@vitessce/vit-s 3.4.9 → 3.4.10

package/dist/index.js

@@ -24826,6 +24826,9 @@ const configSchema1_0_16 = configSchema1_0_13.extend({
     coordinationScopesBy: componentCoordinationScopesBy.optional()
   }))
 });
+const configSchema1_0_17 = configSchema1_0_16.extend({
+  version: z.literal("1.0.17")
+});
 let getRandomValues;
 const rnds8 = new Uint8Array(16);
 function rng() {
@@ -25739,7 +25742,43 @@ function upgradeFrom1_0_15(config2) {
     version: "1.0.16"
   };
 }
-const latestConfigSchema = configSchema1_0_16;
+function upgradeFrom1_0_16(config2) {
+  const newConfig = cloneDeep(config2);
+  const { datasets } = newConfig;
+  const newDatasets = datasets.map((datasetDef) => {
+    const { files } = datasetDef;
+    const newFiles = files.map((fileDef) => {
+      const { fileType, options } = fileDef;
+      if (fileType === "obsSets.anndata.zarr") {
+        return {
+          ...fileDef,
+          options: {
+            obsSets: options
+          }
+        };
+      }
+      if (fileType === "obsFeatureColumns.anndata.zarr") {
+        return {
+          ...fileDef,
+          options: {
+            obsFeatureColumns: options
+          }
+        };
+      }
+      return fileDef;
+    });
+    return {
+      ...datasetDef,
+      files: newFiles
+    };
+  });
+  return {
+    ...newConfig,
+    datasets: newDatasets,
+    version: "1.0.17"
+  };
+}
+const latestConfigSchema = configSchema1_0_17;
 const SCHEMA_HANDLERS = [
   [configSchema0_1_0, upgradeFrom0_1_0],
   [configSchema1_0_0, upgradeFrom1_0_0],
@@ -25757,7 +25796,8 @@ const SCHEMA_HANDLERS = [
   [configSchema1_0_12, upgradeFrom1_0_12],
   [configSchema1_0_13, upgradeFrom1_0_13],
   [configSchema1_0_14, upgradeFrom1_0_14],
-  [configSchema1_0_15, upgradeFrom1_0_15]
+  [configSchema1_0_15, upgradeFrom1_0_15],
+  [configSchema1_0_16, upgradeFrom1_0_16]
 ];
 var re$3 = { exports: {} };
 const SEMVER_SPEC_VERSION = "2.0.0";
@@ -27903,6 +27943,7 @@ const FileType$1 = {
   // Joint file types
   ANNDATA_ZARR: "anndata.zarr",
   ANNDATA_ZARR_ZIP: "anndata.zarr.zip",
+  ANNDATA_H5AD: "anndata.h5ad",
   SPATIALDATA_ZARR: "spatialdata.zarr",
   // Atomic file types
   OBS_EMBEDDING_CSV: "obsEmbedding.csv",
@@ -27943,6 +27984,18 @@ const FileType$1 = {
   OBS_LABELS_ANNDATA_ZARR_ZIP: "obsLabels.anndata.zarr.zip",
   FEATURE_LABELS_ANNDATA_ZARR_ZIP: "featureLabels.anndata.zarr.zip",
   SAMPLE_EDGES_ANNDATA_ZARR_ZIP: "sampleEdges.anndata.zarr.zip",
+  // AnnData - h5ad via reference spec
+  OBS_FEATURE_MATRIX_ANNDATA_H5AD: "obsFeatureMatrix.anndata.h5ad",
+  OBS_FEATURE_COLUMNS_ANNDATA_H5AD: "obsFeatureColumns.anndata.h5ad",
+  OBS_SETS_ANNDATA_H5AD: "obsSets.anndata.h5ad",
+  OBS_EMBEDDING_ANNDATA_H5AD: "obsEmbedding.anndata.h5ad",
+  OBS_SPOTS_ANNDATA_H5AD: "obsSpots.anndata.h5ad",
+  OBS_POINTS_ANNDATA_H5AD: "obsPoints.anndata.h5ad",
+  OBS_LOCATIONS_ANNDATA_H5AD: "obsLocations.anndata.h5ad",
+  OBS_SEGMENTATIONS_ANNDATA_H5AD: "obsSegmentations.anndata.h5ad",
+  OBS_LABELS_ANNDATA_H5AD: "obsLabels.anndata.h5ad",
+  FEATURE_LABELS_ANNDATA_H5AD: "featureLabels.anndata.h5ad",
+  SAMPLE_EDGES_ANNDATA_H5AD: "sampleEdges.anndata.h5ad",
   // SpatialData
   IMAGE_SPATIALDATA_ZARR: "image.spatialdata.zarr",
   LABELS_SPATIALDATA_ZARR: "labels.spatialdata.zarr",
@@ -28194,10 +28247,10 @@ const AUTO_INDEPENDENT_COORDINATION_TYPES = [
   CoordinationType$1.EMBEDDING_OBS_OPACITY
 ];
 const note = "This file is autogenerated by .changeset/post-changelog.mjs.";
-const version = "3.4.9";
