JOSS Paper revisions

[ljwoods2]

No description provided.

[hmacdope]

See comments

[codecov]

Codecov Report

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Additional details and impacted files

[hmacdope]

I would say this is ready to go out for co-author review following some final tweaks! @orbeckst what say you?

1. We should pin to MDAnalysis 2.7.0 until the issue causing CI to fail is resolved.
2. We should mint a 0.3.0 release prior.
3. We should mint Zenodo DOI for said release and other releases going forward: https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content
4. We should add PyPi classifiers, see here and MDAnalysis example

[orbeckst]

The repo already has zenodo activated, see https://zenodo.org/records/13887977

[orbeckst]

I'm not sure if we need to pin MDA to 2.7.0 — the current issues are just in develop and should not show up in 2.8.0 and in any case, the "develop" CI here will always pull the develop branch of MDA, regardless of pins (IIRC).

[orbeckst]

I have to re-read the whole thing. I am putting this in my calendar for Wed.

Definitely have other authors review and confirm in writing on the PR that they agree to be an author and that they agree with the author order. (Add the link to the JOSS page that says what the responsibilities of authors are.) EDIT: also have them add

• affiliation
• ORCID
• any acknowledgements (funding or other)

[orbeckst]

To get zenodo right (same title and authors as JOSS paper), add a CITATION.cff file #69 .

[orbeckst]

Will review on Wed 2024-10-23.

I agree to be an author on the paper and I agree with the author order.

[orbeckst]

I am happy for others to review.

[ljwoods2]

Added the CITATION.cff and associated it with the zenodo doi for "all versions of zarrtraj". I can make it specific to 0.3.0 but I figured more general = better.

I will release a 0.3.0 on merging this PR before JOSS submission.

Also will email and ping all the authors

[ljwoods2]

@yuxuanzhuang @edisj @richardjgowers

We are finishing up this JOSS paper submission PR and would love your review and approval! For authorship in JOSS, just need a few things from you:

• Read and review the paper (paper.md) and give approval in writing here for the paper and that you'd like to be an author once you feel it is ready
• Approve the author list in 'paper.md' and 'citation.cff',
• Add your affiliations, your ORCID, your email address, and any extra acknowledgments you'd like to add to the same two files
• Read and confirm that you're okay with the JOSS authorship requirements (https://joss.readthedocs.io/en/latest/submitting.html#authorship) (copied here):

"Purely financial (such as being named on an award) and organizational (such as general supervision of a research group) contributions are not considered sufficient for co-authorship of JOSS submissions, but active project direction and other forms of non-code contributions are. The authors themselves assume responsibility for deciding who should be credited with co-authorship, and co-authors must always agree to be listed. In addition, co-authors agree to be accountable for all aspects of the work, and to notify JOSS if any retraction or correction of mistakes are needed after publication."

[hmacdope]

Looks good to me, I am happy to be author and accept all JOSS related author responsibilities.

Just one thing, Richard needs affiliation

[orbeckst]

@yuxuanzhuang @edisj @richardjgowers please provide explicit approval on this PR, otherwise we cannot list you as an author and we will move you to Acknowledgements.

Please double-check your name, affiliation, and ORCID. All are needed for submission.

EDIT: And read #68 (comment)

[yuxuanzhuang]

Looking great!

I agree to be an author on the paper and I agree with the author order.

[richardjgowers]

@ljwoods2 I've put in #70 to add my affiliation and made a couple comments, but looks good to me

[edisj]

@ljwoods2 Looks good to me! My orcid is https://orcid.org/0000-0001-8813-6356 if you'd like to add it, or I can fork this repo and open a PR myself, let me know.

I agree to be an author on the paper and I agree with the author order.

I have read and confirm that I'm okay with the JOSS authorship requirements.

[hmacdope]

@ljwoods2 id say we are good to go here! All authors have agreed. Feel free to merge when ready, then submit to JOSS.

[orbeckst]

@ljwoods2 any news from the JOSS paper?