higlass 1.13.1 → 1.13.3

package/README.md

@@ -57,8 +57,6 @@ Useful commands:
 - Run a specific test or "glob" of tests: `npm test -- test/APITests.js [--watch]`
 - Manually run individual tests in an open browser window: `npm test -- --manual`
 
-There can sometimes be import issues due to timeouts when running tests after a clean installation. It is best to run `npm run optimize` prior to running tests for the first time.
-
 **Troubleshooting:**
 
 - If the installation fails due to `sharp` > `node-gyp` try installing the node packages using `python2`:

package/app/globals.d.ts

@@ -1,11 +1,11 @@
-export {}
+export {};
 /* eslint-disable */
 declare global {
   interface Window {
     higlassTracksByType?: {
       [trackType: string]: {
-        config: import('./scripts/configs/tracks-info').TrackInfo
-      }
-    }
+        config: import('./scripts/configs/tracks-info').TrackInfo;
+      };
+    };
   }
 }

package/app/missing-types.d.ts

@@ -5,17 +5,17 @@ declare module 'pub-sub-es' {
   export type Subscription = {
     event: string;
     handler: (news: any) => void;
-  }
+  };
   type PublishOptions = {
     async?: boolean;
     isNoGlobalBroadCast?: boolean;
-  }
+  };
   export type PubSub = {
     publish(event: string, news?: any, options?: PublishOptions): void;
     subscribe(event: string, handler: (news: any) => void): Subscription;
     unsubscribe(subscription: Subscription): void;
     clear(): void;
-  }
+  };
   export function createPubSub(): PubSub;
   export const globalPubSub: PubSub;
 }

package/app/scripts/AddTrackDialog.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import React from 'react';
 import PropTypes from 'prop-types';
 

package/app/scripts/AddTrackPositionMenu.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import PropTypes from 'prop-types';
 import React from 'react';
 import clsx from 'clsx';
@@ -19,14 +20,20 @@ function AddTrackPositionMenu(props) {
       >
         <tbody>
           <tr style={{ height: '30px' }}>
-            <td className={classes['add-track-position-other']} />
+            <td
+              aria-hidden="true"
+              className={classes['add-track-position-other']}
+            />
             <td
               className={classes['add-track-position-top-center']}
               onClick={() => props.onTrackPositionChosen('top')}
             >
               top
             </td>
-            <td className={classes['add-track-position-other']} />
+            <td
+              aria-hidden="true"
+              className={classes['add-track-position-other']}
+            />
           </tr>
           <tr style={{ height: '80px' }}>
             <td
@@ -49,14 +56,20 @@ function AddTrackPositionMenu(props) {
             </td>
           </tr>
           <tr style={{ height: '30px' }}>
-            <td className={classes['add-track-position-other']} />
+            <td
+              aria-hidden="true"
+              className={classes['add-track-position-other']}
+            />
             <td
               className={classes['add-track-position-bottom-middle']}
               onClick={() => props.onTrackPositionChosen('bottom')}
             >
               bottom
             </td>
-            <td className={classes['add-track-position-other']} />
+            <td
+              aria-hidden="true"
+              className={classes['add-track-position-other']}
+            />
           </tr>
         </tbody>
       </table>

package/app/scripts/Annotations1dTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { color } from 'd3-color';
 import PixiTrack from './PixiTrack';
 

package/app/scripts/Annotations2dTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import createPubSub from 'pub-sub-es';
 
 import TiledPixiTrack from './TiledPixiTrack';

package/app/scripts/ArrowheadDomainsTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import createPubSub from 'pub-sub-es';
 
 import TiledPixiTrack from './TiledPixiTrack';

package/app/scripts/Autocomplete.jsx

@@ -1,3 +1,5 @@
+// @ts-nocheck
+/* eslint-disable react/jsx-props-no-spreading */
 import React from 'react';
 import { findDOMNode } from 'react-dom';
 import scrollIntoView from 'dom-scroll-into-view';

package/app/scripts/AxisPixi.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { format } from 'd3-format';
 
