Joss-reviews: [PRE REVIEW]: infotheory: A C++/Python package for multivariate information theoretic analysis

[whedon]

Submitting author: @madvn (Madhavun Candadai)
Repository: https://github.com/madvn/infotheory
Version: 1.0
Editor: @poulson
Reviewers: ajgates42, @Autoplectic

Author instructions

Thanks for submitting your paper to JOSS @madvn. Currently, there isn't an JOSS editor assigned to your paper.

@madvn 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 JOSS and may be suitable for this submission.

Editor instructions

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[whedon]

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What happens now?

This submission is currently in a pre-review state which means we are waiting for an editor to be assigned and for them to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience :smile_cat:

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1548 with the following error:

ORCID looks to be the wrong length
/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:123:in block in check_orcids': Problem with ORCID (https://orcid.org/0000-0002-9254-8641) for Madhavun Candadai (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:121:ineach'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:121:in check_orcids' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:81:ininitialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon/processor.rb:36:inset_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/bin/whedon:55: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 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

'

[labarba]

👋 @ madvn — your paper is not compiling; the error appears to be with an ORCID. Can you try to fix, then run @whedon generate pdf here to try the compilation again?

[madvn]

👋 Thanks, @labarba I have updated ORCIDs

[madvn]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[labarba]

@usethedata — would you be able to handle this submission as editor?

[labarba]

@madvn — the paper at the moment feels like a "wall of text." Could you make an extra effort to separate the text into sub-sections, and build up to the specialized content a little more gradually? Bear in mind our documentation says that you should "describing the high-level functionality and purpose of the software for a diverse, non-specialist audience."

[usethedata]

@labarba I'm a bit strapped at the moment, with ongoing elder care issues and a major proposal due at the end of July. If there's anyone else that can do it, that might be better. Otherwise, I can do it, but I'll be slower in getting to things than I'd prefer.

[labarba]

@poulson — Might you be able to handle this submission? A bit out of your landscape, but no one editor is perfect for this one and you have scads of C++ experience.

[madvn]

Thanks, @labarba. I have reorganized the paper into sections and included more high-level description of the package.

[madvn]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[poulson]

Hi @labarba, I think I could handle this submission.

[labarba]

@whedon assign @poulson as editor

[whedon]

OK, the editor is @poulson

[poulson]

:wave: Alexander (@ajgates42): Given your expertise in python and information theory, you seem like an ideal reviewer for this submission. Would you have the time and interest to help review this submission? And, would you happen to have any suggestions for other reviewers?

:wave: Fabian (@fsteeg): You have listed expertise in information retrieval, though your languages were given as Java and Scala. Would you feel confident as a reviewer of a C++/Python package on information theory? If so, would you have the time to review?

:wave: Andre (@andremrsantos): You listed experience in python/C++ and in statistics and bioinformatics. Would you feel confident reviewing a submission on information theory? If so, do you have the time and interest in doing so?

[andremrsantos]

Hi @poulson,
although I would love to contribute. My knowledge of information theory is limited and I wouldn't feel confident on review submission on the subject.
I hope you find your reviewers soon.

[ajgates42]

Thanks for the invite @poulson. Looks like a fun project, I would be happy to review it.

[madvn]

@ajgates42 Thanks! Looking forward to hearing your feedback on the project.

@poulson We are continuing to use this project in our research and we have discovered that with some minor changes the multivariate analyses methods in this package can be extended from bi-variate to tri-variate analyses. This would significantly increase the value of the package because, to our knowledge, there are no published packages for tri-variate analyses. Since we are in the pre-review stage, would it be okay for me to update it real quick (in a day or two)?

[poulson]

@whedon add ajgates42 as reviewer

[whedon]

OK, ajgates42 is now a reviewer

[poulson]

Hi @madvn, the purpose of the review is to improve the quality of the software and documentation, so I think waiting for the update would be okay, given that the review hasn't yet started.

I will reach out to a few more potential reviewers in parallel with those changes if that makes sense to you.

[poulson]

:wave: Fabian (@fsteeg) -- You have listed expertise in information retrieval, though your languages were given as Java and Scala. Would you feel confident as a reviewer of a C++/Python package on information theory? If so, would you have the time to review?

@ajgates42 Do you happen to have any further reviewers you would suggest? Our list of information theory experts is modest and it seems you are from this community. Any help here would greatly aid the review process -- and therefore the work itself.

[ajgates42]

I think Ryan James ([email protected], @Autoplectic) would be a great
person to have assess the contributions of this package.

Another good fit would be Georg Martius ([email protected]
, @georgmartius)

On Mon, Jul 22, 2019 at 11:18 AM Jack Poulson [e-mail]
wrote:

👋 Fabian (@fsteeg https://github.com/fsteeg) -- You have listed
expertise in information retrieval, though your languages were given as
Java and Scala. Would you feel confident as a reviewer of a C++/Python
package on information theory? If so, would you have the time to review?

@ajgates42 https://github.com/ajgates42 Do you happen to have any
further reviewers you would suggest? Our list of information theory experts
is modest and it seems you are from this community. Any help here would
greatly aid the review process -- and therefore the work itself.

—
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--
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http://alexandergates.net

[poulson]

Hi Ryan (@autoplectic) -- You have been recommended as an expert in information theory; are you comfortable enough in C++ and/or python to confidently review this submission? And do you have the time an interest to do so?

Hi Georg (@georgmartius) -- You have also been recommended as an information theory expert. Same question as for Ryan: do you feel confident enough to review the submission, and do you have the time and interest to do so?

[georgmartius]

Hi Jack,
an even better qualified person would be Joseph Lizier http://lizier.me/joseph/. He wrote JIDT, a quite comprehensive java package.
I am afraid, I cannot invest the appropriate amount of time into it at the moment.

[poulson]

Hi Joseph (@jlizier) -- your colleague, Georg Martius, recommended you as an expert in information theory software packages. He mentioned that you worked primarily in Java -- would you feel confident reviewing a submission in C++ and Python? And, more importantly, do you have the time and interest to do so?

[jlizier]

Hi @poulson - main challenge for me atm is time as I'm already loaded up with reviews over the next month. I could commit to early Sept, but I'm guessing that's a bit too long for you? If not, whilst my c++ is a bit rusty I think it would be ok for this

[poulson]

Thank you for the fast and candid response, Joseph (@jlizier)! I will try to move forward with finding other reviewers and -- if that turns out to run into substantial delays -- circle back with you in early September.

[poulson]

Hi Ryan (@autoplectic) -- Do you think you would be able to provide input on this submission?

[poulson]

:wave: Fabian (@fsteeg) -- Would you have the time and interest to provide feedback on this submission?

[madvn]

@poulson The package, website and the paper have been updated. Ready to review now. Hope we find the second reviewer soon. Thanks!

[madvn]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[fsteeg]

Fabian (@fsteeg) -- Would you have the time and interest to provide feedback on this submission?

Thanks for getting in touch @poulson, and sorry for the late reply, I was on vacation. My expertise is neither in information theory, nor C++ or Python, so I'm afraid I won't be able to contribute here.

[poulson]

Hi Ryan (@Autoplectic) -- Do you think you would be able to provide input on this submission?

[Autoplectic]

Hi all, sorry for the delayed response. Yes, I can review it but it might take a couple weeks.

[poulson]

@whedon add @Autoplectic as reviewer

[whedon]

OK, @Autoplectic is now a reviewer

[poulson]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1609. Feel free to close this issue now!