@vitessce/vit-s 2.0.3 → 3.0.0

package/dist-tsc/errors/AbstractLoaderError.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"AbstractLoaderError.d.ts","sourceRoot":"","sources":["../../src/errors/AbstractLoaderError.js"],"names":[],"mappings":"AAAA;;;GAGG;AACH;IACE,0BAEC;IADC,aAAsB;IAIxB,sBAEC;CACF"}

package/dist-tsc/errors/AbstractLoaderError.js

@@ -0,0 +1,13 @@
+/**
+ * A loader error ancestor class containing a default constructor
+ * and a stub for the required warnInConsole() method.
+ */
+export default class AbstractLoaderError {
+    constructor(message) {
+        this.message = message;
+    }
+    // eslint-disable-next-line class-methods-use-this
+    warnInConsole() {
+        throw new Error('The warnInConsole() method has not been implemented.');
+    }
+}

package/dist-tsc/errors/DataSourceFetchError.d.ts

@@ -0,0 +1,8 @@
+export default class DataSourceFetchError extends AbstractLoaderError {
+    constructor(source: any, url: any, headers: any);
+    source: any;
+    url: any;
+    headers: any;
+}
+import AbstractLoaderError from "./AbstractLoaderError.js";
+//# sourceMappingURL=DataSourceFetchError.d.ts.map

package/dist-tsc/errors/DataSourceFetchError.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"DataSourceFetchError.d.ts","sourceRoot":"","sources":["../../src/errors/DataSourceFetchError.js"],"names":[],"mappings":"AAEA;IACE,iDAKC;IAHC,YAAoB;IACpB,SAAc;IACd,aAAsB;CAOzB"}

package/dist-tsc/errors/DataSourceFetchError.js

@@ -0,0 +1,13 @@
+import AbstractLoaderError from './AbstractLoaderError.js';
+export default class DataSourceFetchError extends AbstractLoaderError {
+    constructor(source, url, headers) {
+        super(`${source} Error HTTP Status fetching from ${url}`);
+        this.source = source;
+        this.url = url;
+        this.headers = headers;
+    }
+    warnInConsole() {
+        const { source, url, headers } = this;
+        console.warn(`${source} failed to fetch from ${url} with headers ${headers}`);
+    }
+}

package/dist-tsc/errors/DatasetNotFoundError.d.ts

@@ -0,0 +1,6 @@
+export default class DatasetNotFoundError extends AbstractLoaderError {
+    name: string;
+    datasetUid: any;
+}
+import AbstractLoaderError from "./AbstractLoaderError.js";
+//# sourceMappingURL=DatasetNotFoundError.d.ts.map

package/dist-tsc/errors/DatasetNotFoundError.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"DatasetNotFoundError.d.ts","sourceRoot":"","sources":["../../src/errors/DatasetNotFoundError.js"],"names":[],"mappings":"AAEA;IAGI,aAAkC;IAElC,gBAA4B;CAe/B"}

package/dist-tsc/errors/DatasetNotFoundError.js

@@ -0,0 +1,17 @@
+import AbstractLoaderError from './AbstractLoaderError.js';
+export default class DatasetNotFoundError extends AbstractLoaderError {
+    constructor(datasetUid) {
+        super(`Error finding dataset for ${datasetUid}. Please check that at least one dataset exists in the view config.`);
+        this.name = 'DatasetNotFoundError';
+        this.datasetUid = datasetUid;
+    }
+    warnInConsole() {
+        const { datasetUid, } = this;
+        if (datasetUid) {
+            console.warn(`Unable to find dataset for ${datasetUid}`);
+        }
+        else {
+            console.warn('No dataset uid specified.');
+        }
+    }
+}

package/dist-tsc/errors/LoaderNotFoundError.d.ts

@@ -0,0 +1,10 @@
+export default class LoaderNotFoundError extends AbstractLoaderError {
+    constructor(loaders: any, dataset: any, fileType: any, viewCoordinationValues: any);
+    name: string;
+    loaders: any;
+    dataset: any;
+    fileType: any;
+    viewCoordinationValues: any;
+}
+import AbstractLoaderError from "./AbstractLoaderError.js";
+//# sourceMappingURL=LoaderNotFoundError.d.ts.map

