[PRE REVIEW]: Probabilistic Biostatistics with Julia

[whedon]

Submitting author: @tszanalytics (Jeffrey A Mills) Repository: https://github.com/tszanalytics/Juliacon2019/ Editor: @matbesancon Reviewers: @bkamins, @kescobo

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Thanks for submitting your paper to JuliaCon @tszanalytics. The JuliaCon editor @matbesancon, will work with you on this issue to find a reviewer for your submission before creating the main review issue.

@tszanalytics if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JuliaCon and may be suitable for this submission.

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You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #25 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/25 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:incollect!' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon/processor.rb:61:infind_paper_paths' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/bin/whedon:50:in prepare' 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-85c572552d68/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

'

[tszanalytics]

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[tszanalytics]

@matbesancon Here's suggestions from the list of potential reviewers (starting at bottom of list) :

dmbates dmbates@gmail.com kescobo kevbonham@gmail.com bkamins bkamins@sgh.waw.pl

Also, the paper did not appear to compile due to a missing file. I will see if I can fix that. Thanks!

[matbesancon]

Thanks @tszanalytics, note that we cannot start the review while the paper doesn't compile. @bkamins would you be available to review this proceeding?

[matbesancon]

@kescobo would you be available to review?

[bkamins]

@matbesancon - sure - I can help. What would be the process?

[matbesancon]

the review happens in an issue, you provide feedback on the code and paper, can submit issues on the main repo itself, changes can happen gradually. Once the checklist is done and you are satisfied with everything, the review is done

See https://github.com/JuliaCon/proceedings-review/issues/28 for instance

[matbesancon]

@whedon add @bkamins as reviewer

[whedon]

OK, @bkamins is now a reviewer

[tszanalytics]

@matbesancon Hi, sorry I don't know what I need to change to get the paper to compile. I'm unfamiliar with Ruby and latexmk. Do I need to install these on my local machine or is there a way to compile without doing so, and if so how? Thanks!

[matbesancon]

The URL you provided is not in the correct format, it should be the main repo, not the path to the paper file

[bkamins]

@matbesancon: I understand that I wait till the status changes to [REVIEW] and the paper PDF is generated + the list like in #28 is in place. Right?

@tszanalytics: I think it will be easier if I give you the feedback as new issues in https://github.com/tszanalytics/Juliacon2019. OK? Also can you also please guide me where are the runnable codes for your text, as I could not find them in your repository. Finally there are two .tex files in the repo. I understand that one can be removed - right?.

[matbesancon]

I understand that I wait till the status changes to [REVIEW] and the paper PDF is generated + the list like in #28 is in place. Right?

You can start your review now by posting issues on the main repo yes, but this one will likely be closed since the URL is invalid. Once we have a second reviewer, I'll open the review issue exactly

[matbesancon]

@tszanalytics you should submit with https://github.com/tszanalytics/Juliacon2019 as repository if it is your main repo

[kescobo]

I'd love to review, but I'm fairly strapped for time (and off the grid for a week starting Friday). What's the time frame?

[matbesancon]

This would be fine, @bkamins can start the review and you can pick up after you come back

[tszanalytics]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #25 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/25 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:incollect!' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon/processor.rb:61:infind_paper_paths' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/bin/whedon:50:in prepare' 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-85c572552d68/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

'

[matbesancon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[matbesancon]

@whedon add @kescobo as reviewer

[whedon]

OK, @kescobo is now a reviewer

[matbesancon]

@tszanalytics problem fixed :)

[matbesancon]

@whedon start review

[tszanalytics]

@matbesancon Ok, I withdrew and resubmitted using the URL as suggested. It compiled OK this time, thanks for the help!

@bkamins Thanks for agreeing to review my paper. I've removed the additional tex and pdf files from the \paper folder. I just have code snippets in the paper, but I can post more complete runnable examples of julia code and add the URL to the paper. I will do so asap. Let me know if you have anything in particular in mind. Also, giving feedback as an issue on the paper repo would be great. Thanks!

[bkamins]

@tszanalytics I asked about the codes, because if you look at https://github.com/JuliaCon/proceedings-review/issues/28 for example there are the following criteria that the paper must meet (I am copying the relevant ones from General checks, but please review all of them there to make sure that your submission complies with it):

General checks

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

[bkamins]

@matbesancon - I can see that you have started the review, but the "checklist" has not generated yet. Should I wait for it or I have missed something.

@tszanalytics - I can review the paper as is if you prefer not to add working codes to the repository. Please let me know how you see this.

[matbesancon]

thanks for the ping, it hasn't started indeed

[matbesancon]

@whedon start review

[matbesancon]

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[matbesancon]

@whedon start review

[matbesancon]

@arfon not sure why whedon isn't kicking off the review?

[arfon]

@matbesancon - it's showing up as withdrawn on the proceedings site. Is this incorrect?

[matbesancon]

ah point, sorry yup

[tszanalytics]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[tszanalytics]

@matbesancon @bkamins @kescobo

Ok, I believe it is ready to move forward with review now. I've added code to generate the figures, etc. that appear in the paper, as well as code for some of the additional examples in the presentation. Let me know what else needs to be done and I should be able to complete quickly.

Thanks, Jeff

[kescobo]

So why was the issue closed? I'm so confused...

[bkamins]

This one should be used: https://github.com/JuliaCon/proceedings-review/issues/36. @tszanalytics - I am not sure but probably you should re-generate the PDF in #36

[matbesancon]

Indeed that is in #36