[PRE REVIEW]: Python Sorted Containers

[whedon]

Submitting author: @grantjenks (Grant Jenks) Repository: https://github.com/grantjenks/python-sortedcontainers Version: v2.1.0 Editor: @jasonclark Reviewers: @djmitche

Author instructions

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

@grantjenks 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

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@whedon commands

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:

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 #1223 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/1223 (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-c5f29247288e/lib/whedon/processor.rb:57:infind_paper_paths' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c5f29247288e/bin/whedon:47: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-c5f29247288e/bin/whedon:113: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

'

[danielskatz]

This software looks useful, even though there's a problem compiling the paper. You can make changes to the source, then enter @whedon compile pdf as a new comment here to try to fix it.

Another issue I have is that it's not clear to me that this is research software according to the JOSS guidelines:

JOSS publishes articles about research software. This definition includes software that: solves complex modeling problems in a scientific context (physics, mathematics, biology, medicine, social science, neuroscience, engineering); supports the functioning of research instruments or the execution of research experiments; extracts knowledge from large data sets; offers a mathematical library, or similar.

Can you help me understand this?

[grantjenks]

Regarding the guidelines, I think it fits under:

supports the functioning of research instruments or the execution of research experiments

But I may be wrong. I had JOSS suggested to me by the creator of IPython. And I received a GitHub Issue asking how to cite the project. Consider some of the users:

• Zipline, an algorithmic trading library from Quantopian
• Angr, a binary analysis platform from UC Santa Barbara
• Trio, an async I/O library
• Dask Distributed, a distributed computation library supported by Continuum Analytics
• Astropy, a community Python library for astronomy

Does that satisfy?

Also, I looked through GitHub issues trying to understand how the PDF is generated:

• https://github.com/openjournals/joss/issues/370
• https://github.com/openjournals/joss/issues/379
• https://github.com/openjournals/whedon
• https://gist.github.com/mhucka/5ecb18aa2fd088c055de07366f70135e
• https://github.com/openbases/builder-pdf

But I was unable to reproduce the problem. (Maybe those links will be useful for a future visitor). There seems to be a "paper.md" file that is missing. Is that something I generate? I'm happy to accommodate, just not sure what's necessary. I could see how the project README may not be as useful for a paper as say the Performance Comparison, Implementation Details, or Performance at Scale materials.

[arfon]

Hi @grantjenks - please take a look at the submission guidelines and prepare a paper.md and paper.bib file and include them in your repository (https://github.com/grantjenks/python-sortedcontainers). Once you've uploaded them, Whedon (the robot here) will be able to compile the paper.

In your paper, please be sure to address each of the points listed in the section what should my paper contain?.

[danielskatz]

Regarding the research application, the problem is that your package is not used by end users for research, but according to your comment, is used by other libraries and packages, some of which then are used for research. I think that's fine, but want to hear from @arfon before we go on.

[arfon]

I think that's fine, but want to hear from @arfon before we go on.

👍 I think that's OK too. Please go ahead and prepare a paper to accompany this submission @grantjenks.

[danielskatz]

I'll mark this as paused until then - please let us know when you are ready to proceed.

[grantjenks]

Sorry for the delay. February has been a busy month. It’s on the schedule for early March.

[grantjenks]

I published the paper.md and paper.bib files this morning. I believe I covered each of the requirements as to "What should my paper contain?" It is ready to be un-paused. I believe that was pre-review. Let me see if I can get whedon to compile the PDF.

[grantjenks]

@whedon compile pdf

[kyleniemeyer]

@whedon compile pdf

[kyleniemeyer]

@arfon looks like @whedon isn't responding in here?

[danielskatz]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1223 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon.rb:83:in check_fields': Paper YAML header is missing expected fields: affiliations (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon.rb:69:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon/processor.rb:32:inset_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/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-01ece1d1d135/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

'

[grantjenks]

Ooops, updated paper.

[grantjenks]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1223 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon.rb:117:in parse_affiliations': undefined methodeach' for nil:NilClass (NoMethodError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon.rb:103:in parse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon.rb:73:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon/processor.rb:32:inset_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/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-01ece1d1d135/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

'

[grantjenks]

Hi all, I'm not sure what you want for "affiliations". I was not attending college when I developed the project. But I can put where I graduated. Should I put my company? Please advise.

[arfon]

@grantjenks - you can have an affiliation of 'None', but the YAML header of the paper needs to match this example: https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography

[grantjenks]

Ok, try 2.

[grantjenks]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[labarba]

Looks like we're ready to get this submission into review now!

@jasonclark — from a first look, I'd like to assign this to you. Hope that you can find a couple of reviewers and steer this one!

[labarba]

@whedon assign @jasonclark as editor

[whedon]

OK, the editor is @jasonclark

[jasonclark]

Hi, @grantjenks. I'll be working through the editing. Thanks for your work so far.

[jasonclark]

Hi, @djmitche. Would you have time to review this software in the next 2 weeks? It's more of a software library implementation and your software testing background perspective would be really helpful. cc @grantjenks

[djmitche]

Happy to.

[jasonclark]

Thanks, @djmitche! I'll set up the review and assign you. cc @grantjenks

[whedon]

OK, the reviewer is @reviewer

[jasonclark]

@whedon assign @djmitche as reviewer

[whedon]

OK, the reviewer is @djmitche

[jasonclark]

@whedon start review magic-word=bananas

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1330. Feel free to close this issue now!

[jasonclark]

@djmitche the review is set up at https://github.com/openjournals/joss-reviews/issues/1330. cc @grantjenks