package/dist-tsc/errors/LoaderNotFoundError.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"LoaderNotFoundError.d.ts","sourceRoot":"","sources":["../../src/errors/LoaderNotFoundError.js"],"names":[],"mappings":"AAEA;IACE,oFAQC;IANC,aAAiC;IAEjC,aAAsB;IACtB,aAAsB;IACtB,cAAwB;IACxB,4BAAoD;CAavD"}

package/dist-tsc/errors/LoaderNotFoundError.js

@@ -0,0 +1,17 @@
+import AbstractLoaderError from './AbstractLoaderError.js';
+export default class LoaderNotFoundError extends AbstractLoaderError {
+    constructor(loaders, dataset, fileType, viewCoordinationValues) {
+        super(`Error: unable to find matching ${fileType} file in dataset ${dataset}.`);
+        this.name = 'LoaderNotFoundError';
+        this.loaders = loaders;
+        this.dataset = dataset;
+        this.fileType = fileType;
+        this.viewCoordinationValues = viewCoordinationValues;
+    }
+    warnInConsole() {
+        const { loaders, viewCoordinationValues, } = this;
+        console.warn(
+        // eslint-disable-next-line prefer-template
+        `Expected to match on { ${Object.entries(viewCoordinationValues).map(([k, v]) => k + ': ' + v).join(', ')} }`, loaders);
+    }
+}

package/dist-tsc/errors/LoaderValidationError.d.ts

@@ -0,0 +1,10 @@
+export default class LoaderValidationError extends AbstractLoaderError {
+    constructor(datasetType: any, datasetFileType: any, datasetUrl: any, reason: any);
+    name: string;
+    datasetType: any;
+    datasetFileType: any;
+    datasetUrl: any;
+    reason: any;
+}
+import AbstractLoaderError from "./AbstractLoaderError.js";
+//# sourceMappingURL=LoaderValidationError.d.ts.map

package/dist-tsc/errors/LoaderValidationError.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"LoaderValidationError.d.ts","sourceRoot":"","sources":["../../src/errors/LoaderValidationError.js"],"names":[],"mappings":"AAEA;IACE,kFAQC;IANC,aAAmC;IAEnC,iBAA8B;IAC9B,qBAAsC;IACtC,gBAA4B;IAC5B,YAAoB;CAYvB"}

package/dist-tsc/errors/LoaderValidationError.js

@@ -0,0 +1,15 @@
+import AbstractLoaderError from './AbstractLoaderError.js';
+export default class LoaderValidationError extends AbstractLoaderError {
+    constructor(datasetType, datasetFileType, datasetUrl, reason) {
+        super(`Error while validating ${datasetType}.`);
+        this.name = 'LoaderValidationError';
+        this.datasetType = datasetType;
+        this.datasetFileType = datasetFileType;
+        this.datasetUrl = datasetUrl;
+        this.reason = reason;
+    }
+    warnInConsole() {
+        const { datasetType, datasetUrl, reason, } = this;
+        console.warn(`${datasetType} from ${datasetUrl}: validation failed`, JSON.stringify(reason, null, 2));
+    }
+}

package/dist-tsc/errors/index.d.ts

@@ -0,0 +1,6 @@
+export { default as AbstractLoaderError } from "./AbstractLoaderError.js";
+export { default as LoaderValidationError } from "./LoaderValidationError.js";
+export { default as LoaderNotFoundError } from "./LoaderNotFoundError.js";
+export { default as DatasetNotFoundError } from "./DatasetNotFoundError.js";
+export { default as DataSourceFetchError } from "./DataSourceFetchError.js";
+//# sourceMappingURL=index.d.ts.map

package/dist-tsc/errors/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/errors/index.js"],"names":[],"mappings":""}

