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[PRE REVIEW]: PyBIDS: Python tools for BIDS datasets #1289

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whedon opened this Issue Feb 28, 2019 · 13 comments

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whedon commented Feb 28, 2019

Submitting author: @tyarkoni (Tal Yarkoni)
Repository: https://github.com/bids-standard/pybids
Version: 0.8.0
Editor: Pending
Reviewer: Pending

Author instructions

Thanks for submitting your paper to JOSS @tyarkoni. Currently, there isn't an JOSS editor assigned to your paper.

@tyarkoni 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 whedon added the pre-review label Feb 28, 2019

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whedon commented Feb 28, 2019

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

What happens now?

This submission is currently in a pre-review state which means we are waiting for an editor to be assigned and for them to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience 😸

You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.

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whedon commented Feb 28, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Feb 28, 2019

PDF failed to compile for issue #1289 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon.rb:83:in check_fields': Paper YAML header is missing expected fields: affiliations (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon.rb:69:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon/processor.rb:32:in set_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/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-01ece1d1d135/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

'

@whedon whedon added Python TeX labels Feb 28, 2019

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danielskatz commented Feb 28, 2019

👋 @cMadan - the submitting author requested you as the editor - is this ok?

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danielskatz commented Feb 28, 2019

👋 @tyarkoni - your paper.md authors and affiliations aren't formatted right - see https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography for an example of how this needs to be.

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tyarkoni commented Feb 28, 2019

Re: editor, I would have requested @arokem because of his Python expertise, but he's a contributor to the repository, so it seemed like a conflict of interest.

There's a PR that I think fixes the issues. Let's see...

@whedon generate pdf from branch joss

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danielskatz commented Feb 28, 2019

Whedon commands need to be new comments

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danielskatz commented Feb 28, 2019

@whedon generate pdf from branch joss

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whedon commented Feb 28, 2019

Attempting PDF compilation from custom branch joss. Reticulating splines etc...
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whedon commented Feb 28, 2019

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danielskatz commented Feb 28, 2019

ok, looks good

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grlee77 commented Mar 1, 2019

I am interested in volunteering as a reviewer for this submission. I have MRI neuroimaging and python expertise.
I do not have any conflicts to report (I have contributed to one of the project's dependencies, NiBabel, but have not had any involvement with BIDS or pyBIDS).

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danielskatz commented Mar 1, 2019

Thanks @grlee77 - reviewer decisions will be made by the editor, hopefully @cMadan once he accepts

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