Table plugin ts

[AlexSurtees]

Description

1. Merges dev, including roi selector plugin. ROI selector and table plugin work separately (and should work together, but UI conflicts needs to be resolved)
2. Refactors anndata zarr plugin to typescript
3. Refactors plugin to prepare for different table backends e.g. csv rather than anndata.
   Fixes # (issue)
   Related to # (if applicable)

#58
#83

Type of change

• 🐛 Bug fix (non-breaking change that resolves an issue)
• ✨ New feature (non-breaking change that adds functionality)
• ⚡ Optimisation (non-breaking improvement to performance or efficiency)
• 🧩 Documentation (adds or improves documentation)
• 🧱 Maintenance (refactor, dependency update, CI/CD, etc.)
• 🔥 Breaking change (fix or feature that causes existing functionality to change)

Checklist

• All tests pass (eg. npm test)
• Pre-commit hooks run successfully (eg. pre-commit run --all-files)
• Documentation updated (if required)

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[AlexSurtees]

Fixed error in test runner, which was caused by the transitive dependency wgsl_reflect (deck.gl/core -> luma.gl/engine -> luma.gl/shadertools -> wgsl_reflect). I added an override to the package.json file to prevent updating to the breaking 1.3.0. The shadertools version we are depending on is 2 years old and could do with updating, which would be a better solution (e.g. upgrading deck.gl version). Output of pnpm why wgsl_reflect:

dependencies:
@deck.gl/core 9.0.41
├─┬ @luma.gl/engine 9.0.28
│ └─┬ @luma.gl/shadertools 9.0.28
│ └── wgsl_reflect 1.3.0
└─┬ @luma.gl/shadertools 9.0.28
└── wgsl_reflect 1.3.0
@deck.gl/geo-layers 9.0.41
├─┬ @deck.gl/core 9.0.41 peer
│ ├─┬ @luma.gl/engine 9.0.28
│ │ └─┬ @luma.gl/shadertools 9.0.28
│ │ └── wgsl_reflect 1.3.0
│ └─┬ @luma.gl/shadertools 9.0.28
│ └── wgsl_reflect 1.3.0
├─┬ @deck.gl/extensions 9.0.41 peer
│ ├─┬ @deck.gl/core 9.0.41 peer
│ │ ├─┬ @luma.gl/engine 9.0.28
│ │ │ └─┬ @luma.gl/shadertools 9.0.28
│ │ │ └── wgsl_reflect 1.3.0
│ │ └─┬ @luma.gl/shadertools 9.0.28
│ │ └── wgsl_reflect 1.3.0
│ ├─┬ @luma.gl/engine 9.0.28 peer
│ │ └─┬ @luma.gl/shadertools 9.0.28
│ │ └── wgsl_reflect 1.3.0
│ └─┬ @luma.gl/shadertools 9.0.28
│ └── wgsl_reflect 1.3.0
└─┬ @deck.gl/layers 9.0.41 peer
└─┬ @deck.gl/core 9.0.41 peer
├─┬ @luma.gl/engine 9.0.28
│ └─┬ @luma.gl/shadertools 9.0.28
│ └── wgsl_reflect 1.3.0
└─┬ @luma.gl/shadertools 9.0.28
└── wgsl_reflect 1.3.0

 and after:
 
 dependencies:

@deck.gl/core 9.0.41
├─┬ @luma.gl/engine 9.0.28
│ └─┬ @luma.gl/shadertools 9.0.28
│ └── wgsl_reflect 1.2.0
└─┬ @luma.gl/shadertools 9.0.28
└── wgsl_reflect 1.2.0
@deck.gl/geo-layers 9.0.41
├─┬ @deck.gl/core 9.0.41 peer
│ ├─┬ @luma.gl/engine 9.0.28
│ │ └─┬ @luma.gl/shadertools 9.0.28
│ │ └── wgsl_reflect 1.2.0
│ └─┬ @luma.gl/shadertools 9.0.28
│ └── wgsl_reflect 1.2.0
├─┬ @deck.gl/extensions 9.0.41 peer
│ ├─┬ @deck.gl/core 9.0.41 peer
│ │ ├─┬ @luma.gl/engine 9.0.28
│ │ │ └─┬ @luma.gl/shadertools 9.0.28
│ │ │ └── wgsl_reflect 1.2.0
│ │ └─┬ @luma.gl/shadertools 9.0.28
│ │ └── wgsl_reflect 1.2.0
│ ├─┬ @luma.gl/engine 9.0.28 peer
│ │ └─┬ @luma.gl/shadertools 9.0.28
│ │ └── wgsl_reflect 1.2.0
│ └─┬ @luma.gl/shadertools 9.0.28
│ └── wgsl_reflect 1.2.0
└─┬ @deck.gl/layers 9.0.41 peer
└─┬ @deck.gl/core 9.0.41 peer
├─┬ @luma.gl/engine 9.0.28
│ └─┬ @luma.gl/shadertools 9.0.28
│ └── wgsl_reflect 1.2.0
└─┬ @luma.gl/shadertools 9.0.28
└── wgsl_reflect 1.2.0

  Likely shadertools does not specify wgsl_reflect version in a narrow enough range and some difference caused pnpm to install 1.3.0 rather than 1.2.0.
  
  Opened an issue for upgrading deck.gl here #98 

[LucaAnce]

@AlexSurtees Tested out the impact on the ROI plugin as requested. Every core functionality works fine including the import of ROIs saved in the zarr!

Only one minor feature is impacted, which is the 'Go to ROI' one. It can still toggle visibility, and move Z/T axis, but the 'zooming in' feature is not working anymore. The write channel the ROI plugin calls to move the camera silently fails since setViewState was removed from onViewerStateChange in VizarrViewer.tsx, so at runtime the property is just undefined

I believe this feature to not be crucial but still useful so I would suggest fixing this.

[AlexSurtees]

Thanks @LucaAnce. For the purposes of this PR, I think we will have to make a decision here about which is the lesser of two evils:

1. Infinite re-render issue which does not seem to cause any functionality issues, but will no doubt affect performance of the viewer/browser.
2. Ability for 'Go to ROI' functionality to match the correct zoom level for the ROI.

@davehorsfall what do you think?

[LucaAnce]

Understood, I missed the reason why that was removed. With this infinite re-render issue in mind, I understand your concerns and potentially support the removal of the go-to feature if no other solution is found.

[codecov]

Codecov Report

❌ Patch coverage is 50.88496% with 111 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
anndata-zarr/src/anndata.ts	34.82%	68 Missing and 5 partials ⚠️
anndata-zarr/src/hooks.ts	36.36%	35 Missing ⚠️
anndata-zarr/src/utils.ts	96.77%	1 Missing ⚠️
anndata-zarr/src/zarr.ts	91.66%	1 Missing ⚠️
viewer/src/io.ts	93.33%	1 Missing ⚠️

📢 Thoughts on this report? Let us know!