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[REVIEW]: ComplexRegions.jl: A Julia package for regions in the complex plane #1811

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whedon opened this issue Oct 15, 2019 · 101 comments
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[REVIEW]: ComplexRegions.jl: A Julia package for regions in the complex plane #1811

whedon opened this issue Oct 15, 2019 · 101 comments
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@whedon whedon commented Oct 15, 2019

Submitting author: @tobydriscoll (Tobin Driscoll)
Repository: https://github.com/complexvariables/ComplexRegions.jl
Version: v0.1.1
Editor: @drvinceknight
Reviewer: @dlfivefifty, @dpsanders
Archive: 10.5281/zenodo.3548866

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/73e8c56985d88c36b918c58cc1346d7a"><img src="https://joss.theoj.org/papers/73e8c56985d88c36b918c58cc1346d7a/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/73e8c56985d88c36b918c58cc1346d7a/status.svg)](https://joss.theoj.org/papers/73e8c56985d88c36b918c58cc1346d7a)

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) by leaving comments 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

@dlfivefifty & @dpsanders, 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: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @drvinceknight know.

Please try and complete your review in the next two weeks

Review checklist for @dlfivefifty

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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?
  • Contribution and authorship: Has the submitting author (@tobydriscoll) 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 functionality 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

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @dpsanders

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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?
  • Contribution and authorship: Has the submitting author (@tobydriscoll) 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 functionality 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

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?
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@whedon whedon commented Oct 15, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @dlfivefifty, @dpsanders it looks like you're currently assigned to review 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 a 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

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf
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@whedon whedon commented Oct 15, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Oct 15, 2019

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@dlfivefifty dlfivefifty commented Oct 15, 2019

@whedon commands

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@whedon whedon commented Oct 15, 2019

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

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@dlfivefifty dlfivefifty commented Oct 15, 2019

I think my review is essentially done. The main thing is referencing related work of IntervalSets.jl and DomainSets.jl, see

complexvariables/ComplexRegions.jl#1

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@drvinceknight drvinceknight commented Oct 16, 2019

Thank you @dlfivefifty 👍 💪

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@dpsanders dpsanders commented Oct 22, 2019

@whedon generate pdf

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@whedon whedon commented Oct 22, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Oct 22, 2019

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@dpsanders dpsanders commented Oct 22, 2019

My main review is now complete.

There is basically nothing written down about how to contribute to the package, but I think it's understood this is done initially via issues, which seems fine to me.

I opened a couple of issues in the repo with suggestions for improvements.

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@drvinceknight drvinceknight commented Oct 23, 2019

Thank @dpsanders and @dlfivefifty, @tobydriscoll if you could confirm when you've addressed the comments that would be great.

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@tobydriscoll tobydriscoll commented Nov 1, 2019

@whedon generate pdf

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@whedon whedon commented Nov 1, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 1, 2019

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@dpsanders dpsanders commented Nov 1, 2019

There seems to be a problem with unicode characters in the Julia source code. @drvinceknight what can be done about that?

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@tobydriscoll tobydriscoll commented Nov 1, 2019

I'm not married to using unicode for this submission. I've pushed a change that avoids it.

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@tobydriscoll tobydriscoll commented Nov 1, 2019

@drvinceknight I think I have addressed the reviewers' comments. Both were quite helpful.

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@drvinceknight drvinceknight commented Nov 4, 2019

@whedon generate pdf

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@whedon whedon commented Nov 4, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 4, 2019

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@drvinceknight drvinceknight commented Nov 4, 2019

@dpsanders and @dlfivefifty could you confirm you're happy with the requested modifications? (Thanks again for your time 👍)

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@whedon whedon commented Nov 21, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Nov 21, 2019


OK DOIs

- 10/dnvcn7 is OK
- 10.2514/3.9819 is OK
- 10.1006/jcph.1993.1175 is OK
- 10.1016/0022-247X(79)90086-6 is OK
- 10/gf9fzf is OK
- 10.1137/0911035 is OK
- 10.1007/bf01418327 is OK
- 10.1016/0377-0427(86)90133-0 is OK
- 10.1109/22.156612 is OK
- 10.1137/0910031 is OK
- 10.1016/0377-0427(86)90141-x is OK
- 10.1063/1.331373 is OK
- 10.1109/tmi.2004.831226 is OK
- 10.1137/060659119 is OK
- 10.1093/imamat/hxw028 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Nov 21, 2019

PDF failed to compile for issue #1811 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e13363a737a/lib/whedon/bibtex_parser.rb:74:in doi_citation': undefined method encode' for nil:NilClass (NoMethodError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e13363a737a/lib/whedon/bibtex_parser.rb:61:in make_citation' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e13363a737a/lib/whedon/bibtex_parser.rb:47:in block in generate_citations'
from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.0.0/lib/bibtex/bibliography.rb:149:in each' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.0.0/lib/bibtex/bibliography.rb:149:in each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e13363a737a/lib/whedon/bibtex_parser.rb:41:in generate_citations' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e13363a737a/lib/whedon/compilers.rb:245:in crossref_from_markdown'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e13363a737a/lib/whedon/compilers.rb:21:in generate_crossref' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e13363a737a/lib/whedon/processor.rb:95:in compile'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e13363a737a/bin/whedon:79:in compile' 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-0e13363a737a/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

'

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@kthyng kthyng commented Nov 21, 2019

hmm, almost done but need to see what the problem is here. @arfon can you help here?

