feat: add capabilities for spatial layout type

[sehilyi]

This PR implements the ability to specify a view to use a spatial layout. This allows the user to supply a "model" file that associates genomic regions with xyz coordinates in space.

Prototypical version of the editor with these capabilities is deployed at https://3d.gosling-lang.org

basic use

{
  "views": [
    {
      "layout": {
        "type": "spatial",
        "model": {
          "type": "csv",
          "url": "https://.../yeast_model.csv",
          "xyz": ["x", "y", "z"],
          "chromosome": "chr",
          "position": "coord"
        }
      },
      "tracks": [
        { /* ... */ }
      ]
    }
  ]
}

TODO (MVP)

When these are resolved, we should be able to merge

• switch to using uchimata (+ use the new unified API)
  • fix: filtering only works on first refresh, not when switching to subsequent examples in the editor UI
• fix types (pnpm build-types should run without issues)
• Better solution for the hard-coded data.sampleLength = 30000 (in demo/renderer/main.ts, line ~163)

TODO (extras)

Document here but likely work on in separate PRs after merging this one

• simple linking of views via synchronized camera

Change List

• adds two new dependencies: uchimata, to facilitate rendering of 3D data; and flechette for working with Arrow IPC format.

Checklist

• Ensure the PR works with all demos on the online editor
• Unit tests added or updated
• Examples added or updated
• Documentation updated (e.g., added API functions)
• Screenshots for visual changes (e.g., new encoding support or UI change on Editor)

[dvdkouril]

@sehilyi Since you opened this PR, I can't assign you as reviewer. Could you take a look if there's anything critical that would prevent from merging this so that we can start using it in GD?

It's not perfect, but the CI checks are green, and we can iron out the other issues while working on the GD UI integration, since this will still end up in the alpha version of Gosling.

[sehilyi]

Thanks for letting me know - I somehow did not notice that the PR is ready to review. I will review this now and let you know here.

[sehilyi]

It makes sense to have this here, especially given the tight timeline.

But, given that we now have more layout options, and some of them have specialized properties (circular layouts also have some properties, like innerRadius), I think we should consider having more scoped types in the future. For example, several circular-specific properties are defined in CommonTrackDef that will also need to be moved out, in addition to locus and spatial, e.g.,

type SingleTrackBase = SingleTrackBaseLinear | SingleTrackBaseCircular | SingleTrackBaseSpatial;

[dvdkouril]

Yea, I definitely took the easy way right now. Will be happy to revisit the types when there's some more time.

[sehilyi]

@dvdkouril I tested locally, and I can confirm that this works in VEC. Thanks for making this change - I'm excited to include this in our alpha version.

Please feel free to merge this when you feel ready. Also, after you merged it, can you try releasing a new alpha version based on the description I wrote on v2/CONTRIBUTING.md?