=bananas

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/549. Feel free to close this issue now!