[REVIEW]: lifelines: survival analysis in Python #1317

whedon · Mar 12, 2019

Submitting author: @CamDavidsonPilon (Cameron Davidson-Pilon)
Repository: https://github.com/camdavidsonpilon/lifelines
Version: 0.21.1
Editor: @trallard
Reviewer: @becarioprecario, @sunhwan
Archive: 10.5281/zenodo.805993

Status

Status badge code:

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Markdown: [![status](http://joss.theoj.org/papers/cd6f19605906416d5196f9cdd3841a76/status.svg)](http://joss.theoj.org/papers/cd6f19605906416d5196f9cdd3841a76)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@becarioprecario & @sunhwan, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @trallard know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @becarioprecario

Conflict of interest

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Version: 0.21.1
Authorship: Has the submitting author (@CamDavidsonPilon) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Authors: Does the paper.md file include a list of authors with their affiliations?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @sunhwan

Conflict of interest

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Version: 0.21.1
Authorship: Has the submitting author (@CamDavidsonPilon) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Authors: Does the paper.md file include a list of authors with their affiliations?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

whedon · Mar 12, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @becarioprecario, it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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

@whedon commands

whedon · Mar 12, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Mar 12, 2019

👉 Check article proof 📄 👈

trallard · Mar 12, 2019

👋 @becarioprecario and @sunhwan this is the issue for the review. Each of you has a checklist of the items you have to look at while conducting your review ⬆

Please use this issue to comment, make suggestions and discuss anything related to the submission. If you need to request changes or go in detail on something it is advisable to make an issue on the software repo https://github.com/camdavidsonpilon/lifelines and reference this issue to keep track of the process.

If any of you or @CamDavidsonPilon has any questions at any point feel free to ping me.

Happy reviewing 🔎💻

trallard · Apr 1, 2019

Hi @becarioprecario and @sunhwan I have not seen much activity on this repo for a bit so I was wondering if there is anything you need help with?

sunhwan · Apr 1, 2019

Thanks for reminding me. I'll work on this soon.

becarioprecario · Apr 1, 2019

Thanks for reminding me. I’ll try to look into this asap. Virgilio

…

El 1 abr 2019, a las 19:37, Tania Allard ***@***.***> escribió: Hi @becarioprecario and @sunhwan I have not seen much activity on this repo for a bit so I was wondering if there is anything you need help with? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

sunhwan · Apr 10, 2019

@trallard I went through the checklist and I was satisfied with most of the item in the list. I found a few problems running some script/file. I left a comment in the repository. CamDavidsonPilon/lifelines#703

This package looks great and I'm okay to accept after the author address the minor issue. Are reviewers expected to write a separate review?

trallard · May 4, 2019

Fantastic @sunhwan thanks a lot for your review.

@becarioprecario is there anything we can help with to move this review forward ?

kyleniemeyer · Jun 3, 2019

Hi @becarioprecario, just wanted to check on your review.

trallard · Jun 11, 2019

ping! @becarioprecario do you have any updates on the review?

becarioprecario · Jun 11, 2019

Hi, I have been a bit stuck with other stuff. Please, may I ask you to send me the guidelines again on how to make the review. Thanks! Virgilio

trallard · Jun 17, 2019

Hi @becarioprecario the checklist for the review is at the top of this issue 👆🏼

For reference the guidelines for reviewers are located here: https://joss.theoj.org/about#reviewer_guidelines

becarioprecario · Jun 24, 2019

Hi,

I am done with my review now. The package and its documentation are excellent!! I had some troubles with the installation, but due to my local configuration. Installing the package with pip run smoothly.

Best,

Virgilio

trallard · Jul 1, 2019

Thanks for your time and reviews @becarioprecario and @sunhwan 🙏🏼

@CameronDevine I can confirm your paper has been accepted now! 🎉 Let's move this to publication, please complete the following actions and let me know once this is done

Final check on article: DOIS are present, authors are correctly listed
Create a new tag for the software and add let me know what final version is
Deposit the software in Zenodo and share the DOI here

trallard · Jul 1, 2019

@whedon generate pdf

whedon · Jul 1, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 1, 2019

👉 Check article proof 📄 👈

trallard · Jul 1, 2019

@whedon check references

whedon · Jul 1, 2019

Attempting to check references...

whedon · Jul 1, 2019


OK DOIs

- 10.5281/zenodo.275519 is OK
- 10.5281/zenodo.1472929 is OK
- 10.1111/j.1751-5823.2009.00095_1.x is OK
- 10.1111/ajps.12176 is OK
- 10.1002/sim.2864 is OK
- 10.1007/s10654-016-0149-3 is OK
- 10.1111/j.1751-5823.2009.00095_1.x is OK
- 10.1007/s40471-016-0089-1 is OK
- 10.18637/jss.v070.i08 is OK

MISSING DOIs

- https://doi.org/10.1002/(sici)1097-0258(19960229)15:4<361::aid-sim168>3.0.co;2-4 may be missing for title: Multivariable prognostic models: issues in developing models, evaluating assumptions and adequacy, and measuring and reducing errors.