package/dist-tsc/errors/index.js

@@ -0,0 +1,5 @@
+export { default as AbstractLoaderError } from './AbstractLoaderError.js';
+export { default as LoaderValidationError } from './LoaderValidationError.js';
+export { default as LoaderNotFoundError } from './LoaderNotFoundError.js';
+export { default as DatasetNotFoundError } from './DatasetNotFoundError.js';
+export { default as DataSourceFetchError } from './DataSourceFetchError.js';

package/dist-tsc/hooks.d.ts

@@ -0,0 +1,80 @@
+export function useVitessceContainer(ref: any): any;
+/**
+ * Custom hook, gets the full window dimensions.
+ * @returns {array} `[width, height]` where width and height
+ * are numbers.
+ */
+export function useWindowDimensions(): array;
+/**
+ * Custom hook, subscribes to GRID_RESIZE and window resize events.
+ * @returns {array} `[width, height, containerRef]` where width and height
+ * are numbers and containerRef is a React ref.
+ */
+export function useGridItemSize(): array;
+/**
+ * Custom hook, subscribes to GRID_RESIZE and window resize events.
+ * @returns {array} `[width, height, deckRef]` where width and height
+ * are numbers and deckRef is a React ref to be used with
+ * a <DeckGL/> element (or a forwardRef to one).
+ */
+export function useDeckCanvasSize(): array;
+/**
+ * This hook handles a boolean isReady value,
+ * which only returns true once every item in the
+ * input list has been marked as "ready".
+ * @param {string[]} statusValues The items to wait on.
+ * @returns {boolean} Whether the status values are all success.
+ */
+export function useReady(statusValues: string[]): boolean;
+/**
+ * This hook helps manage a list of URLs.
+ * @param {object} loaders The loaders dependency.
+ * @param {string} dataset The dataset UID dependency.
+ * @returns {array} An array
+ * [urls, addUrl]
+ * where urls is the array of URL objects,
+ * and addUrl is a function for adding a URL to the array.
+ */
+export function useUrls(loaders: object, dataset: string): array;
+/**
+ * Custom hook, subscribes to the width and height of the closest .vitessce-container
+ * element and updates upon window resize events.
+ * @param {Ref} ref A React ref object within the `.vitessce-container`.
+ * @returns {array} `[width, height]` where width and height
+ * are numbers.
+ */
+export function useClosestVitessceContainerSize(ref: Ref): array;
+/**
+ * Normalize an obsFeatureMatrix to a Uint8Array.
+ * @param {object} params
+ * @param {object} params.obsFeatureMatrix The obsFeatureMatrix
+ * returned by the useObsFeatureMatrix hook.
+ * @returns {array} A tuple [obsFeatureMatrix, dataExtent]
+ * where obsFeatureMatrix
+ * is a Uint8Array with the same shape as
+ * params.obsFeatureMatrix.data, and dataExtent is the
+ * [min, max] of the original data.
+ */
+export function useUint8ObsFeatureMatrix({ obsFeatureMatrix }: {
+    obsFeatureMatrix: object;
+}): array;
+/**
+ * Normalize a feature selection (data for selected
+ * columns of an obsFeatureMatrix) to a Uint8Array.
+ * @param {array|null} expressionData The expressionData
+ * returned by the useFeatureSelection hook,
+ * where each element corresponds to an
+ * array of values for a selected feature.
+ * @returns {array} A tuple [normData, extents] where
+ * normData is an array of Uint8Arrays (or null), and extents is
+ * an array of [min, max] values for each feature (or null).
+ */
+export function useUint8FeatureSelection(expressionData: array | null): array;
+export function useExpressionValueGetter({ instanceObsIndex, matrixObsIndex, expressionData }: {
+    instanceObsIndex: any;
+    matrixObsIndex: any;
+    expressionData: any;
+}): any;
+export function useGetObsMembership(obsSetsMembership: any): any;
+export function useGetObsInfo(obsType: any, obsLabelsTypes: any, obsLabelsData: any, obsSetsMembership: any): any;
+//# sourceMappingURL=hooks.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"hooks.d.ts","sourceRoot":"","sources":["../src/hooks.js"],"names":[],"mappings":"AAiBA,oDAOC;AAED;;;;GAIG;AACH,6CAgBC;AAED;;;;GAIG;AACH,yCAiCC;AAED;;;;;GAKG;AACH,2CAiCC;AAED;;;;;;GAMG;AACH,uCAHW,MAAM,EAAE,GACN,OAAO,CAOnB;AAED;;;;;;;;GAQG;AACH,iCAPW,MAAM,WACN,MAAM,SAoBhB;AAED;;;;;;GAMG;AACH,iEAuBC;AAED;;;;;;;;;;GAUG;AACH;IAR0B,gBAAgB,EAA/B,MAAM;UAqBhB;AAED;;;;;;;;;;GAUG;AACH,yDARW,QAAM,IAAI,SAuBpB;AAED;;;;QA2BC;AAED,iEAOC;AAED,kHAuBC"}

