@vitessce/statistical-plots 3.4.8 → 3.4.10

package/dist/{deflate-9b949812.js → deflate-0e765bf3.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { B as BaseDecoder } from "./index-ff4d0660.js";
+import { B as BaseDecoder } from "./index-ce54e46a.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{index-ff4d0660.js → index-ce54e46a.js}

@@ -979,6 +979,7 @@ 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",
@@ -1019,6 +1020,18 @@ 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",
@@ -8968,6 +8981,9 @@ 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")
+});
 configSchema1_0_0.shape.coordinationSpace.unwrap();
 configSchema1_0_0.shape.layout.element.shape.coordinationScopes.unwrap();
 function upgradeReplaceViewProp(prefix2, view, coordinationSpace) {
@@ -9439,7 +9455,43 @@ 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: files2 } = datasetDef;
+    const newFiles = files2.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],
@@ -9457,7 +9509,8 @@ 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$7 = { exports: {} };
 const SEMVER_SPEC_VERSION$1 = "2.0.0";
@@ -11728,10 +11781,11 @@ 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];
     }
@@ -11816,7 +11870,7 @@ 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.'"),
@@ -11824,9 +11878,15 @@ 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;
@@ -11949,7 +12009,7 @@ z.object({
     scoreColumn: z.string().optional()
   }))
 });
-z.object({
+const anndataZarrSchema = z.object({
   obsLabels: z.union([
     annDataObsLabels,
     z.array(annDataConvenienceObsLabelsItem)
@@ -11959,7 +12019,7 @@ z.object({
     z.array(annDataConvenienceFeatureLabelsItem)
   ]),
   obsFeatureMatrix: annDataObsFeatureMatrix,
-  obsSets: annDataObsSets,
+  obsSets: annDataObsSetsArr,
   obsSpots: annDataObsSpots,
   obsPoints: annDataObsPoints,
   obsLocations: annDataObsLocations,
@@ -11970,6 +12030,9 @@ 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)?
@@ -133128,16 +133191,16 @@ function addDecoder(cases2, importFn) {
   }
   cases2.forEach((c2) => registry$1.set(c2, importFn));
 }
-addDecoder([void 0, 1], () => import("./raw-18214a1e.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-f9f89edb.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-57e07f3f.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-a4e25d69.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-9d65dc0f.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-9b949812.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-92275192.js").then((m2) => m2.default));
-addDecoder(34887, () => import("./lerc-5d951898.js").then((m2) => m2.default));
-addDecoder(50001, () => import("./webimage-6f128314.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-0907c241.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-0e765bf3.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-b0989382.js").then((m2) => m2.default));
+addDecoder(34887, () => import("./lerc-28ed0c74.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-21c51b36.js").then((m2) => m2.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset5 = 0;

package/dist/index.js

@@ -1,4 +1,4 @@
-import { c, C, b, a, e, D, d, E, F } from "./index-ff4d0660.js";
+import { c, C, b, a, e, D, d, E, F } from "./index-ce54e46a.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{jpeg-9d65dc0f.js → jpeg-0907c241.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ff4d0660.js";
+import { B as BaseDecoder } from "./index-ce54e46a.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lerc-5d951898.js → lerc-28ed0c74.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-ff4d0660.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-ce54e46a.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lzw-f9f89edb.js → lzw-a4e25d69.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ff4d0660.js";
+import { B as BaseDecoder } from "./index-ce54e46a.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{packbits-92275192.js → packbits-b0989382.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ff4d0660.js";
+import { B as BaseDecoder } from "./index-ce54e46a.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{raw-18214a1e.js → raw-57e07f3f.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ff4d0660.js";
+import { B as BaseDecoder } from "./index-ce54e46a.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{webimage-6f128314.js → webimage-21c51b36.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ff4d0660.js";
+import { B as BaseDecoder } from "./index-ce54e46a.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/statistical-plots",
-  "version": "3.4.8",
+  "version": "3.4.10",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -28,12 +28,12 @@
     "react-aria": "^3.28.0",
     "internmap": "^2.0.3",
     "uuid": "^9.0.0",
-    "@vitessce/constants-internal": "3.4.8",
-    "@vitessce/sets-utils": "3.4.8",
-    "@vitessce/utils": "3.4.8",
-    "@vitessce/vega": "3.4.8",
-    "@vitessce/vit-s": "3.4.8",
-    "@vitessce/gl": "3.4.8"
+    "@vitessce/constants-internal": "3.4.10",
+    "@vitessce/sets-utils": "3.4.10",
+    "@vitessce/utils": "3.4.10",
+    "@vitessce/vega": "3.4.10",
+    "@vitessce/vit-s": "3.4.10",
+    "@vitessce/gl": "3.4.10"
   },
   "devDependencies": {
     "react": "^18.0.0",