 // Configs

package/app/scripts/BarTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { scaleLinear } from 'd3-scale';
 import { zoomIdentity } from 'd3-zoom';
 

package/app/scripts/BedLikeTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import boxIntersect from 'box-intersect';
 import { median, range } from 'd3-array';
 import { scaleBand, scaleLinear } from 'd3-scale';

package/app/scripts/Button.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import React from 'react';
 import PropTypes from 'prop-types';
 

package/app/scripts/CNVIntervalTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { scaleBand } from 'd3-scale';
 import { range } from 'd3-array';
 import { segmentsToRows } from './utils';

package/app/scripts/CenterTiledPlot.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import React from 'react';
 
 function CenterTiledPlot() {

package/app/scripts/CenterTrack.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import PropTypes from 'prop-types';
 import React from 'react';
 import { brush, brushX, brushY } from 'd3-brush';

package/app/scripts/Chromosome2DAnnotations.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { color } from 'd3-color';
 
 import PixiTrack from './PixiTrack';

package/app/scripts/Chromosome2DLabels.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import boxIntersect from 'box-intersect';
 
 import PixiTrack from './PixiTrack';

package/app/scripts/ChromosomeGrid.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import PixiTrack from './PixiTrack';
 import ChromosomeInfo from './ChromosomeInfo';
 import SearchField from './SearchField';

package/app/scripts/ChromosomeInfo.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { tsvParseRows } from 'd3-dsv';
 import { tileProxy } from './services';
 import { absToChr, chrToAbs, parseChromsizesRows } from './utils';

package/app/scripts/CloseTrackMenu.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import PropTypes from 'prop-types';
 import React from 'react';
 

package/app/scripts/CombinedTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import slugid from 'slugid';
 
 class CombinedTrack {

package/app/scripts/ConfigTrackMenu.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import React from 'react';
 import clsx from 'clsx';
 import { mix } from './mixwith';

package/app/scripts/ConfigViewMenu.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import React from 'react';
 import PropTypes from 'prop-types';
 import clsx from 'clsx';

package/app/scripts/ConfigureSeriesMenu.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import React from 'react';
 
 import ContextMenuContainer from './ContextMenuContainer';

package/app/scripts/ContextMenuContainer.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import PropTypes from 'prop-types';
 import React from 'react';
 import ReactDOM from 'react-dom';

package/app/scripts/ContextMenuItem.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import PropTypes from 'prop-types';
 import React from 'react';
 

package/app/scripts/Cross.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import React from 'react';
 
 import classes from '../styles/Cross.module.scss';

package/app/scripts/CrossRule.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { colorToHex } from './utils';
 import { mix } from './mixwith';
 

package/app/scripts/CustomTrackDialog.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import React from 'react';
 import PropTypes from 'prop-types';
 
@@ -11,6 +12,7 @@ class CustomTrackDialog extends React.PureComponent {
     const childrenWithProp = [];
     this.props.children.forEach((Child, i) => {
       const key = `customTrackDialog_${i}`;
+      // eslint-disable-next-line react/jsx-props-no-spreading
       childrenWithProp.push(<Child key={key} {...this.props.bodyProps[i]} />);
     });
 
@@ -33,6 +35,9 @@ CustomTrackDialog.defaultProps = {};
 
 CustomTrackDialog.propTypes = {
   onCancel: PropTypes.func.isRequired,
+  title: PropTypes.string,
+  bodyProps: PropTypes.array,
+  children: PropTypes.array,
 };
 
 export default CustomTrackDialog;

package/app/scripts/Dialog.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import React from 'react';
 import PropTypes from 'prop-types';
 import clsx from 'clsx';

package/app/scripts/DivergentBarTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { scaleLinear, scaleLog } from 'd3-scale';
 
 import BarTrack from './BarTrack';

package/app/scripts/DragListeningDiv.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import PropTypes from 'prop-types';
 import React from 'react';
 import slugid from 'slugid';

