@vitessce/all 2.0.3 → 3.0.0

package/dist/index.mjs

@@ -1,11 +0,0 @@
-import { V } from "./index.7dac8670.mjs";
-import { registerPluginCoordinationType, registerPluginFileType, registerPluginJointFileType, registerPluginViewType } from "@vitessce/vit-s";
-import "react";
-import "react-dom";
-export {
-  V as Vitessce,
-  registerPluginCoordinationType,
-  registerPluginFileType,
-  registerPluginJointFileType,
-  registerPluginViewType
-};

package/src/index.js

@@ -1,7 +0,0 @@
-export { Vitessce } from './setup';
-export {
-  registerPluginFileType,
-  registerPluginViewType,
-  registerPluginCoordinationType,
-  registerPluginJointFileType,
-} from '@vitessce/vit-s';

package/src/setup.js

@@ -1,143 +0,0 @@
-/* eslint-disable max-len */
-import { useState, useLayoutEffect } from 'react';
-import { VitS, registerPluginFileType } from '@vitessce/vit-s';
-
-// Register view type plugins
-import { register as registerDescription } from '@vitessce/description';
-import { register as registerObsSetsManager } from '@vitessce/obs-sets-manager';
-import { register as registerScatterplotEmbedding } from '@vitessce/scatterplot-embedding';
-import { register as registerScatterplotGating } from '@vitessce/scatterplot-gating';
-import { register as registerSpatial } from '@vitessce/spatial';
-import { register as registerHeatmap } from '@vitessce/heatmap';
-import { register as registerFeatureList } from '@vitessce/feature-list';
-import { register as registerLayerController } from '@vitessce/layer-controller';
-import { register as registerStatus } from '@vitessce/status';
-import { registerCellSetExpression, registerCellSetSizes, registerExpressionHistogram } from '@vitessce/statistical-plots';
-import { registerHiglass, registerGenomicProfiles } from '@vitessce/genomic-profiles';
-
-// Register file type plugins
-import {
-  // CSV
-  CsvSource,
-  ObsSetsCsvLoader,
-  ObsEmbeddingCsvLoader,
-  ObsLocationsCsvLoader,
-  ObsLabelsCsvLoader,
-  ObsFeatureMatrixCsvLoader,
-  FeatureLabelsCsvLoader,
-} from '@vitessce/csv';
-import {
-  // JSON
-  JsonSource,
-  JsonLoader,
-  ObsSegmentationsJsonLoader,
-  ObsSetsJsonLoader,
-  // Legacy
-  RasterJsonAsImageLoader,
-  RasterJsonAsObsSegmentationsLoader,
-  ClustersJsonAsObsFeatureMatrixLoader,
-  GenesJsonAsObsFeatureMatrixLoader,
-  CellsJsonAsObsLabelsLoader,
-  CellsJsonAsObsEmbeddingLoader,
-  CellsJsonAsObsLocationsLoader,
-  CellsJsonAsObsSegmentationsLoader,
-  MoleculesJsonAsObsLocationsLoader,
-  MoleculesJsonAsObsLabelsLoader,
-} from '@vitessce/json';
-import {
-  // AnnData
-  AnnDataSource,
-  ObsFeatureMatrixAnndataLoader,
-  ObsEmbeddingAnndataLoader,
-  ObsLocationsAnndataLoader,
-  ObsSegmentationsAnndataLoader,
-  ObsSetsAnndataLoader,
-  ObsLabelsAnndataLoader,
-  FeatureLabelsAnndataLoader,
-  // MuData
-  MuDataSource,
-  // OME
-  OmeZarrLoader,
-  // Legacy
-  ZarrDataSource,
-  MatrixZarrAsObsFeatureMatrixLoader,
-  GenomicProfilesZarrLoader,
-} from '@vitessce/zarr';
-import { FileType, DataType } from '@vitessce/constants-internal';
-
-function setup() {
-  // View types
-  registerDescription();
-  registerObsSetsManager();
-  registerScatterplotEmbedding();
-  registerScatterplotGating();
-  registerSpatial();
-  registerHeatmap();
-  registerFeatureList();
-  registerLayerController();
-  registerStatus();
-  // Statistical plots
-  registerCellSetExpression();
-  registerCellSetSizes();
-  registerExpressionHistogram();
-  // Higlass
-  registerHiglass();
-  registerGenomicProfiles();
-
-  // File types
-  // All CSV file types
-  registerPluginFileType(FileType.OBS_SETS_CSV, DataType.OBS_SETS, ObsSetsCsvLoader, CsvSource);
-  registerPluginFileType(FileType.OBS_EMBEDDING_CSV, DataType.OBS_EMBEDDING, ObsEmbeddingCsvLoader, CsvSource);
-  registerPluginFileType(FileType.OBS_LOCATIONS_CSV, DataType.OBS_LOCATIONS, ObsLocationsCsvLoader, CsvSource);
-  registerPluginFileType(FileType.OBS_LABELS_CSV, DataType.OBS_LABELS, ObsLabelsCsvLoader, CsvSource);
-  registerPluginFileType(FileType.OBS_FEATURE_MATRIX_CSV, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixCsvLoader, CsvSource);
-  registerPluginFileType(FileType.FEATURE_LABELS_CSV, DataType.FEATURE_LABELS, FeatureLabelsCsvLoader, CsvSource);
