[REVIEW]: lifelines: survival analysis in Python

whedon commented 5 years ago

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

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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

[x] 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

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

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Version: v0.22.2
[x] Authorship: Has the submitting author (@CamDavidsonPilon) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

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

Review checklist for @sunhwan

Conflict of interest

[x] 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

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

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Version: v0.22.2
[x] Authorship: Has the submitting author (@CamDavidsonPilon) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

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

whedon commented 5 years ago

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 :tada:.

:star: Important :star:

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:

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

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

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whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

trallard commented 5 years ago

👋 @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 commented 5 years ago

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 commented 5 years ago

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

becarioprecario commented 5 years ago

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

Virgilio

El 1 abr 2019, a las 19:37, Tania Allard notifications@github.com 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 commented 5 years ago

@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. https://github.com/CamDavidsonPilon/lifelines/issues/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 commented 5 years ago

Fantastic @sunhwan thanks a lot for your review.

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

kyleniemeyer commented 5 years ago

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

trallard commented 5 years ago

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

becarioprecario commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

trallard commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


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 commented 5 years ago

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

trallard commented 5 years ago

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

CamDavidsonPilon commented 5 years ago

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

trallard commented 5 years ago

@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 commented 5 years ago

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

Latest version is 0.21.1

trallard commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

trallard commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

trallard commented 5 years ago

@whedon set 0.21.1 as version

whedon commented 5 years ago

OK. 0.21.1 is the version.

whedon commented 5 years ago


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 commented 5 years ago

@whedon set 10.5281/zenodo.805993 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.805993 is the archive.

trallard commented 5 years ago

@whedon accept

whedon commented 5 years ago

Attempting dry run of processing paper acceptance...

whedon commented 5 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/847

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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 commented 5 years ago

@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 commented 5 years ago

@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 commented 5 years ago

ooops wrong wording you are correct!!! sorry!

danielskatz commented 5 years ago

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

danielskatz commented 5 years ago

Sorry for the delay in seeing this - I was expecting you to say you had merged the PR, which would have led to a GH notification.

@labarba - this was in the midst of acceptance, perhaps as the on-duty @openjournals/joss-eics you can continue the process

labarba commented 5 years ago

@whedon accept

whedon commented 5 years ago

Attempting dry run of processing paper acceptance...

whedon commented 5 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/879

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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 commented 5 years ago

@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 commented 5 years ago

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 commented 5 years ago

Okay, both those should be done @labarba

openjournals / joss-reviews