[PRE REVIEW]: lifelines: survival analysis in Python

[whedon]

Submitting author: @CamDavidsonPilon (Cameron Davidson-Pilon) Repository: https://github.com/camdavidsonpilon/lifelines Version: 0.20.0 Editor: @trallard Reviewers: @becarioprecario, @sunhwan

Author instructions

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

@CamDavidsonPilon 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 #1305 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

'

[CamDavidsonPilon]

@becarioprecario @sunhwan are you two interested in reviewing this submission?

[CamDavidsonPilon]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

[CamDavidsonPilon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1305 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

'

[CamDavidsonPilon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1305 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 13 0 13 0 0 235 0 --:--:-- --:--:-- --:--:-- 236 Error reading bibliography ./paper.bib (line 9, column 10): unexpected "," expecting white space Error running filter pandoc-citeproc: Filter returned error status 1 Looks like we failed to compile the PDF

[CamDavidsonPilon]

SORRY ABOUT THE NOISE 🔈

I think I got it.

[CamDavidsonPilon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1305 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 13 0 13 0 0 115 0 --:--:-- --:--:-- --:--:-- 116 Error reading bibliography ./paper.bib (line 51, column 44): unexpected "\" expecting white space or "," Error running filter pandoc-citeproc: Filter returned error status 1 Looks like we failed to compile the PDF

[CamDavidsonPilon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[CamDavidsonPilon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1305 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 13 0 13 0 0 124 0 --:--:-- --:--:-- --:--:-- 125 Error reading bibliography ./paper.bib (line 24, column 1): unexpected "@" expecting space, ",", white space or "}" Error running filter pandoc-citeproc: Filter returned error status 1 Looks like we failed to compile the PDF

[CamDavidsonPilon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[kyleniemeyer]

@Cameron Davidson-Pilon before we get this review started and work on reviewers, we first need to assign an editor to handle it—hang tight.

[kyleniemeyer]

@trallard would you be able/interested to edit this submission?

[CamDavidsonPilon]

Whoops, I got confused by the OP I guess. Thanks @kyleniemeyer

[trallard]

Hi @kyleniemeyer yes I would be happy to edit this submission

[kyleniemeyer]

@trallard thanks!

[kyleniemeyer]

@whedon assign @trallard as editor

[whedon]

OK, the editor is @trallard

[trallard]

Hi @CamDavidsonPilon I will be editing this paper let's ping the reviewers. Once we have found 2 reviewers we can proceed to the review of the software

---

Dear potential reviewers,

Based on your expertise I would like to ask if you can help out with this JOSS submission.

Title: lifelines: survival analysis in Python

Summary: lifelines is a pure Python implementation of the best parts of survival analysis. We'd love to hear if you are using lifelines, please leave an Issue and let us know your thoughts on the library.

Article proof: https://github.com/openjournals/joss-papers/blob/joss.01305/joss.01305/10.21105.joss.01305.pdf

Submitting author: @CamDavidsonPilon (Cameron Davidson-Pilon)

Version: 0.20.0

Repository: https://github.com/CamDavidsonPilon/lifelines

---

@becarioprecario: Virgilio, are you able to and interested in taking this review? @sunhwan: Sunhwan, are you able to and interested in taking this review?

[becarioprecario]

Hi,

Yes. I will be happy to review this paper. Please, do you have a link with the instructions on how to make reviews. Best, Virgilio

[trallard]

Thanks @becarioprecario Let's wait and see if @sunhwan is willing to act as a reviewer too.

In the meantime you can find the reviewers and authors' guidelines here: 📖 https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

[trallard]

@whedon assign @becarioprecario as reviewer

[whedon]

OK, the reviewer is @becarioprecario

[sunhwan]

@trallard I will be happy to review this paper.

[trallard]

fab thanks @sunhwan! I will then start the review issue and close this one

[trallard]

@whedon add @sunhwan as reviewer

[whedon]

OK, @sunhwan is now a reviewer

[trallard]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1317. Feel free to close this issue now!