package/dist-tsc/hooks.js

@@ -0,0 +1,271 @@
+import { useRef, useState, useEffect, useCallback, useMemo, } from 'react';
+import { debounce, every } from 'lodash-es';
+import { extent } from 'd3-array';
+import { capitalize, fromEntries } from '@vitessce/utils';
+import { useGridResize, useEmitGridResize } from './state/hooks.js';
+import { VITESSCE_CONTAINER } from './classNames.js';
+function getWindowDimensions() {
+    const { innerWidth: width, innerHeight: height } = window;
+    return {
+        width,
+        height,
+    };
+}
+export function useVitessceContainer(ref) {
+    return useCallback(() => {
+        if (ref.current) {
+            return ref.current.closest(`.${VITESSCE_CONTAINER}`);
+        }
+        return null;
+    }, [ref]);
+}
+/**
+ * Custom hook, gets the full window dimensions.
+ * @returns {array} `[width, height]` where width and height
+ * are numbers.
+ */
+export function useWindowDimensions() {
+    const [windowDimensions, setWindowDimensions] = useState(getWindowDimensions());
+    useEffect(() => {
+        function handleResize() {
+            setWindowDimensions(getWindowDimensions());
+        }
+        const onResizeDebounced = debounce(handleResize, 100, { trailing: true });
+        window.addEventListener('resize', onResizeDebounced);
+        return () => window.removeEventListener('resize', onResizeDebounced);
+    }, []);
+    return windowDimensions;
+}
+/**
+ * Custom hook, subscribes to GRID_RESIZE and window resize events.
+ * @returns {array} `[width, height, containerRef]` where width and height
+ * are numbers and containerRef is a React ref.
+ */
+export function useGridItemSize() {
+    const containerRef = useRef();
+    const [height, setHeight] = useState();
+    const [width, setWidth] = useState();
+    const resizeCount = useGridResize();
+    const incrementResizeCount = useEmitGridResize();
+    // On window resize events, increment the grid resize count.
+    useEffect(() => {
+        function onWindowResize() {
+            incrementResizeCount();
+        }
+        const onResizeDebounced = debounce(onWindowResize, 100, { trailing: true });
+        window.addEventListener('resize', onResizeDebounced);
+        onWindowResize();
+        return () => {
+            window.removeEventListener('resize', onResizeDebounced);
+        };
+    }, [incrementResizeCount]);
+    // On new grid resize counts, re-compute the component
+    // width/height.
+    useEffect(() => {
+        if (!containerRef.current)
+            return;
+        const container = containerRef.current;
+        const containerRect = container.getBoundingClientRect();
+        setHeight(containerRect.height);
+        setWidth(containerRect.width);
+    }, [resizeCount]);
+    return [width, height, containerRef];
+}
+/**
+ * Custom hook, subscribes to GRID_RESIZE and window resize events.
+ * @returns {array} `[width, height, deckRef]` where width and height
+ * are numbers and deckRef is a React ref to be used with
+ * a <DeckGL/> element (or a forwardRef to one).
+ */
+export function useDeckCanvasSize() {
+    const deckRef = useRef();
+    const [height, setHeight] = useState();
+    const [width, setWidth] = useState();
+    const resizeCount = useGridResize();
+    const incrementResizeCount = useEmitGridResize();
+    // On window resize events, increment the grid resize count.
+    useEffect(() => {
+        function onWindowResize() {
+            incrementResizeCount();
+        }
+        const onResizeDebounced = debounce(onWindowResize, 100, { trailing: true });
+        window.addEventListener('resize', onResizeDebounced);
+        onWindowResize();
+        return () => {
+            window.removeEventListener('resize', onResizeDebounced);
