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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HTML: <a href="https://joss.theoj.org/papers/73e8c56985d88c36b918c58cc1346d7a"><img src="https://joss.theoj.org/papers/73e8c56985d88c36b918c58cc1346d7a/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/73e8c56985d88c36b918c58cc1346d7a)
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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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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:
Updates:
I have avoided trying to summarize credit for IntervalSets. The paper links to it, where the full history is easy to see.
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
MISSING DOIs
INVALID DOIs
@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
MISSING DOIs
INVALID DOIs
@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
MISSING DOIs
INVALID DOIs
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:inload'
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:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in
```Reference check summary:
OK DOIs
MISSING DOIs
INVALID DOIs
@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
MISSING DOIs
INVALID DOIs
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
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