package/app/scripts/DraggableDiv.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { drag } from 'd3-drag';
 import { pointer, select } from 'd3-selection';
 import PropTypes from 'prop-types';

package/app/scripts/ExportLinkDialog.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import React from 'react';
 import PropTypes from 'prop-types';
 

package/app/scripts/FixedTrack.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import React from 'react';
 import TrackArea from './TrackArea';
 

package/app/scripts/GalleryTracks.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import PropTypes from 'prop-types';
 import React from 'react';
 import clsx from 'clsx';

package/app/scripts/GenomePositionSearchBox.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { select } from 'd3-selection';
 import React from 'react';
 import slugid from 'slugid';
@@ -856,6 +857,7 @@ GenomePositionSearchBox.propTypes = {
   autocompleteServer: PropTypes.string,
   chromInfoId: PropTypes.string,
   chromInfoServer: PropTypes.string,
+  chromInfoPath: PropTypes.string,
   hideAvailableAssemblies: PropTypes.bool,
   isFocused: PropTypes.bool,
   pubSub: PropTypes.object,

package/app/scripts/HeatmapOptions.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import PropTypes from 'prop-types';
 import React from 'react';
 import Dialog from './Dialog';

package/app/scripts/HeatmapTiledPixiTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import ndarray from 'ndarray';
 import { brushY } from 'd3-brush';
 import { format } from 'd3-format';

package/app/scripts/HiGlassComponent.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import React from 'react';
 import PropTypes from 'prop-types';
 import { select, pointer } from 'd3-selection';

package/app/scripts/HiGlassTrackComponent.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import PropTypes from 'prop-types';
 import React from 'react';
 

package/app/scripts/Horizontal1dHeatmapTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { scaleLinear } from 'd3-scale';
 import HorizontalLine1DPixiTrack from './HorizontalLine1DPixiTrack';
 

package/app/scripts/Horizontal2DDomainsTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import TiledPixiTrack from './TiledPixiTrack';
 
 import { tileProxy } from './services';

package/app/scripts/HorizontalChromosomeLabels.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import boxIntersect from 'box-intersect';
 import { scaleLinear } from 'd3-scale';
 import { format, precisionPrefix, formatPrefix } from 'd3-format';

package/app/scripts/HorizontalGeneAnnotationsTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import boxIntersect from 'box-intersect';
 import classifyPoint from 'robust-point-in-polygon';
 

package/app/scripts/HorizontalHeatmapTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import HeatmapTiledPixiTrack from './HeatmapTiledPixiTrack';
 
 // Services

package/app/scripts/HorizontalItem.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import React from 'react';
 import { SortableElement } from 'react-sortable-hoc';
 

package/app/scripts/HorizontalLine1DPixiTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { format } from 'd3-format';
 import { scaleLinear } from 'd3-scale';
 

package/app/scripts/HorizontalMultivecTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { format } from 'd3-format';
 
 import HeatmapTiledPixiTrack from './HeatmapTiledPixiTrack';

package/app/scripts/HorizontalPoint1DPixiTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { scaleLinear, scaleLog } from 'd3-scale';
 import HorizontalLine1DPixiTrack from './HorizontalLine1DPixiTrack';
 import { colorToHex, dictValues } from './utils';

package/app/scripts/HorizontalRule.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 /* eslint-disable max-classes-per-file */
 
 import { mix, Mixin } from './mixwith';

package/app/scripts/HorizontalTiled1DPixiTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import Tiled1DPixiTrack from './Tiled1DPixiTrack';
 import AxisPixi from './AxisPixi';
 

package/app/scripts/HorizontalTiledPlot.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import PropTypes from 'prop-types';
 import React from 'react';
 import { brushX } from 'd3-brush';

package/app/scripts/HorizontalTrack.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import React from 'react';
 
 import MoveableTrack from './MoveableTrack';

package/app/scripts/Id2DTiledPixiTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import HeatmapTiledPixiTrack from './HeatmapTiledPixiTrack';
 