-const date = "2024-07-26";
+const version = "3.4.10";
+const date = "2024-09-01";
 const branch = "changeset-release/main";
-const hash = "9582ddcf";
+const hash = "26b1c2d6";
 const META_VERSION = {
   note,
   version,
@@ -28369,10 +28422,11 @@ function makeConstantWithDeprecationMessage(currObj, oldObj) {
   const handler = {
     get(obj, prop) {
       const oldKeys = Object.keys(oldObj);
-      if (oldKeys.includes(prop)) {
-        console.warn(`Notice about the constant mapping ${prop}: '${oldObj[prop][0]}':
-${oldObj[prop][1]}`);
-        return oldObj[prop];
+      const propKey = String(prop);
+      if (oldKeys.includes(propKey)) {
+        console.warn(`Notice about the constant mapping ${propKey}: '${oldObj[propKey][0]}':
+${oldObj[propKey][1]}`);
+        return oldObj[propKey];
       }
       return obj[prop];
     }
@@ -28528,7 +28582,7 @@ const annDataObsFeatureMatrix = z.object({
   featureFilterPath: z.string().optional().describe("If the feature index should be filtered, put a boolean column here (analogous to the previous geneFilter option). e.g., var/in_obsm_X_small_matrix"),
   initialFeatureFilterPath: z.string().optional().describe("If only a subset of the matrix should be loaded initially, put a boolean column along the feature axis here (analogous to the previous matrixGeneFilter option). e.g., var/highly_variable")
 });
-const annDataObsSets = z.array(z.object({
+const annDataObsSetsArr = z.array(z.object({
   name: z.string().describe("The display name for the set, like 'Cell Type' or 'Louvain.'"),
   path: z.union([
     z.string().describe("The location in the AnnData store for the set, like 'obs/louvain' or 'obs/celltype.'"),
@@ -28536,9 +28590,15 @@ const annDataObsSets = z.array(z.object({
   ]),
   scorePath: z.string().optional().describe("The location in the AnnData store for the set confidence scores, like 'obs/celltype_prediction_score.'")
 }));
-z.array(z.object({
+const annDataObsSets = z.object({
+  obsSets: annDataObsSetsArr
+});
+const annDataObsFeatureColumnsArr = z.array(z.object({
   path: z.string()
 }));
+z.object({
+  obsFeatureColumns: annDataObsFeatureColumnsArr
+});
 const annDataObsSpots = annDataObsm;
 const annDataObsPoints = annDataObsm;
 const annDataObsLocations = annDataObsm;
@@ -28661,7 +28721,7 @@ z.object({
     scoreColumn: z.string().optional()
   }))
 });
-z.object({
+const anndataZarrSchema = z.object({
   obsLabels: z.union([
     annDataObsLabels,
     z.array(annDataConvenienceObsLabelsItem)
@@ -28671,7 +28731,7 @@ z.object({
     z.array(annDataConvenienceFeatureLabelsItem)
   ]),
   obsFeatureMatrix: annDataObsFeatureMatrix,
-  obsSets: annDataObsSets,
+  obsSets: annDataObsSetsArr,
   obsSpots: annDataObsSpots,
   obsPoints: annDataObsPoints,
   obsLocations: annDataObsLocations,
@@ -28682,6 +28742,9 @@ z.object({
   ]),
   sampleEdges: annDataSampleEdges
 }).partial();
+anndataZarrSchema.extend({
+  refSpecUrl: z.string()
+});
 z.object({
   // TODO: should `image` be a special schema
   // to allow specifying fileUid (like for embeddingType)?
@@ -36964,6 +37027,7 @@ function createLoaders(datasets, configDescription, fileTypes, coordinationTypes
           url,
           fileType,
           requestInit: requestInit2,
+          refSpecUrl: options == null ? void 0 : options.refSpecUrl,
           // Optionally, pass a Zarrita store to the data source,
           // if one was mapped to this URL.
           store: stores == null ? void 0 : stores[url]

