Changed package structure to no langer have deck.gl as dependency

packages/file-types/spatial-zarr/package.json

@@ -26,25 +26,27 @@
     "dist-tsc"
   ],
   "scripts": {
-    "bundle": "pnpm exec vite build -c ../../../scripts/vite.config.mjs",
+    "bundle": "pnpm exec vite build -c ../../../scripts/vite.config2.mjs",
     "test": "pnpm exec vitest --run"
   },
   "dependencies": {
     "@vitessce/abstract": "workspace:*",
     "@vitessce/error": "workspace:*",
-    "@vitessce/gl": "workspace:*",
     "@vitessce/spatial-utils": "workspace:*",
     "@vitessce/image-utils": "workspace:*",
     "@vitessce/zarr": "workspace:*",
     "@vitessce/config": "workspace:*",
     "@vitessce/globals": "workspace:*",
+    "@math.gl/core": "catalog:",
     "d3-array": "catalog:",
     "lodash-es": "catalog:",
-    "zarrita": "catalog:",
     "apache-arrow": "catalog:",
     "parquet-wasm": "catalog:",
     "ol": "^10.2.1"
   },
+  "peerDependencies": {
+    "zarrita": "catalog:"
+  },
   "devDependencies": {
     "@vitessce/types": "workspace:*",
     "@zarrita/storage": "catalog:"

packages/file-types/spatial-zarr/src/ome-loaders/OmeZarrAsObsSegmentationsLoader.js

@@ -1,8 +1,8 @@
 import { CoordinationLevel as CL } from '@vitessce/config';
 import { LoaderResult } from '@vitessce/abstract';
-import { GLSL_COLORMAP_DEFAULT } from '@vitessce/gl';
-import OmeZarrLoader from './OmeZarrLoader.js';
 
+import OmeZarrLoader from './OmeZarrLoader.js';
+const GLSL_COLORMAP_DEFAULT = 'plasma';
 export default class OmeZarrAsObsSegmentationsLoader extends OmeZarrLoader {
   async load() {
     const { obsTypesFromChannelNames } = this.options || {};

packages/file-types/spatial-zarr/src/spatialdata-loaders/SpatialDataObsSegmentationsLoader.js

@@ -5,12 +5,12 @@ import { CoordinationLevel as CL } from '@vitessce/config';
 import {
   coordinateTransformationsToMatrixForSpatialData,
 } from '@vitessce/spatial-utils';
-import { GLSL_COLORMAP_DEFAULT, math } from '@vitessce/gl';
+import { Vector2 } from '@math.gl/core';
 import {
   OLD_SHAPES_DEFAULT_AXES,
   OLD_SHAPES_DEFAULT_COORDINATE_TRANSFORMATIONS,
 } from './old-defaults.js';
-
+const GLSL_COLORMAP_DEFAULT = 'plasma';
 function getGeometryPath(path) {
   return `${path}/geometry`;
 }
@@ -63,7 +63,7 @@ export default class SpatialDataObsSegmentationsLoader extends AbstractTwoStepLo
 
       // Apply transformation matrix to the coordinates
       const transformedCoords = polygons.map(polygon => polygon.map((coord) => {
-        const transformed = new math.Vector2(coord[0], coord[1])
+        const transformed = new Vector2(coord[0], coord[1])
           .transformAsPoint(modelMatrix);
         return [transformed[0], transformed[1]];
       }));

packages/file-types/spatial-zarr/src/spatialdata-loaders/SpatialDataObsSpotsLoader.js

@@ -6,7 +6,7 @@ import { CoordinationLevel as CL } from '@vitessce/config';
 import {
   coordinateTransformationsToMatrixForSpatialData,
 } from '@vitessce/spatial-utils';
-import { math } from '@vitessce/gl';
+import { Vector2 } from '@math.gl/core';
 import {
   OLD_SHAPES_DEFAULT_AXES,
   OLD_SHAPES_DEFAULT_COORDINATE_TRANSFORMATIONS,
@@ -86,7 +86,7 @@ export default class SpatialDataObsSpotsLoader extends AbstractTwoStepLoader {
       for (let i = 0; i < this.locations.shape[1]; i++) {
         const xCoord = this.locations.data[0][i];
         const yCoord = this.locations.data[1][i];
-        const transformed = new math.Vector2(xCoord, yCoord)
+        const transformed = new Vector2(xCoord, yCoord)
           .transformAsPoint(modelMatrix);
         // eslint-disable-next-line prefer-destructuring
         this.locations.data[0][i] = transformed[0];