[REVIEW]: smot: a python package and CLI tool for contextual phylogenetic subsampling

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@arendsee@Bisaloo<!--end-editor-- Reviewers: @Chjulian, @marekborowiec Archive: 10.5281/zenodo.7458325

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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

@Chjulian & @marekborowiec, 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 @Bisaloo 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 @Chjulian

📝 Checklist for @marekborowiec

editorialbot commented 1 year ago

Done! version is now v1.0.0

Bisaloo commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1371/journal.pone.0009490 is OK
- 10.1093/nar/gkw857 is OK
- 10.1128/mSphere.00275-16 is OK
- 10.1093/molbev/mst010 is OK
- 10.1126/science.1189132 is OK
- 10.1038/nature08182 is OK
- 10.1128/JVI.00459-15 is OK
- 10.1371/journal.pcbi.1002947 is OK
- 10.1126/science.1117727 is OK
- 10.22269/210921 is OK
- 10.1016/s0168-9525(03)00112-4 is OK
- 10.1186/s12859-018-2164-8 is OK
- 10.1186/1756-0500-6-145 is OK
- 10.1101/2021.02.13.431075 is OK
- 10.1093/molbev/msz053 is OK
- 10.1101/2021.01.21.427647 is OK
- 10.1186/s12864-018-4620-2 is OK
- 10.1093/bioinformatics/btq228 is OK
- 10.1093/bioinformatics/btp163 is OK
- 10.1128/mra.00673-19 is OK
- 10.12688/f1000research.10446.1 is OK
- 10.1093/molbev/msz053 is OK
- 10.1093/molbev/msw046 is OK
- 10.1016/j.softx.2020.100436 is OK
- 10.1111/2041-210X.12628 is OK
- 10.1093/molbev/msw046 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/ese-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/3830, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 1 year ago

@arendsee - the track editor for this paper is currently out, so I'm helping. I've proofread your paper and have a few small changes in https://github.com/flu-crew/smot/pull/7 - please merge this or let me know you disagree with. In addition, there's a word missing at the end of the first sentence of the caption of Figure 3. Please let me know when this is fixed.

tkanderson commented 1 year ago

@danielskatz Thank you. I agree with the suggestions, and have revised the Figure 3 legend. @arendsee could you also please have one last read of the proof. Thank you very much to all for the constructive reviews and process!

danielskatz commented 1 year ago

@editorialbot recommend-accept

this will create a new proof - please let me know when you are happy with it

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1371/journal.pone.0009490 is OK
- 10.1093/nar/gkw857 is OK
- 10.1128/mSphere.00275-16 is OK
- 10.1093/molbev/mst010 is OK
- 10.1126/science.1189132 is OK
- 10.1038/nature08182 is OK
- 10.1128/JVI.00459-15 is OK
- 10.1371/journal.pcbi.1002947 is OK
- 10.1126/science.1117727 is OK
- 10.22269/210921 is OK
- 10.1016/s0168-9525(03)00112-4 is OK
- 10.1186/s12859-018-2164-8 is OK
- 10.1186/1756-0500-6-145 is OK
- 10.1101/2021.02.13.431075 is OK
- 10.1093/molbev/msz053 is OK
- 10.1101/2021.01.21.427647 is OK
- 10.1186/s12864-018-4620-2 is OK
- 10.1093/bioinformatics/btq228 is OK
- 10.1093/bioinformatics/btp163 is OK
- 10.1128/mra.00673-19 is OK
- 10.12688/f1000research.10446.1 is OK
- 10.1093/molbev/msz053 is OK
- 10.1093/molbev/msw046 is OK
- 10.1016/j.softx.2020.100436 is OK
- 10.1111/2041-210X.12628 is OK
- 10.1093/molbev/msw046 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/ese-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/3835, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

tkanderson commented 1 year ago

@danielskatz Looks good, thanks.

danielskatz commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 1 year ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 year 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/3836
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04193
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 1 year ago

Congratulations to @arendsee (Zebulun Arendsee) and @tkanderson and co-author on your publication!!

And thanks to @Chjulian and @marekborowiec for reviewing, and to @Bisaloo for editing! We couldn't do this without you

danielskatz commented 1 year ago

Note that there's an issue with the PDF not appearing, so I'll keep this open until we resolve it

danielskatz commented 1 year ago

@openjournals/dev - Can you see what the issue is with the PDF, which I don't see, though the DOI resolves correctly?

danielskatz commented 1 year ago

There was a problem with GitHub pages that's been fixed, so this should now be working. It still isn't working for me, but it is for other people, so it appears I have a caching issue. So I'm going to go ahead and close the issue.

editorialbot commented 1 year ago

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

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[![DOI](https://joss.theoj.org/papers/10.21105/joss.04193/status.svg)](https://doi.org/10.21105/joss.04193)

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</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04193/status.svg
   :target: https://doi.org/10.21105/joss.04193

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