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

whedon commented 5 years ago

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

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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:

Make sure you're logged in to your GitHub account
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

[x] I confirm that I read and will adhere to the JOSS 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

[x] I confirm that I read and will adhere to the JOSS 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?

dlfivefifty commented 4 years ago

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.

tobydriscoll commented 4 years ago

@whedon check references

whedon commented 4 years ago

Attempting to check references...

whedon commented 4 years ago


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 commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

tobydriscoll commented 4 years ago

DOIs fixed and package names updated in the references.

drvinceknight commented 4 years ago

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).

tobydriscoll commented 4 years ago

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

I hope it's all in order. Thanks!

drvinceknight commented 4 years ago

@whedon set 10.5281/zenodo.3548866 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3548866 is the archive.

drvinceknight commented 4 years ago

@whedon set v0.1.1 as version

whedon commented 4 years ago

OK. v0.1.1 is the version.

drvinceknight commented 4 years ago

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

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

kthyng commented 4 years ago

@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.

kthyng commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

kthyng commented 4 years ago

Also a PR for spacing I missed before.

kthyng commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

kthyng commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago


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 commented 4 years ago

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<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

'

kthyng commented 4 years ago

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

arfon commented 4 years ago

@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

kthyng commented 4 years ago

@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 commented 4 years ago

@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 commented 4 years ago

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

Kevin-Mattheus-Moerman commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 4 years ago

@kthyng did you want to finish processing this one?

Kevin-Mattheus-Moerman commented 4 years ago

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

Kevin-Mattheus-Moerman commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

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<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 commented 4 years ago


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 commented 4 years ago

@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.

arfon commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago


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 commented 4 years ago

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

Kevin-Mattheus-Moerman commented 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago

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

whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 4 years ago

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

openjournals / joss-reviews