-  // All JSON file types
-  registerPluginFileType(FileType.OBS_SEGMENTATIONS_JSON, DataType.OBS_SEGMENTATIONS, ObsSegmentationsJsonLoader, JsonSource);
-  registerPluginFileType(FileType.OBS_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource);
-  // All AnnData file types
-  registerPluginFileType(FileType.OBS_SETS_ANNDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, AnnDataSource);
-  registerPluginFileType(FileType.OBS_EMBEDDING_ANNDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, AnnDataSource);
-  registerPluginFileType(FileType.OBS_LOCATIONS_ANNDATA_ZARR, DataType.OBS_LOCATIONS, ObsLocationsAnndataLoader, AnnDataSource);
-  registerPluginFileType(FileType.OBS_LABELS_ANNDATA_ZARR, DataType.OBS_LABELS, ObsLabelsAnndataLoader, AnnDataSource);
-  registerPluginFileType(FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, AnnDataSource);
-  registerPluginFileType(FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, AnnDataSource);
-  registerPluginFileType(FileType.FEATURE_LABELS_ANNDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, AnnDataSource);
-  // All MuData file types
-  registerPluginFileType(FileType.OBS_SETS_MUDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, MuDataSource);
-  registerPluginFileType(FileType.OBS_EMBEDDING_MUDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, MuDataSource);
-  registerPluginFileType(FileType.OBS_LOCATIONS_MUDATA_ZARR, DataType.OBS_LOCATIONS, ObsLocationsAnndataLoader, MuDataSource);
-  registerPluginFileType(FileType.OBS_LABELS_MUDATA_ZARR, DataType.OBS_LABELS, ObsLabelsAnndataLoader, MuDataSource);
-  registerPluginFileType(FileType.OBS_FEATURE_MATRIX_MUDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, MuDataSource);
-  registerPluginFileType(FileType.OBS_SEGMENTATIONS_MUDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, MuDataSource);
-  registerPluginFileType(FileType.FEATURE_LABELS_MUDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, MuDataSource);
-  // All OME file types
-  registerPluginFileType(FileType.IMAGE_OME_ZARR, DataType.IMAGE, OmeZarrLoader, ZarrDataSource);
-
-  // All legacy file types
-  registerPluginFileType(FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR, DataType.OBS_FEATURE_MATRIX, MatrixZarrAsObsFeatureMatrixLoader, ZarrDataSource);
-  registerPluginFileType(FileType.IMAGE_RASTER_JSON, DataType.IMAGE, RasterJsonAsImageLoader, JsonSource);
-  registerPluginFileType(FileType.OBS_SEGMENTATIONS_RASTER_JSON, DataType.OBS_SEGMENTATIONS, RasterJsonAsObsSegmentationsLoader, JsonSource);
-  registerPluginFileType(FileType.OBS_SETS_CELL_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource);
-  registerPluginFileType(FileType.OBS_FEATURE_MATRIX_CLUSTERS_JSON, DataType.OBS_FEATURE_MATRIX, ClustersJsonAsObsFeatureMatrixLoader, JsonSource);
-  registerPluginFileType(FileType.OBS_FEATURE_MATRIX_GENES_JSON, DataType.OBS_FEATURE_MATRIX, GenesJsonAsObsFeatureMatrixLoader, JsonSource);
-  registerPluginFileType(FileType.OBS_LABELS_CELLS_JSON, DataType.OBS_LABELS, CellsJsonAsObsLabelsLoader, JsonSource);
-  registerPluginFileType(FileType.OBS_EMBEDDING_CELLS_JSON, DataType.OBS_EMBEDDING, CellsJsonAsObsEmbeddingLoader, JsonSource);
-  registerPluginFileType(FileType.OBS_LOCATIONS_CELLS_JSON, DataType.OBS_LOCATIONS, CellsJsonAsObsLocationsLoader, JsonSource);
-  registerPluginFileType(FileType.OBS_SEGMENTATIONS_CELLS_JSON, DataType.OBS_SEGMENTATIONS, CellsJsonAsObsSegmentationsLoader, JsonSource);
-  registerPluginFileType(FileType.OBS_LOCATIONS_MOLECULES_JSON, DataType.OBS_LOCATIONS, MoleculesJsonAsObsLocationsLoader, JsonSource);
-  registerPluginFileType(FileType.OBS_LABELS_MOLECULES_JSON, DataType.OBS_LABELS, MoleculesJsonAsObsLabelsLoader, JsonSource);
-  registerPluginFileType(FileType.NEIGHBORHOODS_JSON, DataType.NEIGHBORHOODS, JsonLoader, JsonSource);
-  registerPluginFileType(FileType.GENOMIC_PROFILES_ZARR, DataType.GENOMIC_PROFILES, GenomicProfilesZarrLoader, ZarrDataSource);
-}
-
-export function Vitessce(props) {
-  const [ready, setReady] = useState(false);
-  useLayoutEffect(() => {
-    setup();
-    setReady(true);
-  }, []);
-  return (ready ? (
-    <VitS {...props} />
-  ) : null);
-}