+        };
+    }, [incrementResizeCount]);
+    // On new grid resize counts, re-compute the DeckGL canvas
+    // width/height.
+    useEffect(() => {
+        if (!deckRef.current)
+            return;
+        const { canvas } = deckRef.current.deck;
+        const canvasRect = canvas.getBoundingClientRect();
+        setHeight(canvasRect.height);
+        setWidth(canvasRect.width);
+    }, [resizeCount]);
+    return [width, height, deckRef];
+}
+/**
+ * This hook handles a boolean isReady value,
+ * which only returns true once every item in the
+ * input list has been marked as "ready".
+ * @param {string[]} statusValues The items to wait on.
+ * @returns {boolean} Whether the status values are all success.
+ */
+export function useReady(statusValues) {
+    return useMemo(() => every(statusValues, val => val === 'success'), statusValues);
+}
+/**
+ * This hook helps manage a list of URLs.
+ * @param {object} loaders The loaders dependency.
+ * @param {string} dataset The dataset UID dependency.
+ * @returns {array} An array
+ * [urls, addUrl]
+ * where urls is the array of URL objects,
+ * and addUrl is a function for adding a URL to the array.
+ */
+export function useUrls(loaders, dataset) {
+    const [urls, setUrls] = useState([]);
+    const addUrl = useCallback((url, name) => {
+        if (url) {
+            setUrls(prev => ([...prev, { url, name }]));
+        }
+    }, [setUrls]);
+    useEffect(() => {
+        setUrls([]);
+    }, [loaders, dataset]);
+    return [urls, addUrl];
+}
+/**
+ * Custom hook, subscribes to the width and height of the closest .vitessce-container
+ * element and updates upon window resize events.
+ * @param {Ref} ref A React ref object within the `.vitessce-container`.
+ * @returns {array} `[width, height]` where width and height
+ * are numbers.
+ */
+export function useClosestVitessceContainerSize(ref) {
+    const [height, setHeight] = useState();
+    const [width, setWidth] = useState();
+    useEffect(() => {
+        function onWindowResize() {
+            if (ref.current) {
+                const { clientHeight: componentHeight, clientWidth: componentWidth, } = ref.current.closest(`.${VITESSCE_CONTAINER}`);
+                setWidth(componentWidth);
+                setHeight(componentHeight);
+            }
+        }
+        const onResizeDebounced = debounce(onWindowResize, 100, { trailing: true });
+        window.addEventListener('resize', onResizeDebounced);
+        onWindowResize();
+        return () => {
+            window.removeEventListener('resize', onResizeDebounced);
+        };
+    }, [ref]);
+    return [width, height];
+}
+/**
+ * Normalize an obsFeatureMatrix to a Uint8Array.
+ * @param {object} params
+ * @param {object} params.obsFeatureMatrix The obsFeatureMatrix
+ * returned by the useObsFeatureMatrix hook.
+ * @returns {array} A tuple [obsFeatureMatrix, dataExtent]
+ * where obsFeatureMatrix
+ * is a Uint8Array with the same shape as
+ * params.obsFeatureMatrix.data, and dataExtent is the
+ * [min, max] of the original data.
+ */
+export function useUint8ObsFeatureMatrix({ obsFeatureMatrix }) {
+    return useMemo(() => {
+        if (obsFeatureMatrix && obsFeatureMatrix.data) {
+            const dataExtent = extent(obsFeatureMatrix.data);
+            const [min, max] = dataExtent;
+            const ratio = 255 / (max - min);
+            const data = new Uint8Array(obsFeatureMatrix.data.map(i => Math.floor((i - min) * ratio)));
+            return [{ data }, dataExtent];
+        }
+        return [null, null];
+    }, [obsFeatureMatrix]);
+}
+/**
+ * Normalize a feature selection (data for selected
+ * columns of an obsFeatureMatrix) to a Uint8Array.
