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[REVIEW]: PFEIFER: Preprocessing Framework of Electrograms Intermittently Fiducialized from Experimental Recordings #472

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whedon opened this issue Nov 27, 2017 · 57 comments
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accepted published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review

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@whedon
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whedon commented Nov 27, 2017

Submitting author: @bzenger (Brian Zenger)
Repository: https://github.com/SCIInstitute/PFEIFER
Version: v1.0.0
Editor: @Kevin-Mattheus-Moerman
Reviewer: @CristianaCorsi
Archive: 10.5281/zenodo.1158651

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/b3c9a521d3f2a1bd924c8e6a81f9f8b3"><img src="http://joss.theoj.org/papers/b3c9a521d3f2a1bd924c8e6a81f9f8b3/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/b3c9a521d3f2a1bd924c8e6a81f9f8b3/status.svg)](http://joss.theoj.org/papers/b3c9a521d3f2a1bd924c8e6a81f9f8b3)

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

@CristianaCorsi, 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 @Kevin-Mattheus-Moerman know.

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: Does the release version given match the GitHub release (v1.0.0)?
  • Authorship: Has the submitting author (@bzenger) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

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

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

I suggest to use in the Documentation, figures that describe exactly the windows that open when you run PFEIFER. For example, in Chapter 6, figure 6.1 shows a window slightly different from the DATA_ORGANIZATION window that opens when you run PFEIFER. In the window each section has a specific name and the BEAT PROPAGATION section includes six fields, not four as reported in the figure (Window Length is called Window Width; the fields #Beats before updating and # Beats for updating are missing as well as the flags “Include RMS for Autofiducializing”, “Local Fiducials”, “Update Templates”; and the button !Default Settings!). The design of the window is also different from the one reported in figure 6.1.
I also suggest to include in the Documentation the link to the tutorials available at: http://www.sci.utah.edu/software/pfeifer.html

Software paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
@whedon
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whedon commented Nov 27, 2017

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @CristianaCorsi it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐ Important ⭐

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:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

For a list of things I can do to help you, just type:

@whedon commands

@whedon
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whedon commented Nov 27, 2017

Attempting PDF compilation. Reticulating splines etc...

1 similar comment
@whedon
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whedon commented Nov 27, 2017

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Nov 27, 2017

PDF failed to compile for issue #472 with the following error: 

 /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in `block in find': No such file or directory (Errno::ENOENT)
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in `collect!'
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in `find'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-33e05183aa0d/lib/whedon/processor.rb:49:in `find_paper_paths'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-33e05183aa0d/bin/whedon:32: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>'

1 similar comment
@whedon
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whedon commented Nov 27, 2017

PDF failed to compile for issue #472 with the following error: 

 /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in `block in find': No such file or directory (Errno::ENOENT)
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in `collect!'
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in `find'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-33e05183aa0d/lib/whedon/processor.rb:49:in `find_paper_paths'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-33e05183aa0d/bin/whedon:32: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>'

@Kevin-Mattheus-Moerman
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@CristianaCorsi this is where the review takes place. The review is guided by the tick boxes at the top of this issue which you are able to tick. See our website and reviewer guidelines for more information. If you have comments or issues you want to report for the authors you can leave comments here. You can also post issues on the project repo and link to them here. Thanks you. Let me know if I can help with anything.

@Kevin-Mattheus-Moerman
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@CristianaCorsi could you provide an indication as to when you think you can complete this review? Thanks

@Kevin-Mattheus-Moerman
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@bzenger The initial paper generation did not complete. I am unsure about the error but it looks like it cannot find your paper file. Could you please rename the paper folder and paper file to paper and paper.md respectively? Thanks

@bzenger
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bzenger commented Nov 27, 2017

@Kevin-Mattheus-Moerman This should be updated now. Could we re-run the generation function?

@Kevin-Mattheus-Moerman
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@whedon generate pdf

@whedon
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whedon commented Nov 28, 2017

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Nov 28, 2017

https://github.com/openjournals/joss-papers/blob/joss.00472/joss.00472/10.21105.joss.00472.pdf

@Kevin-Mattheus-Moerman
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@bzenger that seems to have worked. Can you check if the affiliations are complete/correct in your article?

@bzenger
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bzenger commented Nov 29, 2017

@Kevin-Mattheus-Moerman I just updated the affiliations for clarifications. If you could have whedon run again that would be great! Thank you so much!

