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[PRE REVIEW]: mbir: Magnitude-Based Inferences #725

Closed whedon closed 6 years ago

whedon commented 6 years ago

Submitting author: @kdpeterson51 (Kyle Peterson) Repository: https://github.com/kdpeterson51/mbir Version: 1.3 Editor: @leeper Reviewers: @kellieotto

Author instructions

Thanks for submitting your paper to JOSS @kdpeterson51. 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.

@kdpeterson51 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.

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whedon commented 6 years ago

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 commented 6 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 6 years ago

PDF failed to compile for issue #725 with the following error:

/app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-a31a5c2a9125/lib/whedon.rb:78:in check_fields': Paper YAML header is missing expected fields: tags (RuntimeError) from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-a31a5c2a9125/lib/whedon.rb:66:ininitialize' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-a31a5c2a9125/lib/whedon/processor.rb:29:in new' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-a31a5c2a9125/lib/whedon/processor.rb:29:inset_paper' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-a31a5c2a9125/bin/whedon:37:in prepare' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun' 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:indispatch' 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-a31a5c2a9125/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

'

arfon commented 6 years ago

@kdpeterson51 - please take a look at the guidelines for the paper structure http://joss.theoj.org/about#paper_structure and update yours accordingly.

In addition, this package doesn't look like it has a README, license etc. You might want to take a look at the reviewer guidelines to see what your package will be evaluated on.

kdpeterson51 commented 6 years ago

Sincere apologies, Afron.

Tags have been added to YAML header, README and LICENSE files are now up-to-date.

kdpeterson51 commented 6 years ago

@whedon commands

whedon commented 6 years ago

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

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@whedon assign @username as reviewer

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@whedon add @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

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@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Open the review issue
@whedon start review

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# Compile the paper
@whedon generate pdf
kdpeterson51 commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 6 years ago

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

leeper commented 6 years ago

@whedon assign @leeper as editor

whedon commented 6 years ago

OK, the editor is @leeper

leeper commented 6 years ago

Hi, @kdpeterson51. Thanks for your submission. A couple of preliminary things here before we get started:

  1. Can you clarify the license for the functions mentioned in COPYRIGHT? Do you have permission to redistribute this code from the original author? If so, under what license?

  2. It looks like you are generating your R NAMESPACE file by hand rather than through roxygen. Can you delete and reinitialize using devtools::document()?

  3. Should the vignette be included in a typical /vignettes directory in the package itself?

  4. Do you have any suggested reviewers for the package?

kdpeterson51 commented 6 years ago

Hi @leeper. Thank you very much for your assistance.

  1. The copyright was obtained by written permission to use those cited MS Excel spreadsheets.

  2. Original NAMESPACE file has been deleted and replaced with devtools version.

  3. Vignette folder is now up-to-date within /mbir folder.

  4. We do not have any suggested reviewers at this time.

leeper commented 6 years ago

Hi @kdpeterson51, thanks for that. Can I request that you update the COPYRIGHT file to clarify that. As you know, JOSS only publishes software that has a complete open source license and the current wording might be confusing in this respect.

Given that the software is a derivative work (rather than a redistribution of the original spreadsheets), I might suggest that you indicate that the copyright applies to the original spreadsheets, permission was granted to create a derivative work (perhaps list a date that written permission was granted), and indicate that the copyright does not apply to any of the actual code in the package.

Would that be acceptable to you?

kdpeterson51 commented 6 years ago

Your suggestions are appreciated, @leeper. The COPYRIGHT file has been updated to improve the language.

leeper commented 6 years ago

@kellieotto Would you be interested in reviewing this software for JOSS?

kellieotto commented 6 years ago

@leeper Yes, happy to review this.

leeper commented 6 years ago

@whedon assign @kellieotto as reviewer

whedon commented 6 years ago

OK, the reviewer is @kellieotto

leeper commented 6 years ago

@whedon start review magic-word=bananas

whedon commented 6 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/746. Feel free to close this issue now!

leeper commented 6 years ago

@kellieotto Excellent. Thank you! You can find the review issue here: https://github.com/openjournals/joss-reviews/issues/746 Please follow the instructions there, complete the review checklist, and raise any issues questions, or concerns.

Let me know (over there) if you have any questions. Thanks, again!