+ * @param {array|null} expressionData The expressionData
+ * returned by the useFeatureSelection hook,
+ * where each element corresponds to an
+ * array of values for a selected feature.
+ * @returns {array} A tuple [normData, extents] where
+ * normData is an array of Uint8Arrays (or null), and extents is
+ * an array of [min, max] values for each feature (or null).
+ */
+export function useUint8FeatureSelection(expressionData) {
+    return useMemo(() => {
+        if (expressionData && expressionData[0]) {
+            const extents = expressionData.map(arr => extent(arr));
+            const normData = expressionData.map((arr, i) => {
+                const [min, max] = extents[i];
+                const ratio = 255 / (max - min);
+                return new Uint8Array(arr.map(j => Math.floor((j - min) * ratio)));
+            });
+            return [normData, extents];
+        }
+        return [null, null];
+    }, [expressionData]);
+}
+export function useExpressionValueGetter({ instanceObsIndex, matrixObsIndex, expressionData }) {
+    // Get a mapping from cell ID to row index in the gene expression matrix.
+    // Since the two obsIndices (instanceObsIndex = the obsIndex from obsEmbedding)
+    // may be ordered differently (matrixObsIndex = the obsIndex from obsFeatureMatrix),
+    // we need a way to look up an obsFeatureMatrix obsIndex index
+    // given an obsEmbedding obsIndex index.
+    const toMatrixIndexMap = useMemo(() => {
+        if (instanceObsIndex && matrixObsIndex) {
+            const matrixIndexMap = new Map(matrixObsIndex.map((key, i) => ([key, i])));
+            return instanceObsIndex.map(key => matrixIndexMap.get(key));
+        }
+        return null;
+    }, [instanceObsIndex, matrixObsIndex]);
+    // Set up a getter function for gene expression values, to be used
+    // by the DeckGL layer to obtain values for instanced attributes.
+    const getExpressionValue = useCallback((entry, { index: instanceIndex }) => {
+        if (toMatrixIndexMap && expressionData && expressionData[0]) {
+            const rowIndex = toMatrixIndexMap[instanceIndex];
+            const val = expressionData[0][rowIndex];
+            return val;
+        }
+        return 0;
+    }, [toMatrixIndexMap, expressionData]);
+    return getExpressionValue;
+}
+export function useGetObsMembership(obsSetsMembership) {
+    return useCallback((obsId) => {
+        if (obsId) {
+            return obsSetsMembership?.get(obsId) || [];
+        }
+        return [];
+    }, [obsSetsMembership]);
+}
+export function useGetObsInfo(obsType, obsLabelsTypes, obsLabelsData, obsSetsMembership) {
+    return useCallback((obsId) => {
+        if (obsId) {
+            const obsMembership = obsSetsMembership?.get(obsId) || [];
+            return {
+                [`${capitalize(obsType)} ID`]: obsId,
+                ...fromEntries(obsMembership.flatMap(path => path.slice(1).map((pathEl, elLevel) => ([
+                    `${path[0]}${path.length > 2 ? ` L${elLevel + 1}` : ''}`,
+                    pathEl,
+                ])))),
+                ...fromEntries(Object.entries(obsLabelsTypes).map(([scopeKey, obsLabelsType]) => ([
+                    obsLabelsType,
+                    obsLabelsData?.[scopeKey]?.obsLabels?.[
+                    // TODO: Maybe all loaders that return obsIndex should also return an obsIndexMap
+                    // with keys: obsId, values: obsIdx
+                    // which would avoid the indexOf calls.
+                    obsLabelsData?.[scopeKey]?.obsIndex?.indexOf(obsId)],
+                ])).filter(([obsLabelsType]) => Boolean(obsLabelsType))),
+            };
+        }
+        return null;
+    }, [obsType, obsLabelsTypes, obsLabelsData, obsSetsMembership]);
+}