package/dist-tsc/Warning.d.ts

@@ -1,2 +1,2 @@
-export function Warning(props: any): import("../../plugins/node_modules/@types/react/index.js").JSX.Element;
+export function Warning(props: any): import("react").JSX.Element;
 //# sourceMappingURL=Warning.d.ts.map

package/dist-tsc/Warning.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"Warning.d.ts","sourceRoot":"","sources":["../src/Warning.js"],"names":[],"mappings":"AAyCA,4GAoBC"}
+{"version":3,"file":"Warning.d.ts","sourceRoot":"","sources":["../src/Warning.js"],"names":[],"mappings":"AAyCA,iEAoBC"}

package/dist-tsc/state/hooks.d.ts

@@ -287,9 +287,9 @@ export function useEmitGridResize(): Function;
 export const ViewConfigProvider: ({ initialStore, createStore, children, }: {
     initialStore?: import("zustand").UseBoundStore<object> | undefined;
     createStore: () => import("zustand").UseBoundStore<object>;
-    children: import("../../../plugins/node_modules/@types/react/index.js").ReactNode;
-}) => import("../../../plugins/node_modules/@types/react/index.js").FunctionComponentElement<import("../../../plugins/node_modules/@types/react/index.js").ProviderProps<import("zustand").UseBoundStore<object> | undefined>>;
-export const useViewConfigStore: import("zustand/context.js").UseContextStore<object>;
+    children: import("react").ReactNode;
+}) => import("react").FunctionComponentElement<import("react").ProviderProps<import("zustand").UseBoundStore<object> | undefined>>;
+export const useViewConfigStore: import("zustand/context").UseContextStore<object>;
 export const useViewConfigStoreApi: () => {
     getState: import("zustand").GetState<object>;
     setState: import("zustand").SetState<object>;
@@ -299,9 +299,9 @@ export const useViewConfigStoreApi: () => {
 export const AuxiliaryProvider: ({ initialStore, createStore, children, }: {
     initialStore?: import("zustand").UseBoundStore<object> | undefined;
     createStore: () => import("zustand").UseBoundStore<object>;
-    children: import("../../../plugins/node_modules/@types/react/index.js").ReactNode;
-}) => import("../../../plugins/node_modules/@types/react/index.js").FunctionComponentElement<import("../../../plugins/node_modules/@types/react/index.js").ProviderProps<import("zustand").UseBoundStore<object> | undefined>>;
-export const useAuxiliaryStore: import("zustand/context.js").UseContextStore<object>;
+    children: import("react").ReactNode;
+}) => import("react").FunctionComponentElement<import("react").ProviderProps<import("zustand").UseBoundStore<object> | undefined>>;
+export const useAuxiliaryStore: import("zustand/context").UseContextStore<object>;
 export function createViewConfigStore(initialLoaders: any, initialConfig: any): Function;
 export function useComponentLayout(component: any, scopes: any, coordinationScopes: any): Object;
 export function createAuxiliaryStore(): Function;

