Joss-reviews: [PRE REVIEW]: q2-sample-classifier: machine-learning tools for microbiome classification and regression

[whedon]

Submitting author: @nbokulich (Nicholas Bokulich)
Repository: https://github.com/caporaso-lab/sample-classifier-ms
Version: 2018.6
Editor: @yochannah
Reviewers: @rasbt, @luizirber

Author instructions

Thanks for submitting your paper to JOSS @nbokulich. 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.

@nbokulich 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, a robot that can 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]

Failed to discover a valid open source license.

[whedon]

PDF failed to compile for issue #891 with the following error:

/app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/author.rb:36:in block in build_affiliation_string': Problem with affiliations for J Gregory Caporaso, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/author.rb:35:ineach'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/author.rb:35:in build_affiliation_string' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/author.rb:11:ininitialize'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:108:in new' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:108:inblock in parse_authors'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:106:in each' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:106:inparse_authors'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon.rb:73:in initialize' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:32:innew'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:32:in set_paper' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:37:inprepare'
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:ininvoke_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:instart'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:99:in <top (required)>' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:inload'
from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in `

'

[nbokulich]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[yochannah]

@whedon assign @yochannah as editor

[whedon]

OK, the editor is @yochannah

[yochannah]

@nbokulich I think this is ready to be reviewed - do you have any suggestions for reviewers?

[gregcaporaso]

Sebastian Raschka, Dan Knights (though @nbokulich and I have published with Dan, so that might be a conflict of interest) and Holly Bik could be good reviewers for this manuscript.

[yochannah]

@gregcaporaso I'll contact them - thanks for the tips!

[yochannah]

Ok, I've pinged @hollybik @rasbt via email - and now also made them aware in this issue.

[rasbt]

I could review the pkg

[yochannah]

@rasbt fantastic! I'm still looking for a second reviewer so I won't kick the review process off quite yet.

[yochannah]

👋 @luizirber is this something you might be interested in reviewing?

[luizirber]

@yochannah sure!

[yochannah]

Excellent!

[yochannah]

@whedon assign @rasbt as reviewer

[whedon]

OK, the reviewer is @rasbt

[yochannah]

@whedon add @luizirber as reviewer

[whedon]

OK, @luizirber is now a reviewer

[yochannah]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/934. Feel free to close this issue now!