 // Configs

package/app/scripts/IdHorizontal1DTiledPixiTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import HorizontalTiled1DPixiTrack from './HorizontalTiled1DPixiTrack';
 
 // Configs

package/app/scripts/IdVertical1DTiledPixiTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 // Configs
 import { GLOBALS } from './configs';
 

package/app/scripts/LeftAxisTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { axisLeft } from 'd3-axis';
 
 import SVGTrack from './SVGTrack';

package/app/scripts/LeftTrackModifier.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 // Configs
 import { GLOBALS } from './configs';
 

package/app/scripts/ListWrapper.jsx

@@ -1,3 +1,5 @@
+// @ts-nocheck
+/* eslint-disable react/jsx-props-no-spreading */
 import PropTypes from 'prop-types';
 import React from 'react';
 import { arrayMove } from 'react-sortable-hoc';

package/app/scripts/MapboxTilesTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import OSMTilesTrack from './OSMTilesTrack';
 
 /**

package/app/scripts/Modal.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import React from 'react';
 import PropTypes from 'prop-types';
 import clsx from 'clsx';

package/app/scripts/MoveableTrack.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import PropTypes from 'prop-types';
 import React from 'react';
 

package/app/scripts/NestedContextMenu.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import React from 'react';
 import clsx from 'clsx';
 

package/app/scripts/OSMTileIdsTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { initTile, drawTile } from './Id2DTiledPixiTrack';
 import OSMTilesTrack from './OSMTilesTrack';
 

package/app/scripts/OSMTilesTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import slugid from 'slugid';
 
 import PixiTrack from './PixiTrack';

package/app/scripts/OverlayTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import PixiTrack from './PixiTrack';
 
 // Utils

package/app/scripts/PixiTrack.js

@@ -1,4 +1,3 @@
-// @ts-check
 import { formatPrefix, precisionPrefix } from 'd3-format';
 import slugid from 'slugid';
 

package/app/scripts/PlotTypeChooser.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import PropTypes from 'prop-types';
 import React from 'react';
 

package/app/scripts/PopupMenu.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import PropTypes from 'prop-types';
 import React from 'react';
 import ReactDOM from 'react-dom';

package/app/scripts/RasterTilesTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import OSMTilesTrack from './OSMTilesTrack';
 
 /**

package/app/scripts/RuleMixin.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { Mixin } from './mixwith';
 
 const RuleMixin = Mixin(

package/app/scripts/SVGTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { select } from 'd3-selection';
 import slugid from 'slugid';
 

package/app/scripts/SearchField.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { bisector } from 'd3-array';
 import { format } from 'd3-format';
 import absToChr from './utils/abs-to-chr';

package/app/scripts/SeriesListItems.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import React from 'react';
 
 import ContextMenuItem from './ContextMenuItem';

package/app/scripts/SeriesListMenu.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import React from 'react';
 import clsx from 'clsx';
 

package/app/scripts/SeriesListSubmenuMixin.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import React from 'react';
 import { Mixin } from './mixwith';
 

package/app/scripts/SketchInlinePicker.jsx

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import PropTypes from 'prop-types';
 import { rgb as d3rgb } from 'd3-color';
 import React from 'react';

package/app/scripts/SortableList.jsx

@@ -1,3 +1,5 @@
+// @ts-nocheck
+/* eslint-disable react/jsx-props-no-spreading */
 import React from 'react';
 import { SortableContainer } from 'react-sortable-hoc';
 

package/app/scripts/SquareMarkersTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import TiledPixiTrack from './TiledPixiTrack';
 
 import { tileProxy } from './services';

package/app/scripts/Tiled1DPixiTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { scaleLinear } from 'd3-scale';
 
 import TiledPixiTrack from './TiledPixiTrack';

package/app/scripts/TiledPixiTrack.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { scaleLinear, scaleLog, scaleQuantile } from 'd3-scale';
 import { median, range, ticks } from 'd3-array';
 import slugid from 'slugid';