@Kevin-Mattheus-Moerman
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@whedon generate pdf

@whedon
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whedon commented Nov 29, 2017

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Nov 29, 2017

PDF failed to compile for issue #472 with the following error: 

 /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in `parse': (tmp/472/paper/paper.md): mapping values are not allowed in this context at line 37 column 9 (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>'

@wgood
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wgood commented Nov 29, 2017

@whedon generate pdf

@whedon
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whedon commented Nov 29, 2017

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Nov 29, 2017

PDF failed to compile for issue #472 with the following error: 

 /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in `parse': (tmp/472/paper/paper.md): mapping values are not allowed in this context at line 38 column 8 (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>'

@wgood
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wgood commented Nov 29, 2017

@whedon generate pdf

@whedon
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whedon commented Nov 29, 2017

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Nov 29, 2017

PDF failed to compile for issue #472 with the following error: 

 /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in `parse': (tmp/472/paper/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-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
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arfon commented Nov 29, 2017

@bzenger - sorry for the unhelpful errors from @whedon. I've made some fixes to your paper YAML header that were obvious (to me 😄) problems: SCIInstitute/PFEIFER#24

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whedon commented Nov 30, 2017

Attempting PDF compilation. Reticulating splines etc...

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whedon commented Nov 30, 2017

https://github.com/openjournals/joss-papers/blob/joss.00472/joss.00472/10.21105.joss.00472.pdf

@Kevin-Mattheus-Moerman
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@arfon. Perhaps we can fix this by always starting the DOI link on a new line.

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arfon commented Dec 1, 2017

@arfon. Perhaps we can fix this by always starting the DOI link on a new line.

Perhaps. Not sure how we would do that though?

@Kevin-Mattheus-Moerman
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I've added some statements over at openjournals/whedon#14.

@Kevin-Mattheus-Moerman
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@CristianaCorsi how are you getting on? Let me know if I can help with anything.

@CristianaCorsi
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Hi. I downloaded all the material. I hope I will be able to provide the review in ten days. If I need help I will let you know. Thank you!

@Kevin-Mattheus-Moerman
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@CristianaCorsi thanks for the update! Our review guidelines are here and you can find the tick-boxes at the top of this issue. Thanks for your help reviewing!

@Kevin-Mattheus-Moerman
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@bzenger @CristianaCorsi Happy New Year! 🎉
@CristianaCorsi how are you getting on? Are you able to finalize the review process soon? Let me know if I can help with anything.

@CristianaCorsi
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CristianaCorsi commented Jan 22, 2018 via email

@Kevin-Mattheus-Moerman
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@ChristianaCorsi 🎉 excellent thanks for completing the review process. We will handle things from here on. Can you and @bzenger confirm the comments to the documentation have been implemented? Can you link to an issue (if an issue was used)?

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bzenger commented Jan 22, 2018 via email

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CristianaCorsi commented Jan 23, 2018 via email

@Kevin-Mattheus-Moerman
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@bzenger can you respond to @CristianaCorsi 's comments?

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bzenger commented Jan 23, 2018

@Kevin-Mattheus-Moerman @CristianaCorsi the doc is updated in the github repo. Thanks!

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bzenger commented Jan 24, 2018

@Kevin-Mattheus-Moerman let us know if there is anything else you need us to do!

@Kevin-Mattheus-Moerman
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Okay it looks like we are all set here! 🚀 🎉
@bzenger 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? @arfon can then move forward with accepting the submission.
Thanks @CristianaCorsi for the review!

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bzenger commented Jan 24, 2018

DOI

@Kevin-Mattheus-Moerman is this all I need for that process?

@Kevin-Mattheus-Moerman
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Yes all set. @arfon will take it from here.

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arfon commented Jan 24, 2018

@whedon set 10.5281/zenodo.1158651 as archive

@whedon
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whedon commented Jan 24, 2018

OK. 10.5281/zenodo.1158651 is the archive.

@arfon arfon added the accepted label Jan 24, 2018
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arfon commented Jan 24, 2018

@CristianaCorsi - many thanks for your review here and to @Kevin-Mattheus-Moerman for editing this one ✨

@bzenger - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00472 ⚡️ 🚀 💥

@arfon arfon closed this as completed Jan 24, 2018
@whedon
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whedon commented Jan 24, 2018

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippet:

[![DOI](http://joss.theoj.org/papers/10.21105/joss.00472/status.svg)](https://doi.org/10.21105/joss.00472)

This is how it will look in your documentation:

DOI

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