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@arfon arfon commented Nov 21, 2019

@kthyng - there are a couple of DOIs that are non-standard in format. There look to be alternative (standard-form) DOIs for the same records and I've updated them in complexvariables/ComplexRegions.jl#7

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@kthyng kthyng commented Nov 22, 2019

@tobydriscoll Can you merge the PR from @arfon?

@arfon why are those errors only picked up when trying to accept instead of when generating the pdf?

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@arfon arfon commented Nov 23, 2019

@arfon why are those errors only picked up when trying to accept instead of when generating the pdf?

They're been generated when we create the Crossref metadata (which we don't do until towards the end of the process).

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@kthyng kthyng commented Nov 23, 2019

@arfon got it, makes sense. I know better what to look for when this happens in the future.

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@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman commented Nov 28, 2019

@whedon generate pdf

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@whedon whedon commented Nov 28, 2019

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

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@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman commented Nov 28, 2019

@kthyng did you want to finish processing this one?

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@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman commented Dec 1, 2019

I checked the archive on Zenodo and the paper and all looks good.

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@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman commented Dec 1, 2019

@whedon accept

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@whedon whedon commented Dec 1, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Dec 1, 2019

PDF failed to compile for issue #1811 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon/bibtex_parser.rb:74:in doi_citation': undefined method encode' for nil:NilClass (NoMethodError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon/bibtex_parser.rb:61:in make_citation' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon/bibtex_parser.rb:47:in block in generate_citations'
from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.0.1/lib/bibtex/bibliography.rb:149:in each' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.0.1/lib/bibtex/bibliography.rb:149:in each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon/bibtex_parser.rb:41:in generate_citations' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon/compilers.rb:245:in crossref_from_markdown'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon/compilers.rb:21:in generate_crossref' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon/processor.rb:95:in compile'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/bin/whedon:79:in compile' 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-df8b50fe58b8/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

'

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@whedon whedon commented Dec 1, 2019


OK DOIs

- 10/dnvcn7 is OK
- 10.2514/3.9819 is OK
- 10.1006/jcph.1993.1175 is OK
- 10.1016/0022-247X(79)90086-6 is OK
- 10/gf9fzf is OK
- 10.1137/0911035 is OK
- 10.1007/bf01418327 is OK
- 10.1016/0377-0427(86)90133-0 is OK
- 10.1109/22.156612 is OK
- 10.1137/0910031 is OK
- 10.1016/0377-0427(86)90141-x is OK
- 10.1063/1.331373 is OK
- 10.1109/tmi.2004.831226 is OK
- 10.1137/060659119 is OK
- 10.1093/imamat/hxw028 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman commented Dec 1, 2019

@tobydriscoll it looks like you still need to merge this PR complexvariables/ComplexRegions.jl#7. Let me know when you are ready to proceed.

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@arfon arfon commented Dec 2, 2019

@whedon accept

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@whedon whedon commented Dec 2, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Dec 2, 2019


OK DOIs

- 10.1137/0908003 is OK
- 10.2514/3.9819 is OK
- 10.1006/jcph.1993.1175 is OK
- 10.1016/0022-247X(79)90086-6 is OK
- 10.1137/19M125947X is OK
- 10.1137/0911035 is OK
- 10.1007/bf01418327 is OK
- 10.1016/0377-0427(86)90133-0 is OK
- 10.1109/22.156612 is OK
- 10.1137/0910031 is OK
- 10.1016/0377-0427(86)90141-x is OK
- 10.1063/1.331373 is OK
- 10.1109/tmi.2004.831226 is OK
- 10.1137/060659119 is OK
- 10.1093/imamat/hxw028 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Dec 2, 2019

Check final proof 👉 openjournals/joss-papers#1140

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1140, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman commented Dec 2, 2019

@whedon accept deposit=true

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@whedon whedon commented Dec 2, 2019

Doing it live! Attempting automated processing of paper acceptance...
@whedon whedon added the accepted label Dec 2, 2019
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@whedon whedon commented Dec 2, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Dec 2, 2019

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#1143
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01811
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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@whedon whedon commented Dec 2, 2019

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

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

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01811/status.svg)](https://doi.org/10.21105/joss.01811)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01811">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01811/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01811/status.svg
   :target: https://doi.org/10.21105/joss.01811

This is how it will look in your documentation:

DOI

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