INVALID DOIs

- None

CameronDevine · Jul 1, 2019

@CamDavidsonPilon, I just wanted to make sure you saw this since I was mentioned by mistake.

trallard · Jul 8, 2019

HI @CamDavidsonPilon I was wondering if you'd make any progress with the last few tasks for acceptance?

CamDavidsonPilon · Jul 8, 2019

hi @trallard, I have addressed the missing DOI. Anything else? Is there a list I missed?

trallard · Jul 16, 2019

@CamDavidsonPilon Can you please paste the DOI here so I can set it as the archive? As well as the latest version of the package and I can finalise the acceptance

CamDavidsonPilon · Jul 18, 2019

Missing DOI entry: https://github.com/CamDavidsonPilon/lifelines/blob/master/paper/paper.bib#L144-L153

Latest version is 0.21.1

trallard · Jul 19, 2019

@whedon generate pdf

whedon · Jul 19, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 19, 2019

👉 Check article proof 📄 👈

trallard · Jul 19, 2019

@whedon check references

whedon · Jul 19, 2019

Attempting to check references...

trallard · Jul 19, 2019

@whedon set 0.21.1 as version

whedon · Jul 19, 2019

OK. 0.21.1 is the version.

whedon · Jul 19, 2019


OK DOIs

- 10.5281/zenodo.275519 is OK
- 10.5281/zenodo.1472929 is OK
- 10.1111/j.1751-5823.2009.00095_1.x is OK
- 10.1111/ajps.12176 is OK
- 10.1002/sim.2864 is OK
- 10.1007/s10654-016-0149-3 is OK
- 10.1111/j.1751-5823.2009.00095_1.x is OK
- 10.1007/s40471-016-0089-1 is OK
- https://doi.org/10.1002/(SICI)1097-0258(19960229)15:4<361::AID-SIM168>3.0.CO;2-4 is OK
- 10.18637/jss.v070.i08 is OK

MISSING DOIs

- None

INVALID DOIs

- None

trallard · Jul 19, 2019

@whedon set 10.5281/zenodo.805993 as archive

whedon · Jul 19, 2019

OK. 10.5281/zenodo.805993 is the archive.

trallard · Jul 19, 2019

@whedon accept

whedon · Jul 19, 2019

Attempting dry run of processing paper acceptance...

whedon · Jul 19, 2019

Check final proof 👉 openjournals/joss-papers#847

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#847, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

trallard · Jul 19, 2019

@CamDavidsonPilon Lifelines is ready for acceptance to JOSS, let's pass this over to our editor in chief to proceed 🎉🎉

@becarioprecario and @sunhwan thanks for the time and effort put in this review. Your contribution to JOSS is deeply appreciated. 🙏🏼🙌🏼🙂

@openjournals/joss-eics this paper is ready for acceptance 👾

danielskatz · Jul 19, 2019

@trallard - you've jumped the gun slightly. Let's say that you believe Lifelines is ready to be accepted to JOSS - now @openjournals/joss-eics need to do some final checks.

trallard · Jul 19, 2019

ooops wrong wording you are correct!!! sorry!

danielskatz · Jul 19, 2019

@CamDavidsonPilon - please accept the changes in CamDavidsonPilon/lifelines#781, or disagree with the ones that are not adding needed spaces :)

whedon assigned trallard Mar 12, 2019

whedon added the review label Mar 12, 2019

whedon referenced this issue Mar 12, 2019
Closed
[PRE REVIEW]: lifelines: survival analysis in Python #1305

whedon assigned becarioprecario and sunhwan May 6, 2019

trallard added the accepted label Jul 1, 2019

openjournals deleted a comment from whedon Jul 19, 2019

openjournals/joss-reviews

Track tasks and feature requests

[REVIEW]: lifelines: survival analysis in Python #1317

Comments

whedon commented Mar 12, 2019 • edited

Status

Reviewer instructions & questions

Review checklist for @becarioprecario

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @sunhwan

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon assigned trallard Mar 12, 2019

whedon added the review label Mar 12, 2019

whedon referenced this issue Mar 12, 2019

[PRE REVIEW]: lifelines: survival analysis in Python #1305

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