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[REVIEW]: Microbiome.jl and BiobakeryUtils.jl - Julia packages for working with microbial community data #3876

Closed whedon closed 2 years ago

whedon commented 2 years ago

Submitting author: @kescobo (Bonham, Kevin) Repository: https://github.com/EcoJulia/Microbiome.jl Version: v0.8.2 Editor: @will-rowe Reviewer: @adRn-s, @aguang Archive: 10.5281/zenodo.5682344

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Markdown: [![status](https://joss.theoj.org/papers/450fa18f47932c5fd3b837edeac91440/status.svg)](https://joss.theoj.org/papers/450fa18f47932c5fd3b837edeac91440)

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.)

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@adRn-s & @aguang, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @adRn-s

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Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @aguang

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whedon commented 2 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @adRn-s, @aguang it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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whedon commented 2 years ago

Wordcount for paper.md is 963

whedon commented 2 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.06 s (654.1 files/s, 130989.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              4              2              2           4026
Julia                           10            282             53           1178
Markdown                        10            296              0            953
TeX                              1             17              0            182
YAML                             7              4             10            154
TOML                             4              4              0             46
-------------------------------------------------------------------------------
SUM:                            36            605             65           6539
-------------------------------------------------------------------------------

Statistical information for the repository 'ae19e4e1828a385fdaef2501' was
gathered on 2021/11/02.
No commited files with the specified extensions were found.
whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3390/nu13082833 is OK
- 10.3390/microorganisms9081608 is OK
- 10.3389/fmicb.2021.670336 is OK
- 10.1186/s13059-017-1359-z is OK
- 10.1137/141000671 is OK
- 10.5334/jors.151 is OK
- 10.21105/joss.03349 is OK
- 10.7554/eLife.65088 is OK
- 10.5281/zenodo.5566503 is OK

MISSING DOIs

- 10.1186/s13059-017-1359-z may be a valid DOI for title: Experimental design and quantitative analysis of microbial community multiomics

INVALID DOIs

- None
whedon 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:

kescobo commented 2 years ago

Co-authors: @annelle-abatoni @anikaluo @vanjakle

aguang commented 2 years ago

I have finished my review and think the package and paper are a nice contribution to the EcoJulia ecosystem. The documentation is overall solid, I've made a few suggestions to the documentation based on my attempts to run some of the functions on my own data, but those are only suggestions rather than necessary revisions. Nice job, I look forward to trying this package out more extensively soon.

adRn-s commented 2 years ago

It has been an honor for me to be a reviewer for this software. I have made some suggestions in their respective repositories, and all have positively been taken into account. The core functionality of both packages is in perfect condition. I look forward to seeing these software libraries grow into the whole framework functionality that EcoJulia has to offer.

I would like to take the opportunity to urge that more diversity metrics (alpha and beta) be incorporated. Then, this could include measures of computational efficiency that the Julia language provides as a modern basis. This way, benchmark comparisons to other software suits could be made. Of course, these are not requirements to approve the publication of your scientific article.

For my part, as a JOSS reviewer, I suggest to the editors that they accept this work as is.

Congratulations to all the authors, keep up with the good work!

kescobo commented 2 years ago

Thanks @adRn-s and @aguang for the thoughtful reviews and suggestions! I am working on a number of the suggested changes here.

I would like to take the opportunity to urge that more diversity metrics (alpha and beta) be incorporated. Then, this could include measures of computational efficiency that the Julia language provides as a modern basis.

There's been some discussion in the #ecology stream on zulip about incorporating Diversity.jl, which may end up being an even better solution. I think either pulling Diveristy.jl in as a dependency or just making sure CommunityProfiles play nicely, and maybe adding some examples to the doc. I've opened https://github.com/EcoJulia/Microbiome.jl/issues/117 to keep track, and see also https://github.com/EcoJulia/EcoBase.jl/issues/22

kescobo commented 2 years ago

@will-rowe Can you chime in with next steps here?

@adRn-s you didn't check off the "performance" or "state of the field" items in your review - were there specific comments you had on that front?

will-rowe commented 2 years ago

Hi @kescobo. Thanks for the ping and sorry for the delay.

Thanks to @aguang and @adRn-s for some excellent reviews. Given both have recommended acceptance, I'm happy to move forward. (That being said if you can respond @adRn-s regarding the two unchecked boxes, that would be great).

Let me give it another check over and then we can move on to acceptance.

will-rowe commented 2 years ago

@whedon generate pdf

whedon 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:

will-rowe commented 2 years ago

Looks good to me.

@kescobo - can you please create a new tagged release and archive it (in zenodo) and then post back here with the version number and archive DOI

kescobo commented 2 years ago

@will-rowe

will-rowe commented 2 years ago

Hi @kescobo. I'm afraid the author list on the zenodo repository needs to match that of your paper - would you mind updating them?

kescobo commented 2 years ago

Ah, no sweat. Should be set @will-rowe

will-rowe commented 2 years ago

Great - thanks! All looks good to me. The one thing I'd say is that I've not come across a JOSS paper with 2 repositories/archives associated with the paper. I'll tag this submission with the Microbiome.jl archive but the EiC may have some suggestion on how this is usually handled.

will-rowe commented 2 years ago

@whedon set 10.5281/zenodo.5682344 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5682344 is the archive.

will-rowe commented 2 years ago

@whedon set v0.8.2 as version

whedon commented 2 years ago

OK. v0.8.2 is the version.

will-rowe commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3390/nu13082833 is OK
- 10.3390/microorganisms9081608 is OK
- 10.3389/fmicb.2021.670336 is OK
- 10.1186/s13059-017-1359-z is OK
- 10.1137/141000671 is OK
- 10.5334/jors.151 is OK
- 10.21105/joss.03349 is OK
- 10.7554/eLife.65088 is OK
- 10.5281/zenodo.5566503 is OK

MISSING DOIs

- 10.1186/s13059-017-1359-z may be a valid DOI for title: Experimental design and quantitative analysis of microbial community multiomics

INVALID DOIs

- None
whedon 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/2750

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2750, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
kescobo commented 2 years ago

PDF looks good to me! Thanks again everyone :-)

whedon commented 2 years ago

:wave: @adRn-s, please update us on how your review is going (this is an automated reminder).

arfon commented 2 years ago

@whedon accept deposit=true

whedon commented 2 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 2 years ago

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2755
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03876
  3. If everything looks good, then close this review issue.

  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? Notify your editorial technical team...

arfon commented 2 years ago

@adRn-s, @aguang – many thanks for your very speedy reviews here and to @will-rowe 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 ✨

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

whedon commented 2 years ago

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

If you would like to include a link to your paper from your README use the following code snippets:

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HTML:
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