[REVIEW]: pyABC: Efficient and robust easy-to-use approximate Bayesian computation

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@yannikschaelte@osorensen<!--end-editor-- Reviewers: @mattpitkin, @hpesonen, @blakeaw Archive: 10.5281/zenodo.6677826

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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 & @hpesonen, 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 @osorensen 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 @blakeaw

📝 Checklist for @hpesonen

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

yannikschaelte commented 2 years ago

@yannikschaelte please also make sure that Scott A Sisson's name is spelled consistently in the references:

This should be resolved now.

osorensen 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

- 10.1126/science.1069492 is OK
- 10.1093/genetics/145.2.505 is OK
- 10.1038/nrg2509 is OK
- 10.1016/j.cels.2016.12.002 is OK
- 10.1214/07-AOS574 is OK
- 10.1002/jae.3950080507 is OK
- 10.1080/10618600.2017.1302882 is OK
- 10.1093/oxfordjournals.molbev.a026091 is OK
- 10.1093/genetics/162.4.2025 is OK
- 10.1073/pnas.0607208104 is OK
- 10.1111/j.1467-9868.2006.00553.x is OK
- 10.1145/3093172.3093233 is OK
- 10.1093/bioinformatics/btaa078 is OK
- 10.1111/2041-210X.12050 is OK
- 10.1093/bioinformatics/bty361 is OK
- 10.1515/sagmb-2012-0069 is OK
- 10.1007/978-3-319-67471-1_8 is OK
- 10.1038/s41467-019-09879-3 is OK
- 10.1371/journal.pcbi.1009149 is OK
- 10.7554/eLife.56265 is OK
- 10.1038/s41586-021-03965-7 is OK
- 10.1063/5.0010764 is OK
- 10.1101/2022.02.10.479738 is OK
- 10.7554/eLife.55665 is OK
- 10.1088/1475-7516/2021/08/027 is OK
- 10.1016/j.compbiomed.2018.10.015 is OK
- 10.1002/eap.2442 is OK
- 10.1101/2021.07.29.454327 is OK
- 10.1214/16-BA1002 is OK
- 10.1214/12-STS406 is OK
- 10.1111/j.1467-9868.2011.01010.x is OK
- 10.5705/ss.202015.0340 is OK
- 10.1016/j.jcp.2020.109999 is OK
- 10.1101/2022.03.18.484896 is OK
- 10.1515/sagmb-2013-0010 is OK
- 10.1093/bioinformatics/btaa397 is OK
- 10.1111/rssb.12312 is OK
- 10.1515/sagmb-2012-0043 is OK
- 10.1111/j.1541-0420.2010.01410.x is OK
- 10.1137/141000671 is OK
- 10.1093/bioinformatics/btl485 is OK
- 10.1371/journal.pcbi.1008646 is OK
- 10.1093/bioinformatics/btab227 is OK
- 10.1093/bioinformatics/btp619 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: https://github.com/openjournals/joss-papers/pull/3294

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3294, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 2 years ago

@yannikschaelte

I checked the archive meta-data (title and authors) and all looks good. :+1:
I checked the version tag for the review and archive and have the following comments:
[x] This review says it is currently for 0.12.4 however the archive says version 1. If I inspect the project repository I see a tag for 0.12.5. Can you please comment on what the version should be? The version should be the same for this review and the archive. I get the impression both should be 0.12.5 but do let me know which it should be. You may need to manually edit the ZENODO archive to have the correct version label.
I proofread the paper and all seems fine :+1:

yannikschaelte commented 2 years ago

Hi @Kevin-Mattheus-Moerman , thanks for proofreading! You are right, it should be 0.12.5 (I created a new version with the latest changes esp. from the review process). I updated the zenodo accordingly.

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot set 10.5281/zenodo.6677826 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6677826

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot set 10.5281/zenodo.6677826 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6677826

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot set 0.12.5 as version

editorialbot commented 2 years ago

Done! version is now 0.12.5

Kevin-Mattheus-Moerman 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/3304
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04304
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 2 years ago

@yannikschaelte congratulations on your publication in JOSS!

Thanks for editing this one @osorensen! And thank you @mattpitkin, @hpesonen, @blakeaw for your review efforts!!! :tada:

editorialbot commented 2 years ago

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

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Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.04304/status.svg)](https://doi.org/10.21105/joss.04304)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.04304/status.svg" alt="DOI badge" >
</a>

reStructuredText:
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   :target: https://doi.org/10.21105/joss.04304

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