Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

Closed
whedon opened this issue Mar 12, 2019 · 74 comments

Comments

@whedon
Copy link
Collaborator

commented Mar 12, 2019

Submitting author: @CamDavidsonPilon (Cameron Davidson-Pilon)
Repository: https://github.com/camdavidsonpilon/lifelines
Version: v0.22.2
Editor: @trallard
Reviewer: @becarioprecario, @sunhwan
Archive: 10.5281/zenodo.805993

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/cd6f19605906416d5196f9cdd3841a76"><img src="http://joss.theoj.org/papers/cd6f19605906416d5196f9cdd3841a76/status.svg"></a>
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:

  1. Make sure you're logged in to your GitHub account
  2. 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

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: v0.22.2
  • 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

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: v0.22.2
  • 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

This comment has been minimized.

Copy link
Collaborator Author

commented 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:

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

watching

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

notifications

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

@whedon commands
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Mar 12, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Mar 12, 2019

@trallard

This comment has been minimized.

Copy link
Collaborator

commented 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

This comment has been minimized.

Copy link
Collaborator

commented 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

This comment has been minimized.

Copy link

commented Apr 1, 2019

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

@becarioprecario

This comment has been minimized.

Copy link

commented Apr 1, 2019

@sunhwan

This comment has been minimized.

Copy link

commented 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

This comment has been minimized.

Copy link
Collaborator

commented 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

This comment has been minimized.

Copy link

commented Jun 3, 2019

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

@trallard

This comment has been minimized.

Copy link
Collaborator

commented Jun 11, 2019

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

@becarioprecario

This comment has been minimized.

Copy link

commented Jun 11, 2019

@trallard

This comment has been minimized.

Copy link
Collaborator

commented 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

This comment has been minimized.

Copy link

commented 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

This comment has been minimized.

Copy link
Collaborator

commented 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 trallard added the accepted label Jul 1, 2019

@trallard

This comment has been minimized.

Copy link
Collaborator

commented Jul 1, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jul 1, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jul 1, 2019

@trallard

This comment has been minimized.

Copy link
Collaborator

commented Jul 1, 2019

@whedon check references

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jul 1, 2019

Attempting to check references...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented 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

This comment has been minimized.

Copy link
Collaborator

commented Jul 1, 2019

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

@trallard

This comment has been minimized.

Copy link
Collaborator

commented Jul 8, 2019

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

@CamDavidsonPilon

This comment has been minimized.

Copy link

commented Jul 8, 2019

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

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 3, 2019

Check final proof 👉 openjournals/joss-papers#879

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#879, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
@labarba

This comment has been minimized.

Copy link
Member

commented Aug 3, 2019

@CamDavidsonPilon — the listing on the bottom of page 2 bleeds into the margin. Could you add some line breaks to make that render better?

@labarba

This comment has been minimized.

Copy link
Member

commented Aug 3, 2019

Also, I had a look at the Zenodo archive here: http://doi.org/10.5281/zenodo.805993
It shows a long list of authors, possibly an automatic listing from the commits.

We request that authors modify the Zenodo-archive metadata so that the title and author list match the JOSS paper. You may also want to add your ORCID to the metadata.

@CamDavidsonPilon

This comment has been minimized.

Copy link

commented Aug 3, 2019

Okay, both those should be done @labarba

@labarba

This comment has been minimized.

Copy link
Member

commented Aug 3, 2019

I see your latest tagged release is v0.22.2, but here we have 0.21.1 — could you double check which version we should be associating the JOSS paper with?

@labarba

This comment has been minimized.

Copy link
Member

commented Aug 3, 2019

Also, the Zenodo archive shows the repo name as title. Could you edit the metadata to match the JOSS paper title?

@CamDavidsonPilon

This comment has been minimized.

Copy link

commented Aug 3, 2019

I see your latest tagged release is v0.22.2, but here we have 0.21.1 — could you double check which version we should be associating the JOSS paper with?

If I change the JOSS paper to be associated to 0.22.2, does it need to be re-reviewed, etc.? If not, v0.22.2 is correct.

@labarba

This comment has been minimized.

Copy link
Member

commented Aug 3, 2019

@whedon set v0.22.2 as archive

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 3, 2019

v0.22.2 doesn't look like an archive DOI.

@labarba

This comment has been minimized.

Copy link
Member

commented Aug 3, 2019

@whedon set v0.22.2 as version

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 3, 2019

OK. v0.22.2 is the version.

@labarba

This comment has been minimized.

Copy link
Member

commented Aug 4, 2019

@whedon accept

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 4, 2019

Attempting dry run of processing paper acceptance...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 4, 2019

Check final proof 👉 openjournals/joss-papers#882

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#882, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
@labarba

This comment has been minimized.

Copy link
Member

commented Aug 4, 2019

@CamDavidsonPilon — just one more tweak on the comment line that bleeds into the margin, please!

@labarba

This comment has been minimized.

Copy link
Member

commented Aug 4, 2019

You can run @whedon generate pdf right here to see the proof.

@CamDavidsonPilon

This comment has been minimized.

Copy link

commented Aug 4, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 4, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 4, 2019

@labarba labarba referenced this issue Aug 4, 2019

Merged

fix typos #797

@labarba

This comment has been minimized.

Copy link
Member

commented Aug 4, 2019

@whedon accept deposit=true

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 4, 2019

Doing it live! Attempting automated processing of paper acceptance...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 4, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 4, 2019

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#883
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01317
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

@labarba

This comment has been minimized.

Copy link
Member

commented Aug 4, 2019

Congratulations, @CamDavidsonPilon, your JOSS paper is published! 🚀

Huge thanks to our editor: @trallard, and the reviewers: @becarioprecario, @sunhwan — we greatly appreciate your contribution to JOSS 🙏

@ooo

This comment has been minimized.

Copy link

commented Aug 4, 2019

👋 Hey @labarba...

Letting you know, @trallard is currently OOO until Monday, August 19th 2019. ❤️

@labarba labarba closed this Aug 4, 2019

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 4, 2019

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01317/status.svg)](https://doi.org/10.21105/joss.01317)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01317">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01317/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01317/status.svg
   :target: https://doi.org/10.21105/joss.01317

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

@CamDavidsonPilon

This comment has been minimized.

Copy link

commented Aug 5, 2019

@ooo

This comment has been minimized.

Copy link

commented Aug 5, 2019

👋 Hey @CamDavidsonPilon...

Letting you know, @trallard is currently OOO until Monday, August 19th 2019. ❤️

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
9 participants
You can’t perform that action at this time.