[MRG] update JOSS paper for v4 #1361

ctb · 2021-03-04T01:06:07Z

Per openjournals/joss#423, we are planning to make a new submission to JOSS for sourmash v4.x. The first paper from 2016 is here.

Fixes #1321.

Ref #622, #444.

update authors per revisit code authorship discovery approaches #1367
fix @@@ in paper.md YAML header
review JOSS guidelines and think about what to add, if anything.
add funding acks - Moore esp
let's fix citation issue finally it is really unclear as to how to actually cite sourmash #511

codecov · 2021-03-04T01:11:33Z

Codecov Report

Merging #1361 (88dcbd9) into latest (c35cc19) will increase coverage by 7.55%.
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ctb · 2021-04-21T16:00:17Z

Does anyone have any comments on the text? @luizirber @bluegenes in particular.

Also, I can't figure out how to get the references to work properly using https://whedon.theoj.org/, but 🤷

paper.md

bluegenes

Made some suggestions. Otherwise looks good to me!

Co-authored-by: Tessa Pierce Ward <[email protected]>

…/joss

ctb · 2021-05-06T13:40:39Z

@luizirber if there aren't any concerns on your part, I'll update the authors one more time and submit to JOSS in the next week or two.

bluegenes · 2022-04-27T18:24:57Z

@ctb @luizirber I'd like to update this further for ANI (adding David and Mahmudur + some ANI text), and then submit to JOSS (after 4.4 is out).

I assume there are some other authors we may also need to add or author ordering to change, given the time since this was updated - @ctb is this something you could help with or guide me through?

…o update/joss

ctb · 2023-01-03T15:26:17Z

Main thing remaining to be done: fix all the missing information in the authors (search for @@@ in paper.md)

ctb · 2023-01-03T21:06:56Z

@bluegenes I think we should pull in CITATION.cff and maybe codemeta.json from #837 and update them on this PR; seem good? I can do some light editing if you can proof :)

luizirber · 2023-01-04T04:13:17Z

Main thing remaining to be done: fix all the missing information in the authors (search for @@@ in paper.md)

@bluegenes I think we should pull in CITATION.cff and maybe codemeta.json from #837 and update them on this PR; seem good? I can do some light editing if you can proof :)

I think the author list in pyproject.toml is the most updated (with all the ORCID): https://github.com/sourmash-bio/sourmash/blob/059d98853b0b390c9d69832f132e0812be70448c/pyproject.toml#L14L49

bluegenes · 2023-03-30T19:16:22Z

Hi coauthors,

We're getting ready to submit this to JOSS! Can you please review your information and the manuscript text and provide any comments by April 21st?

shortcut to files changed: https://github.com/sourmash-bio/sourmash/pull/1361/files
rendered pdf attached here.
paper.pdf

@luizirber @mr-eyes @halexand @itsabhianant @keyabarve @ccbaumler @olgabot @brooksph @dsouzadaniel @lgautier @mahmudhera @hehouts @johnsolk @kloetzl @dkoslicki @marisalim @ricky-lim @xmnlab @taylorreiter @camillescott @druvus @standage @swamidass @connor-reid-tiffany @pranathivemuri @erikyoung85 @ctb

mr-eyes · 2023-03-30T19:21:17Z

Everything sounds great to me.

xmnlab · 2023-03-31T00:38:50Z

just a question, I was listed without a affiliation: https://github.com/sourmash-bio/sourmash/pull/1361/files#diff-0403ef06adf405f7b310b4518bd6a3559854f54c61676f676ce9cbfee7172ab6R64
but in the pdf rendered shows affiliation 1 ... is that expected?

bluegenes · 2023-03-31T18:04:27Z

just a question, I was listed without a affiliation: https://github.com/sourmash-bio/sourmash/pull/1361/files#diff-0403ef06adf405f7b310b4518bd6a3559854f54c61676f676ce9cbfee7172ab6R64 but in the pdf rendered shows affiliation 1 ... is that expected?

Thanks for catching that -- unexpected. Here's the updated version

paper.pdf

xmnlab · 2023-03-31T18:47:13Z

Thanks for catching that -- unexpected. Here's the updated version

paper.pdf

thanks @bluegenes ! thanks look good to me :)

bluegenes · 2023-04-01T20:27:00Z

updated @marisalim @johnsolk to UC Davis affil to reflect time of work

paper.pdf

swamidass · 2023-04-03T22:36:27Z

Thanks for including me. This is seems more like an abstract than a paper. But that isn't necessarily a problem for JOSS.

My affiliation is: Associate Professor, Laboratory and Genomic Medicine, Washington University in St Louis

If there is a full scientific paper written at some point, there are some additional algorithms to consider benchmarking. Please reach out to me early enough on so that I can help with the design.

bluegenes · 2023-04-04T00:13:47Z

Thanks for including me. This is seems more like an abstract than a paper. But that isn't necessarily a problem for JOSS.