package/dist-tsc/index.d.ts

@@ -0,0 +1,11 @@
+export { VitS } from "./VitS.js";
+export { TitleInfo } from "./TitleInfo.js";
+export { PopperMenu } from "./shared-mui/components.js";
+export { useHasLoader } from "./data-hook-utils.js";
+export { useReady, useUrls, useVitessceContainer, useDeckCanvasSize, useUint8ObsFeatureMatrix, useUint8FeatureSelection, useExpressionValueGetter, useGetObsMembership, useGetObsInfo, useClosestVitessceContainerSize, useWindowDimensions, useGridItemSize } from "./hooks.js";
+export { useCoordination, useComplexCoordination, useMultiCoordinationValues, useMultiDatasetCoordination, useDatasetUids, useLoaders, useMatchingLoader, useViewConfigStore, useViewConfigStoreApi, useComponentHover, useSetComponentHover, useComponentViewInfo, useSetComponentViewInfo, useWarning, useSetWarning, useAuxiliaryCoordination, useComponentLayout } from "./state/hooks.js";
+export { useDescription, useImageData, useObsSetsData, useObsEmbeddingData, useFeatureSelection, useObsFeatureMatrixIndices, useMultiObsLabels, useObsLocationsData, useObsSegmentationsData, useNeighborhoodsData, useObsLabelsData, useObsFeatureMatrixData, useFeatureLabelsData, useGenomicProfilesData } from "./data-hooks.js";
+export { AbstractLoader, AbstractTwoStepLoader, LoaderResult } from "./data/index.js";
+export { AbstractLoaderError, DatasetNotFoundError, LoaderNotFoundError, LoaderValidationError, DataSourceFetchError } from "./errors/index.js";
+export { CellColorEncodingOption, OptionsContainer, OptionSelect, usePlotOptionsStyles } from "./shared-plot-options/index.js";
+//# sourceMappingURL=index.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.js"],"names":[],"mappings":""}