package/dist-tsc/state/hooks.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"hooks.d.ts","sourceRoot":"","sources":["../../src/state/hooks.js"],"names":[],"mappings":"AAmCA;;;;;;GAMG;AACH,8CAJW,GAAC,mBAEC,MAAM,GAAC,SAAS,CA4B5B;AAED;;;;;;;GAOG;AACH,gDALW,GAAC,wBACD,GAAC,qBAEC,MAAM,GAAC,SAAS,CA0C5B;AAED;;;;;GAKG;AACH,6CAJW,MAAM,sBACN,GAAC,GACC,MAAM,GAAC,SAAS,CAI5B;AAED;;;;;;GAMG;AACH,+CALW,MAAM,mDACN,GAAC,wBACD,GAAC,GACC,MAAM,GAAC,SAAS,CAc5B;AA4RD;;;;;;;;;GASG;AACH,mDALW,MAAM,EAAE,sBACR,MAAM,GAEJ,MAAM,CAclB;AAED;;;;;;;;;;;;;;;GAeG;AACH,4CATW,MAAM,EAAE,sBACR,MAAM,GAEJ,KAAK,CAmCjB;AAED,yFAKC;AAED,gGAqBC;AAED,0IA4BC;AAED,iJAkEC;AAED,yFAmBC;AAED;;;;GAIG;AACH,mDAHW,MAAM,GACJ,MAAM,CAIlB;AAED;;;;;;;;;;;;;GAaG;AACH,mDAXW,MAAM,EAAE,sBACR,MAAM,wBACN,MAAM,UAEN,MAAM,GAEJ,KAAK,CA2EjB;AAED;;;;;GAKG;AACH,0DAHW,MAAM,GACJ,MAAM,CAiBlB;AAED;;;;;;GAMG;AACH,4DAJW,MAAM,wBACN,MAAM,GACJ,MAAM,CAgBlB;AAED;;;;;;;GAOG;AACH,4DANW,MAAM,EAAE,iDACR,MAAM,eACN,MAAM,iBACN,MAAM,SAuEhB;AAGD;;;;;;;;;;;GAWG;AACH,wDATW,MAAM,EAAE,sBACR,MAAM,wBACN,MAAM,GAEJ,KAAK,CAUjB;AA6BD;;;;;;;;;;;;;;;GAeG;AACH,qDATW,MAAM,EAAE,sBACR,MAAM,GAEJ,KAAK,CAgCjB;AAED;;;;;GAKG;AACH,8BAHa,MAAM,CAKlB;AAGD;;;;;;;;;;;;GAYG;AACH,2CARW,MAAM,WACN,MAAM,YACN,MAAM,0BACN,MAAM,OAoBhB;AAED;;;;;;;;;;;;GAYG;AACH,2CARW,MAAM,WACN,MAAM,YACN,MAAM,0BACN,MAAM,OAShB;AAED;;;;;GAKG;AACH,6BAHa,MAAM,EAAE,CAKpB;AAED;;;;;GAKG;AACH,+CAEC;AAED;;;;;GAKG;AACH,0EAEC;AAED;;;;;GAKG;AACH,uEAEC;AAED;;;;;GAKG;AACH,4CAEC;AAED;;;;;GAKG;AACH,0CAEC;AAED;;;;;GAKG;AACH,iDAEC;AAED;;;;;GAKG;AACH,oEAIC;AAED;;;;;GAKG;AACH,qCAHa,MAAM,CAKlB;AAED;;;;;GAKG;AACH,iDAEC;AAED;;;;;GAKG;AACH,8BAHa,MAAM,CAKlB;AAED;;;;;GAKG;AACH,0CAEC;AAED;;;;;GAKG;AACH,iDAHa,MAAM,CAKlB;AAED;;;;;GAKG;AACH,6DAOC;AAED;;;;GAIG;AACH,iCAFa,MAAM,CAIlB;AAED;;;;;GAKG;AACH,8CAEC;AA5oCD;;;;aAPG,OAAO,kCAAkC,OAAO,sEAOO;AAC1D,mFAA0D;AAC1D;;;;;EAAgE;AAOhE;;;;mIAAwD;AACxD,kFAAwD;AAiIjD,yFA+KJ;AAOI,0FAFM,MAAM,CAOlB;AAcM,iDAUJ"}