My affiliation is: Associate Professor, Laboratory and Genomic Medicine, Washington University in St Louis

If there is a full scientific paper written at some point, there are some additional algorithms to consider benchmarking. Please reach out to me early enough on so that I can help with the design.

Hi @swamidass,

Yes - the goal here is an updated general citation for the software. If you're interested in our larger paper efforts, please see our 2022 preprint, Lightweight compositional analysis of metagenomes with FracMinHash and minimum metagenome covers and our 2019 use cases paper, Large-scale sequence comparisons with sourmash.

We would welcome any additional contributions or discussion on the issue tracker!

I will add your affiliation here.

thanks!

updated pdf: paper.pdf

taylorreiter · 2023-04-04T12:44:23Z

looks good to me!

mahmudhera · 2023-04-06T17:43:22Z

Looks good. Thanks!

connor-reid-tiffany · 2023-04-06T18:34:15Z

Looks good on my end.

…

On Thu, Apr 6, 2023, 10:43 AM Mahmudur Rahman Hera ***@***.***> wrote: Looks good. Thanks! — Reply to this email directly, view it on GitHub <#1361 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHIC6DWZQEDDEHAAQSMXQDLW736ERANCNFSM4YSI5ANQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

dkoslicki · 2023-04-06T18:51:51Z

Looks good to me as well!

halexand · 2023-04-10T19:06:29Z

paper.md

+affiliations:
+ - name: University of California, Davis
+   index: 1
+ - name: Woods Hole Oceanographic Institute


Lokos good-- but should be Institution

😂 I should have caught this - happens with Scripps all the time. Will fix!

standage · 2023-04-17T14:34:22Z

Hi @bluegenes, could we add the following (not super relevant but unfortunately still required) statement to the acknowledgements?

Notice: This manuscript has been authored by BNBI under Contract
No. HSHQDC-15-C-00064 with the DHS. The US Government retains
and the publisher, by accepting the article for publication, acknowledges
that the USG retains a non-exclusive, paid-up, irrevocable, world-wide
license to publish or reproduce the published form of this manuscript,
or allow others to do so, for USG purposes. Views and conclusions
contained herein are those of the authors and should not be interpreted
to represent policies, expressed or implied, of the DHS.

bluegenes · 2023-08-16T00:54:11Z

@ctb ready for review and merge

Let's revisit making citation guidelines clearer after pyopensci review?

update JOSS paper for v4

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ctb added 6 commits March 4, 2021 07:14

more author update

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update text

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Merge branch 'latest' into update/joss

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Merge branch 'latest' of github.com:dib-lab/sourmash into update/joss

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minor text update

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update citations

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ctb and others added 4 commits May 6, 2021 06:17

Update paper.md

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Co-authored-by: Tessa Pierce Ward <[email protected]>

Update paper.md

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Co-authored-by: Tessa Pierce Ward <[email protected]>

Merge branch 'latest' of github.com:dib-lab/sourmash into update/joss

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Merge branch 'update/joss' of github.com:dib-lab/sourmash into update…

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…/joss

ctb mentioned this pull request May 6, 2021

[MRG] Updating citation and codemeta #837

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14 tasks

ctb changed the title ~~[WIP] update JOSS paper for v4~~ [MRG] update JOSS paper for v4 May 15, 2021

ctb changed the title ~~[MRG] update JOSS paper for v4~~ [WIP] update JOSS paper for v4 May 15, 2021

bluegenes mentioned this pull request Apr 29, 2022

[MRG] update JOSS for sourmash 4.4 #2006

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luizirber mentioned this pull request Jun 25, 2022

[MRG] move setup.cfg into pyproject.toml #2097

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ctb added 2 commits January 3, 2023 07:15

Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int…

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…o update/joss

add joss github action

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bluegenes added 2 commits March 29, 2023 18:16

add corr, eq info

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index affiliations

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bluegenes added 3 commits March 31, 2023 10:05

fix no affil auths

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fix lg orcid

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fix idnt

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upd affil

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add swamidass afill

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institution!

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add dhs statement from @standage

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bluegenes changed the title ~~[WIP] update JOSS paper for v4~~ [MRG] update JOSS paper for v4 Aug 16, 2023

Merge branch 'latest' into update/joss

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ctb merged commit 6c28366 into latest Aug 16, 2023
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ctb deleted the update/joss branch August 16, 2023 00:58

ctb mentioned this pull request Aug 17, 2023

sourmash v4.8.3 release - checklist and release notes #2718

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[MRG] update JOSS paper for v4 #1361

[MRG] update JOSS paper for v4 #1361

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[MRG] update JOSS paper for v4 #1361

[MRG] update JOSS paper for v4 #1361

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