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

whedon · 2019-10-15T12:08:55Z

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 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:

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✨ 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

I confirm that I read and will adhere to the JOSS 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

I confirm that I read and will adhere to the JOSS 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?

The text was updated successfully, but these errors were encountered:

whedon · 2019-10-15T12:08:58Z

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:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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

whedon · 2019-10-15T12:08:59Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-10-15T12:09:26Z

👉 Check article proof 📄 👈

dlfivefifty · 2019-10-15T19:52:48Z

@whedon commands

whedon · 2019-10-15T19:52:50Z

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

dlfivefifty · 2019-10-15T19:58:18Z

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

drvinceknight · 2019-10-16T07:56:38Z

Thank you @dlfivefifty 👍 💪

dpsanders · 2019-10-22T18:18:36Z

@whedon generate pdf

whedon · 2019-10-22T18:18:39Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-10-22T18:19:10Z

👉 Check article proof 📄 👈

dpsanders · 2019-10-22T18:32:32Z

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.

drvinceknight · 2019-10-23T09:05:16Z

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

tobydriscoll · 2019-11-01T20:13:09Z

@whedon generate pdf

whedon · 2019-11-01T20:13:12Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-11-01T20:13:42Z

👉 Check article proof 📄 👈

dpsanders · 2019-11-01T20:36:58Z

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

tobydriscoll · 2019-11-01T21:02:26Z

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

tobydriscoll · 2019-11-01T21:14:05Z

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

drvinceknight · 2019-11-04T17:42:49Z

@whedon generate pdf

whedon · 2019-11-04T17:42:52Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-11-04T17:43:18Z

👉 Check article proof 📄 👈

drvinceknight · 2019-11-04T17:44:29Z

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

arfon · 2019-11-21T23:27:29Z

@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

kthyng · 2019-11-22T22:15:01Z

@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?

arfon · 2019-11-23T06:47:19Z

@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).

kthyng · 2019-11-23T13:42:58Z

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

Kevin-Mattheus-Moerman · 2019-11-28T21:36:04Z

@whedon generate pdf

whedon · 2019-11-28T21:36:07Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-11-28T21:36:33Z

👉 Check article proof 📄 👈

Kevin-Mattheus-Moerman · 2019-11-28T21:37:08Z

@kthyng did you want to finish processing this one?

Kevin-Mattheus-Moerman · 2019-12-01T21:30:24Z

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

Kevin-Mattheus-Moerman · 2019-12-01T21:32:06Z

@whedon accept

whedon · 2019-12-01T21:32:09Z

Attempting dry run of processing paper acceptance...

whedon · 2019-12-01T21:32:27Z

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

'

whedon · 2019-12-01T21:32:31Z


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

Kevin-Mattheus-Moerman · 2019-12-01T21:34:11Z

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

arfon · 2019-12-02T14:12:22Z

@whedon accept

whedon · 2019-12-02T14:12:25Z

Attempting dry run of processing paper acceptance...

whedon · 2019-12-02T14:12:52Z


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

whedon · 2019-12-02T14:13:05Z

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

Kevin-Mattheus-Moerman · 2019-12-02T14:30:37Z

@whedon accept deposit=true

whedon · 2019-12-02T14:30:40Z

Doing it live! Attempting automated processing of paper acceptance...

whedon · 2019-12-02T14:31:21Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2019-12-02T14:31:22Z

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

Here's what you must now do:

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

Any issues? notify your editorial technical team...

whedon · 2019-12-02T14:32:20Z

🎉🎉🎉 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:

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whedon added the review label Oct 15, 2019

whedon assigned drvinceknight Oct 15, 2019

whedon mentioned this issue Oct 15, 2019

[PRE REVIEW]: ComplexRegions.jl: A Julia package for regions in the complex plane #1780

Closed

whedon assigned dlfivefifty Oct 16, 2019

whedon assigned dpsanders Oct 17, 2019

dpsanders mentioned this issue Oct 22, 2019

Documentation fixes complexvariables/ComplexRegions.jl#2

Closed

This was referenced Oct 22, 2019

Meaning of / -- use broadcast instead? complexvariables/ComplexRegions.jl#3

Closed

Paper modifications complexvariables/ComplexRegions.jl#4

Closed

arfon mentioned this issue Nov 23, 2019

Whedon should catch erroneous DOIs sooner openjournals/whedon-api#74

Open

whedon added the accepted label Dec 2, 2019

Kevin-Mattheus-Moerman closed this as completed Dec 2, 2019

whedon added published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. labels Mar 2, 2020

editorialbot mentioned this issue Oct 6, 2023

[PRE REVIEW]: RationalFunctionApproximation.jl: A Julia package for approximation by rational functions #5929

Closed

editorialbot mentioned this issue Dec 2, 2024

[PRE REVIEW]: ConleyDynamics.jl: A Julia package for multivector dynamics on Lefschetz complexes #7543

Open

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

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

Comments

whedon commented Oct 15, 2019 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @dlfivefifty

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @dpsanders

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Oct 15, 2019

whedon commented Oct 15, 2019

whedon commented Oct 15, 2019

dlfivefifty commented Oct 15, 2019

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dlfivefifty commented Oct 15, 2019

drvinceknight commented Oct 16, 2019

dpsanders commented Oct 22, 2019

whedon commented Oct 22, 2019

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dpsanders commented Oct 22, 2019

drvinceknight commented Oct 23, 2019

tobydriscoll commented Nov 1, 2019

whedon commented Nov 1, 2019

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dpsanders commented Nov 1, 2019

tobydriscoll commented Nov 1, 2019

tobydriscoll commented Nov 1, 2019

drvinceknight commented Nov 4, 2019

whedon commented Nov 4, 2019

whedon commented Nov 4, 2019

drvinceknight commented Nov 4, 2019

arfon commented Nov 21, 2019

kthyng commented Nov 22, 2019

arfon commented Nov 23, 2019

kthyng commented Nov 23, 2019

Kevin-Mattheus-Moerman commented Nov 28, 2019

whedon commented Nov 28, 2019

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Kevin-Mattheus-Moerman commented Dec 1, 2019

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whedon commented Dec 1, 2019

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Kevin-Mattheus-Moerman commented Dec 1, 2019

arfon commented Dec 2, 2019

whedon commented Dec 2, 2019

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Kevin-Mattheus-Moerman commented Dec 2, 2019

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whedon commented Oct 15, 2019 •

edited

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