Joss-reviews: [REVIEW]: ComplexRegions.jl: A Julia package for regions in the complex plane

Created on 15 Oct 2019  ·  101Comments  ·  Source: openjournals/joss-reviews

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

  • [x] 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

  • [x] Repository: Is the source code for this software available at the repository url?
  • [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • [x] 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

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

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

  • [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • [x] 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

  • [x] 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

  • [x] Repository: Is the source code for this software available at the repository url?
  • [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • [x] 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

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

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

  • [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • [x] 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?
accepted published recommend-accept review

All 101 comments

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 :tada:.

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@whedon check references

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

https://github.com/complexvariables/ComplexRegions.jl/issues/1

Thank you @dlfivefifty :+1: 💪

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

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.

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

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

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

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

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

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

@dpsanders and @dlfivefifty could you confirm you're happy with the requested modifications? (Thanks again for your time :+1:)

Good for me, thanks.

The References heading in the PDF didn't come out right.

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

@dpsanders I needed to put in a blank line. References header is ok now.

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

@dlfivefifty could you confirm you're now happy with the paper?

Good for me, thanks.

@dpsanders I've taken the liberty to tick the two remaining boxes on your check list ("Community guidelines", "State of the field" and "Reference").

Two comments:

  1. The citation for IntervalSets.jl gives Huybrechs and myself (Olver) too much credit: we’ve made contributions but it was created by @mronian, with many contributions by @timholy
  2. The use of “.jl” in package names should be consistent between “ComplexRegions” and “IntervalSets.jl and DomainSets.jl”.

Updates:

  1. I have avoided trying to summarize credit for IntervalSets. The paper links to it, where the full history is easy to see.

  2. I have decided to go without .jl on all the package names. It's an editorial choice, but seeing it over and over is really clunky.

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

Ok one last comment: add references for DomainSets and IntervalSets as otherwise it’s not clear how to find them. This could just be links to the github pages

My mistake. I thought adding them as markdown links would get through. I put them in the Refs section instead.

@whedon generate pdf

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

sigh Forgot to brace my capital Js. Trying again.

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

@whedon check references

Attempting to check references...

```Reference check summary:

OK DOIs

  • 10/gf9fzf is OK
  • 10.1109/tmi.2004.831226 is OK
  • 10.1137/060659119 is OK
  • 10.1093/imamat/hxw028 is OK

MISSING DOIs

INVALID DOIs

  • None
    ```

@tobydriscoll it looks like a number of DOIs are missing, would you be able to add those please?

@dlfivefifty I believe the references you asked for are included now (but if you could confirm you're happy for this to be accepted that would be great :+1:)

id Suggest adding “.jl” to the references, even if it’s not used in the paper itself: this seems more consistent with how things are cited, particularly with packages whose names otherwise might be confusing (DifferentialEquations.jl).

But I’ll leave it to the author/editor whether to incorporate this suggestion.

@whedon check references

Attempting to check references...

```Reference check summary:

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
    ```

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

DOIs fixed and package names updated in the references.

Great, thanks.

It's all looking good to me now.

Could you make a tagged release and archive, and report the version number and archive DOI here (note that the archive title should match the paper title: ComplexRegions.jl: A Julia package for regions in the complex plane).

It's v0.1.1, DOI is 10.5281/zenodo.3548866.

I hope it's all in order. Thanks!

@whedon set 10.5281/zenodo.3548866 as archive

OK. 10.5281/zenodo.3548866 is the archive.

@whedon set v0.1.1 as version

OK. v0.1.1 is the version.

@openjournals/joss-eics this paper is ready to be accepted :)

Thanks @dpsanders and @dlfivefifty again for your work reviewing the paper.

@tobydriscoll Hi! I am taking over from here. I made a few changes to your paper so there are not parentheses around references if they are meant to be inline instead. The PR is here and if you agree with it please merge.

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

Also a PR for spacing I missed before.

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

@whedon accept

Attempting dry run of processing paper acceptance...

```Reference check summary:

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
    ```

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 methodencode' 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:inblock 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:ineach'
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:incrossref_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:incompile'
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:inrun'
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:indispatch'
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 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

'

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

@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 https://github.com/complexvariables/ComplexRegions.jl/pull/7

@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 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).

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

@whedon generate pdf

Attempting PDF compilation. Reticulating splines etc...

@kthyng did you want to finish processing this one?

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

@whedon accept

Attempting dry run of processing paper acceptance...

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 methodencode' 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:inblock 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:ineach'
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:incrossref_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:incompile'
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:inrun'
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:indispatch'
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 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

'

```Reference check summary:

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
    ```

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

@whedon accept

Attempting dry run of processing paper acceptance...

```Reference check summary:

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
    ```

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1140

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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

@whedon accept deposit=true

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

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/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...

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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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