package/dist-tsc/vitessce-grid-utils.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"vitessce-grid-utils.d.ts","sourceRoot":"","sources":["../src/vitessce-grid-utils.js"],"names":[],"mappings":"AAyCA,gHA6CC;AA4BD;;;;;;;;;;GAUG;AACH,wCATW,MAAM,EAAE,qBACR,MAAM,aAEN,cAAc,EAAE,qBAChB,sBAAsB,EAAE,UACxB,MAAM,GACJ,MAAM,CA6DlB"}
+{"version":3,"file":"vitessce-grid-utils.d.ts","sourceRoot":"","sources":["../src/vitessce-grid-utils.js"],"names":[],"mappings":"AAyCA,gHA6CC;AA4BD;;;;;;;;;;GAUG;AACH,wCATW,MAAM,EAAE,qBACR,MAAM,aAEN,cAAc,EAAE,qBAChB,sBAAsB,EAAE,UACxB,MAAM,GACJ,MAAM,CA8DlB"}

package/dist-tsc/vitessce-grid-utils.js

@@ -132,6 +132,7 @@ export function createLoaders(datasets, configDescription, fileTypes, coordinati
                     url,
                     fileType,
                     requestInit,
+                    refSpecUrl: options?.refSpecUrl,
                     // Optionally, pass a Zarrita store to the data source,
                     // if one was mapped to this URL.
                     store: stores?.[url],

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/vit-s",
-  "version": "3.4.9",
+  "version": "3.4.10",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -29,12 +29,12 @@
     "uuid": "^9.0.0",
     "zustand": "^3.5.10",
     "react-aria": "^3.28.0",
-    "@vitessce/constants-internal": "3.4.9",
-    "@vitessce/plugins": "3.4.9",
-    "@vitessce/schemas": "3.4.9",
-    "@vitessce/utils": "3.4.9",
-    "@vitessce/sets-utils": "3.4.9",
-    "@vitessce/config": "3.4.9"
+    "@vitessce/constants-internal": "3.4.10",
+    "@vitessce/plugins": "3.4.10",
+    "@vitessce/schemas": "3.4.10",
+    "@vitessce/utils": "3.4.10",
+    "@vitessce/sets-utils": "3.4.10",
+    "@vitessce/config": "3.4.10"
   },
   "devDependencies": {
     "@testing-library/jest-dom": "^5.16.4",
@@ -42,7 +42,7 @@
     "react": "^18.0.0",
     "vite": "^4.3.0",
     "vitest": "^0.32.2",
-    "@vitessce/types": "3.4.9"
+    "@vitessce/types": "3.4.10"
   },
   "peerDependencies": {
     "react": "^16.8.0 || ^17.0.0 || ^18.0.0"

package/src/vitessce-grid-utils.js

@@ -164,6 +164,7 @@ export function createLoaders(datasets, configDescription, fileTypes, coordinati
           url,
           fileType,
           requestInit,
+          refSpecUrl: options?.refSpecUrl,
           // Optionally, pass a Zarrita store to the data source,
           // if one was mapped to this URL.
           store: stores?.[url],