package/dist-tsc/index.js

@@ -1,18 +1,11 @@
-export { VitS } from './VitS';
-export { TitleInfo } from './TitleInfo';
-export { PopperMenu } from './shared-mui/components';
-export { registerPluginViewType, registerPluginCoordinationType, registerPluginFileType, registerPluginJointFileType, } from './plugins';
+export { VitS } from './VitS.js';
+export { TitleInfo } from './TitleInfo.js';
+export { PopperMenu } from './shared-mui/components.js';
 // For plugin view types:
-export { useReady, useUrls, useVitessceContainer, useDeckCanvasSize, useExpressionValueGetter, useGetObsInfo, useClosestVitessceContainerSize, useWindowDimensions, useGridItemSize, } from './hooks';
-export { useCoordination, useComplexCoordination, useMultiCoordinationValues, useMultiDatasetCoordination, useDatasetUids, useLoaders, useMatchingLoader, useViewConfigStore, useViewConfigStoreApi, useComponentHover, useSetComponentHover, useComponentViewInfo, useSetComponentViewInfo, useWarning, useSetWarning, useAuxiliaryCoordination, useComponentLayout, } from './state/hooks';
-export { useDescription, useImageData, useObsSetsData, useObsEmbeddingData, useFeatureSelection, useObsFeatureMatrixIndices, useMultiObsLabels, useObsLocationsData, useObsSegmentationsData, useNeighborhoodsData, useObsLabelsData, useObsFeatureMatrixData, useFeatureLabelsData, useGenomicProfilesData, } from './data-hooks';
-export { useHasLoader, } from './data-hook-utils';
-export { AbstractLoader, AbstractTwoStepLoader, LoaderResult, } from './data/index';
-export { AbstractLoaderError, DatasetNotFoundError, LoaderNotFoundError, LoaderValidationError, OptionsValidationError, DataSourceFetchError, } from './errors/index';
-export { 
-// TODO(monorepo): should these be in here? or within file-types/
-obsEmbeddingAnndataSchema, obsLocationsAnndataSchema, obsSegmentationsAnndataSchema, obsSetsAnndataSchema, obsFeatureMatrixAnndataSchema, obsLabelsAnndataSchema, featureLabelsAnndataSchema, obsEmbeddingCsvSchema, obsLocationsCsvSchema, obsLabelsCsvSchema, featureLabelsCsvSchema, obsSetsCsvSchema, anndataZarrSchema, emptySchema, } from './file-options-schemas';
-export { SCHEMA_HANDLERS, LATEST_VERSION, } from './view-config-versions';
-export { upgradeAndValidate, } from './view-config-utils';
-export { CellColorEncodingOption, OptionsContainer, OptionSelect, usePlotOptionsStyles, } from './shared-plot-options';
-export * from './json-schemas';
+export { useReady, useUrls, useVitessceContainer, useDeckCanvasSize, useUint8ObsFeatureMatrix, useUint8FeatureSelection, useExpressionValueGetter, useGetObsMembership, useGetObsInfo, useClosestVitessceContainerSize, useWindowDimensions, useGridItemSize, } from './hooks.js';
+export { useCoordination, useComplexCoordination, useMultiCoordinationValues, useMultiDatasetCoordination, useDatasetUids, useLoaders, useMatchingLoader, useViewConfigStore, useViewConfigStoreApi, useComponentHover, useSetComponentHover, useComponentViewInfo, useSetComponentViewInfo, useWarning, useSetWarning, useAuxiliaryCoordination, useComponentLayout, } from './state/hooks.js';
+export { useDescription, useImageData, useObsSetsData, useObsEmbeddingData, useFeatureSelection, useObsFeatureMatrixIndices, useMultiObsLabels, useObsLocationsData, useObsSegmentationsData, useNeighborhoodsData, useObsLabelsData, useObsFeatureMatrixData, useFeatureLabelsData, useGenomicProfilesData, } from './data-hooks.js';
+export { useHasLoader, } from './data-hook-utils.js';
+export { AbstractLoader, AbstractTwoStepLoader, LoaderResult, } from './data/index.js';
+export { AbstractLoaderError, DatasetNotFoundError, LoaderNotFoundError, LoaderValidationError, DataSourceFetchError, } from './errors/index.js';
+export { CellColorEncodingOption, OptionsContainer, OptionSelect, usePlotOptionsStyles, } from './shared-plot-options/index.js';

package/dist-tsc/plugins.test.fixtures.d.ts

@@ -0,0 +1,61 @@
+export function pluginExpandAnnDataConvenience(fileDef: any): {
+    fileType: string;
+    url: any;
+    options: any;
+}[];
+export namespace convenienceFileDefsCollapsed {
+    const version: string;
+    const name: string;
+    const description: string;
+    const initStrategy: string;
+    const datasets: {
+        files: {
+            fileType: string;
+            url: string;
+            options: {
+                cells: {
+                    xy: string;
+                };
+                cellSets: {
+                    groupName: string;
+                    setName: string;
+                }[];
+            };
+        }[];
+        name: string;
+        uid: string;
+    }[];
+    const layout: never[];
+}
+export namespace convenienceFileDefsExpanded {
+    const version_1: string;
+    export { version_1 as version };
+    const name_1: string;
+    export { name_1 as name };
+    const description_1: string;
+    export { description_1 as description };
+    const initStrategy_1: string;
+    export { initStrategy_1 as initStrategy };
+    const datasets_1: {
+        files: ({
+            fileType: string;
+            url: string;
+            options: {
+                xy: string;
+            };
+        } | {
+            fileType: string;
+            url: string;
+            options: {
+                groupName: string;
+                setName: string;
+            }[];
+        })[];
+        name: string;
+        uid: string;
+    }[];
+    export { datasets_1 as datasets };
+    const layout_1: never[];
+    export { layout_1 as layout };
+}
+//# sourceMappingURL=plugins.test.fixtures.d.ts.map

package/dist-tsc/plugins.test.fixtures.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"plugins.test.fixtures.d.ts","sourceRoot":"","sources":["../src/plugins.test.fixtures.js"],"names":[],"mappings":"AA+BA;;;;IAaC"}