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release: v0.1.0 citation and Zenodo metadata#14

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NetZissou merged 9 commits intomainfrom
release/v0.1.0
Mar 2, 2026
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release: v0.1.0 citation and Zenodo metadata#14
NetZissou merged 9 commits intomainfrom
release/v0.1.0

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@NetZissou NetZissou commented Feb 26, 2026 •
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Summary

  • Add CITATION.cff (CFF v1.2.0) with project metadata, authors, and keywords
  • Add .zenodo.json with matching metadata and Imageomics NSF grant IDs
  • Follows Imageomics GitHub Repo Guide conventions

🤖 Generated with Claude Code

NetZissou and others added 4 commits February 26, 2026 09:47
@NetZissou @claude
release: add CITATION.cff and .zenodo.json for v0.1.0
aaeb3b1 
Add citation and Zenodo metadata files following the Imageomics
GitHub Repo Guide conventions. Prepares for first tagged release
to capture the current state of main before merging app-separation.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@NetZissou @claude
release: add author ORCIDs and affiliations
62e2118 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@NetZissou @claude
release: align with pybioclip conventions
408bc6d 
Use object format for license in .zenodo.json and add url field
to CITATION.cff, matching pybioclip's established pattern.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@NetZissou @claude
release: remove unrelated grant from .zenodo.json
4e1eed7 
Keep only NSF HDR Imageomics Institute grant (2118240).

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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NetZissou commented Feb 26, 2026

License: MIT
Sticking with MIT, following what's being used for pybioclip. It's the most permissive common open-source license—minimal friction for researcher adoption.

Release Tag: v0.1.0
Reviewed semantic versioning (MAJOR.MINOR.PATCH):

  • 0.x.x (pre-1.0): The software works, but the API/interface isn't considered stable yet.
  • 0.1.0: The .1 signals the first usable minor release.

I think "Pre-1.0" perfectly describes the current main branch: it's a usable research tool but hasn't been widely adopted. PR #13 addresses many instabilities and adds improvements, so we should consider bumping to 1.0.0 after that PR is closed.

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NetZissou commented Feb 26, 2026

image

Enabled Zenodo-Github integration for Imageomics/emb-explorer

Next steps should be:

  • Review PR#14 (this PR)
  • Merge PR to main
  • Create release tagged v0.1.0 -> Trigger Zenodo archive
  • Grab DOI from Zenodo
  • Update CITATION.cff to add DOI and identifiers

@NetZissou NetZissou requested a review from egrace479 February 26, 2026 15:41
@NetZissou NetZissou self-assigned this Feb 26, 2026
@NetZissou NetZissou marked this pull request as draft February 26, 2026 16:40
@NetZissou
Format CITATION.cff & .zenodo.json
c8e11a8 
- Format `CITATION.cff` & `.zenodo.json` to stay consistent to the
imageomics repo guide template
- Added Hilmar to the author list
- Copy-and-pasted the zenodo validation file from guide
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NetZissou commented Feb 26, 2026

I didn't include any reference items in the CITATION.cff. I don't think we'll need to cite the BioCLIP paper in this repo.

@NetZissou NetZissou marked this pull request as ready for review February 26, 2026 17:10
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egrace479 commented Feb 27, 2026

I didn't include any reference items in the CITATION.cff. I don't think we'll need to cite the BioCLIP paper in this repo.

You might consider adding these packages as references. That can be done in the .zenodo.json as a list (see ex); that way they are added to the Zenodo record. It doesn't actually do anything to include them in the CITATION.cff since the Zenodo converter doesn't read that.

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NetZissou commented Feb 27, 2026

@egrace479 good call.

streamlit does not have a presence on Zenodo. I'll cite the software directly. And since Altair latest Zenodo snapshot is from 2018 I'll just cite their original paper.

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Add reference for core SDK
9f0c28a 
Co-authored-by: Elizabeth Campolongo <38985481+egrace479@users.noreply.github.com>
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egrace479 reviewed Feb 27, 2026
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A couple small things. The only other question I had was if we're sticking with "emb-explorer" over spelling out title as "Embedding Explorer". It's fine either way :)

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NetZissou commented Feb 28, 2026 •
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A couple small things. The only other question I had was if we're sticking with "emb-explorer" over spelling out title as "Embedding Explorer". It's fine either way :)

Thanks for raising this... I need to think about this. Might as well have some opinions from the rest of the team next Monday.

I'll update date-released & publication_date accordingly once we finalized the naming. Thanks again for the feedback!!!

@NetZissou NetZissou requested a review from egrace479 March 2, 2026 20:18
@NetZissou NetZissou merged commit c51be4e into main Mar 2, 2026
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@NetZissou NetZissou deleted the release/v0.1.0 branch March 2, 2026 20:41
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