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Add basic citation file#309

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msschwartz21 merged 8 commits intomainfrom
add-citation
Aug 26, 2025
Merged

Add basic citation file#309
msschwartz21 merged 8 commits intomainfrom
add-citation

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@DragaDoncila
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@DragaDoncila DragaDoncila commented Aug 21, 2025

Proposed Change

As per zulip discussion, this PR adds a CITATION.cff file listing all current contributors, their affiliations, their ORCIDs and their GitHub usernames. I have listed contributors in the order they appeared on the contributors page, because it was easy for me. Please feel free to rearrange at will. Probs should be alphabetical? Once everyone confirms their details, we can do that. I did not include copilot, pre-commit bot or dependabot, though we are of course very grateful for their contributions.

It also lists a title and the GEFF license. I did not list a GEFF version because otherwise we'd have to keep updating it. We may want to include latest release version and add step that opens a PR to the release action. I'm not sure what other fields of the citation file we may want to include - potentiall a DOI once/if we set one up on zenodo.

I've done my best to spell everything correctly and include correct affiliations and orcids, but I will ping folks individually to check their own details before we merge.

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codecov bot commented Aug 21, 2025

Codecov Report

✅ All modified and coverable lines are covered by tests.

📢 Thoughts on this report? Let us know!

@DragaDoncila
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I refuse to entertain the idea that this PR broke typing 😠

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codspeed-hq bot commented Aug 21, 2025

CodSpeed Performance Report

Merging #309 will improve performances by ×3.6

Comparing add-citation (4f67c75) with main (e516b63)

Summary

⚡ 1 improvements
✅ 6 untouched benchmarks

Benchmarks breakdown

Benchmark BASE HEAD Change
test_bench_read[read_sg-500] 1,726.1 ms 479.4 ms ×3.6

@lxenard
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lxenard commented Aug 21, 2025

Actually, for the typing failure one of the error comes from my trackmate loader. Should I make a commit to try to fix this?

@melisande-c
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I refuse to entertain the idea that this PR broke typing 😠

I think the errors coming from the validate/tracks.py are due to a recent release of types-networkx.

This was a recent change where int is no longer an accepted argument of G.in_degree and G.out_degree
https://github.com/python/typeshed/blame/main/stubs/networkx/networkx/classes/reportviews.pyi#L58-L61

@melisande-c
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I think the errors coming from the validate/tracks.py are due to a recent release of types-networkx.

^ opened and issue python/typeshed#14616

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I updated my affiliation!

Co-authored-by: Yohsuke T. Fukai <ysk@yfukai.net>
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@DragaDoncila I was wondering if we should also add the java contributors here and then add the same file to the geff-java repo. Thoughts?

@msschwartz21 msschwartz21 added the 🔧 maintenance Library maintenance/chore label Aug 21, 2025
@mkitti
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mkitti commented Aug 21, 2025

For Janelians, I wonder if we should mention the Howard Hughes Medical Institute as part of the affiliation.

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I was wondering if we should also add the java contributors here and then add the same file to the geff-java repo. Thoughts?

@msschwartz21 yep, agreed. I'll take a look at that

@DragaDoncila
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For Janelians, I wonder if we should mention the Howard Hughes Medical Institute as part of the affiliation.

@mkitti that's up to you all! I wasn't sure what the "official" affiliation was

@melisande-c
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@DragaDoncila: @ilan-theodoro is missing 🥺

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We probably should acknowledge uncle Howard.

@DragaDoncila
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@DragaDoncila: @ilan-theodoro is missing 🥺

Ooops my bad, I did this manually so I'm not surprised I missed one. Thanks for catching, will fix! Or @ilan-theodoro just add yourself if you'd like

cmalinmayor and others added 2 commits August 25, 2025 16:36
Co-authored-by: Mark Kittisopikul <mkitti@users.noreply.github.com>
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Everyone has approved so we can go ahead and merge this. Thanks for organizing @DragaDoncila!

@msschwartz21 msschwartz21 merged commit 26a2de8 into main Aug 26, 2025
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@msschwartz21 msschwartz21 deleted the add-citation branch August 26, 2025 15:02
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