Fix URLs based on repo transfer and prep for DOI snapshot

[egrace479]

Prepares this repo for a release and Zenodo snapshot:

• Redirects all URLs to Imageomics GitHub
• Clarify license as MIT
• Updates the license based on @samuelstevens first commit: a0f8528, likely no more of the original codebase left.
• Set version for 0.1.0 as @samuelstevens notes "the key is to recognize that it's a rapidly changing codebase that is not stable at any point": updates to CITATION.cff and adds .zenodo.json and associated validation workflow.
  • Set release date for tomorrow (June 10)

[samuelstevens]

Thanks Elizabeth.

1. Did you generate the changes to the docs with just docs or a find+replace? I would prefer to use just docs so that we know it works with all auto-generated docs in the future.
2. Instead of a Github Action, which in my experience is pretty hard to get right, can we include a script to use one of npx, bunx dx or deno run --allow-read? Then we get (1) no Github Actions (2) Flexible Javascript package usage (3) Zenodo validation in the future. It could be a just recipe or a script. Or we could remove the Github Action entirely since the .zenodo.json seems valid already.

bunx zenodraft metadata validate .zenodo.json and deno run --allow-read npm:zenodraft metadata validate .zenodo.json both worked for me. I ran them, saw no errors, edited the .zenodo.json file to remove the 'name' field and both runners then reported an error.

[samuelstevens]

See my comment above.

[egrace479]

1. Did you generate the changes to the docs with just docs or a find+replace? I would prefer to use just docs so that we know it works with all auto-generated docs in the future.

I did case-preserving find+replace and the only remaining instances of OSU-NLP-Group/OSU-NLP in the repo are your notes on whether it should stay there and the output from the notebook install. You can run another method if preferred.

2. Instead of a Github Action, which in my experience is pretty hard to get right, can we include a script to use one of npx, bunx dx or deno run --allow-read? Then we get (1) no Github Actions (2) Flexible Javascript package usage (3) Zenodo validation in the future. It could be a just recipe or a script. Or we could remove the Github Action entirely since the .zenodo.json seems valid already.

The workflow is our standard Zenodo metadata checker using Zenodo's action to validate the formatting. It's set up to only run when that or the .zenodo.json are edited.

[samuelstevens]

The find+replace worked okay.

But I think using a script on developer machines is much, much easier than Github Actions. Can you add a short script scripts/validation-zenodo.sh:

#!/bin/sh
if command -v npx >/dev/null 2>&1; then
    exec npx zenodraft metadata validate .zenodo.json
elif command -v bunx >/dev/null 2>&1; then
    exec bunx zenodraft metadata validate .zenodo.json
elif command -v dx >/dev/null 2>&1; then
    exec dx zenodraft metadata validate .zenodo.json
elif command -v deno >/dev/null 2>&1; then
    exec deno run --allow-read npm:zenodraft metadata validate .zenodo.json
else
    echo "no runner found (tried: npx bunx dx deno)" >&2
    exit 1
fi

And add this runner to the justfile under docs? That will be easiest to maintain in the future. Thanks!

[egrace479]

The find+replace worked okay.

@thompsonmj ran just docs and will push up the changes.

But I think using a script on developer machines is much, much easier than Github Actions. Can you add a short script scripts/validation-zenodo.sh:

...

And add this runner to the justfile under docs? That will be easiest to maintain in the future. Thanks!

Yes, we can add the developer validation script too.

[thompsonmj]

@samuelstevens I think this is ready for a look once more ...

Note that in the README, I changed the citation instructions to point to the use of the CITATION.cff file via the sidebar button. Makes sense to have this single source of truth that tracks with release versions.

If this is good, once this gets an approval, an update can be made to publication dates in .zenodo.json and CITATION.cff.

[thompsonmj]

And a quick note on:

Or we could remove the Github Action entirely since the .zenodo.json seems valid already.

There are occasions when that file should be manually edited (most frequently on version bumps), so the workflow earns its keep when we will inevitably forget to run it manually.

[samuelstevens]

Yeah I'm really not a fan of Github Actions. Can we try without for 6 months? I've really never had much luck with Github Actions being reliable.

earns its keep

smells like LLM to me Matt