[REVIEW]: SeleDiff: A fast and scalable tool for estimating and testing selection differences between populations

whedon commented 5 years ago

Submitting author: @xin-huang (Xin Huang) Repository: https://github.com/xin-huang/SeleDiff Version: v1.1 Editor: @lpantano Reviewer: @stulacy, @suresh-lab Archive: 10.5281/zenodo.3323833

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Markdown: [![status](http://joss.theoj.org/papers/93d0bb9fea95827696628d97d9825dca/status.svg)](http://joss.theoj.org/papers/93d0bb9fea95827696628d97d9825dca)

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) by leaving comments 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

@stulacy & @suresh-lab, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @lpantano know.

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

Review checklist for @stulacy

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: v1.1
[x] Authorship: Has the submitting author (@xin-huang) 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 @suresh-lab

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: v1.1
[x] Authorship: Has the submitting author (@xin-huang) 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. @stulacy, @suresh-lab it looks like you're currently assigned to review 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:

@whedon commands

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:

xin-huang commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

PDF failed to compile for issue #1545 with the following error:

suresh-lab commented 5 years ago

Hi, Am I able to provide written comments for the review in addition to the checklist? Do I attach it as a file here on this thread?

stulacy commented 5 years ago

Can you please add the DOI for Haldane (1924)?

xin-huang commented 5 years ago

Hi @stulacy Yes, I have added the doi for this reprint https://link.springer.com/article/10.1007/BF02459574

lpantano commented 5 years ago

Hi @suresh-lab, for sure you can provide comments. if it will be a long thread you can create an issue in the repository and mention this one. I think is better to write the comments on the issue so they are more accessible. Let me know if that would work. Thanks!

xin-huang commented 5 years ago

Hi @suresh-lab I have revised the community guidelines in README:

"If you are interested in contributing to SeleDiff, please feel free to clone and modify it. You should include unit tests for your modified codes. Besides, you can edit build.gradle to include new dependencies. After your modification, please send a GitHub Pull Request with a clear list of what you've done."

Please let me know whether it is appropriate.

suresh-lab commented 5 years ago

thank you, that's perfect.

lpantano commented 5 years ago

It seems reviewers are done, let me know otherwise. I will start the final step to mark this as accepted.

lpantano commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- 10.1002/ece3.1261 is OK
- 10.1073/pnas.1019276108 is OK
- 10.1007/BF02459574 is OK
- 10.1093/molbev/msw211 is OK
- 10.1101/gr.192336.115 is OK
- 10.1093/molbev/msu211 is OK
- 10.1111/mec.13559 is OK
- 10.1146/annurev-genet-111212-133526 is OK

MISSING DOIs

- https://doi.org/10.2307/1529706 may be missing for title: An Introduction to Population Genetics Theory

INVALID DOIs

- None

lpantano 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:

lpantano commented 5 years ago

@xin-huang, it seems there is another DOI missing:

https://doi.org/10.2307/1529706 may be missing for title: An Introduction to Population Genetics Theory

can you fix it?

And after that, can you make a zenodo archive and give me the DOI? you need to make sure the title and authors there match your paper.

thanks!

lpantano commented 5 years ago

@whedon set v1.1 as version

whedon commented 5 years ago

OK. v1.1 is the version.

xin-huang commented 5 years ago

Hi @lpantano

I think this https://doi.org/10.2307/1529706 is a book review for the book I cited. The book, An Introduction to Population Genetics Theory, is a old book published in 1970s (https://www.amazon.com/Introduction-Population-Genetics-Theory/dp/1932846123), I cannot find a doi related to this book.

The DOI for the zenodo archive is 10.5281/zenodo.3323833

Thank you very much.

lpantano commented 5 years ago

@whedon set 10.5281/zenodo.3323833 as archive

lpantano commented 5 years ago

@whedon set 10.5281/zenodo.3323833 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.3323833 is the archive.

lpantano commented 5 years ago

Hi @openjournals/joss-eics, this is accepted. The only thing is that reference that doesn't have a DOI because it is too old. I don't know if there is a specific way to deal with that. Thanks!

danielskatz commented 5 years ago

Thanks - I'll do the processing tonight or tomorrow

Don't worry about the DOI, whedon provides guidance but is not always right, and everything doesn't have to have a DOI; we just want to make sure that for things that do have a DOI, the DOI is part of the reference.

danielskatz 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:

danielskatz 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/840

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/840, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz commented 5 years ago

@xin-huang - please merge https://github.com/xin-huang/SeleDiff/pull/6 to make a couple of small changes in wording.

xin-huang commented 5 years ago

Hi @danielskatz

I have merged it into the main branch. Thank you very much.

danielskatz 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:

danielskatz 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/841

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/841, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz commented 5 years ago

@whedon accept deposit=true

whedon commented 5 years ago

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

whedon commented 5 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 5 years ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/844
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01545
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

danielskatz commented 5 years ago

Thanks to @stulacy and @suresh-lab for reviewing and to @lpantano for editing!

whedon commented 5 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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