[REVIEW]: swyft: Truncated Marginal Neural Ratio Estimation in Python

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@bkmi@pdebuyl<!--end-editor-- Reviewers: @mattpitkin, @olgadoronina Archive: 10.5281/zenodo.6412465

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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) 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

@mattpitkin & @olgadoronina, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @mattpitkin

📝 Checklist for @olgadoronina

pdebuyl commented 2 years ago

Hi @bkmi thanks for the update. It is in good shape :-) The changes do not impact the code, only the documentation configuration, so that there is no need for a further release.

Can you edit the metadata of the zenodo entry so that it matches the one of the paper?

Title should be "swyft: Truncated Marginal Neural Ratio Estimation in Python"
Authors should be the same and in the same order. If someone is a contributor but not an author of the paper, you can move them to "contributor" on zenodo instead of author.

bkmi commented 2 years ago

The author order is not allowed to be altered? The reason we want to is because the largest code contributor is the PI of the lab. Also, a significant amount of the code, written by some contributors, is ipython notebook output.

Am I understanding it right that it's possible to move people off the author list who have contributed code as long as they're are added to the contributors list?

The other aspects are no problem.

pdebuyl commented 2 years ago

The author order is not allowed to be altered? The reason we want to is because the largest code contributor is the PI of the lab. Also, a significant amount of the code, written by some contributors, is ipython notebook output.

From Zenodo's FAQ:

I only want to change the title of my upload, do I still get a new DOI?

No, as before you can continue to edit the metadata of your upload without creating a new version of a record. You should only create a new version if you want to update the files of your record.

So you can change Zenodo's author order and update the record. You cannot change the files in a record.

JOSS policy is that the author list between the paper and archive must match. See in the editorial guide https://joss.readthedocs.io/en/latest/editing.html#after-reviewers-recommend-acceptance I can't find the same guideline in the "author info" part of our documentation. If this is an issue for you, I'll query the editorial team.

Am I understanding it right that it's possible to move people off the author list who have contributed code as long as they're are added to the contributors list?

Yes. For many JOSS articles, there is a group of main contributors that are authors of the article while some contributors are not authors. See a relevant discussion here for instance: https://github.com/openjournals/joss/issues/815

pdebuyl commented 2 years ago

Hi @bkmi could you settle the authorship issue?

pdebuyl commented 2 years ago

ping @bkmi

bkmi commented 2 years ago

good timing. just got back from vacation. working on that right now.

bkmi commented 2 years ago

Everything looks okay to me now. Do you agree?

pdebuyl commented 2 years ago

Yes, it is all good, thank you :-)

pdebuyl commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.21105/joss.03021 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.3509134 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.5281/zenodo.5712786 is OK
- 10.21105/joss.02505 is OK
- 10.21105/joss.00011 is OK
- 10.1093/bioinformatics/bty361 is OK
- 10.1145/3093172.3093233 is OK
- 10.1093/mnras/stz1960 is OK
- 10.1093/mnras/sty819 is OK
- 10.1093/mnras/stz1900 is OK
- 10.1002/sta4.56 is OK
- 10.1214/20-ba1238 is OK
- 10.1007/s11222-017-9738-6 is OK
- 10.1214/06-ba127 is OK
- 10.1111/j.1365-2966.2007.12353.x is OK
- 10.1111/j.1365-2966.2009.14548.x is OK
- 10.1093/mnras/stv1911 is OK
- 10.1051/0004-6361/201322971 is OK
- 10.1007/s11222-018-9844-0 is OK
- 10.1214/18-ss120 is OK
- 10.1098/rsif.2008.0172 is OK
- 10.1111/j.2517-6161.1984.tb01290.x is OK
- 10.1214/aos/1176346785 is OK
- 10.1093/genetics/145.2.505 is OK
- 10.1007/s11222-009-9116-0 is OK
- 10.2172/4390578 is OK
- 10.1093/biomet/57.1.97 is OK
- 10.1038/s41567-021-01425-7 is OK
- 10.1103/PhysRevLett.127.241103 is OK
- 10.1103/PhysRevLett.124.041102 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3384, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 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/3387
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04205
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon commented 2 years ago

@mattpitkin, @olgadoronina – many thanks for your reviews here and to @pdebuyl for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@bkmi – your paper is now accepted and published in JOSS :zap::rocket::boom:

editorialbot commented 2 years ago

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

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bkmi commented 2 years ago

Thank you all very much, especially for patience and expertise!

openjournals / joss-reviews