npm - @jbrowse/plugin-wiggle - Versions diffs - 2.3.1 → 2.3.3 - Mend

@jbrowse/plugin-wiggle 2.3.1 → 2.3.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (36) hide show

package/dist/CreateMultiWiggleExtension/ConfirmDialog.js CHANGED Viewed

@@ -22,15 +22,18 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __setModuleDefault(result, mod);
     return result;
 };
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
+const Dialog_1 = __importDefault(require("@jbrowse/core/ui/Dialog"));
 const configuration_1 = require("@jbrowse/core/configuration");
 const ConfirmDialog = ({ tracks, onClose, }) => {
     const [val, setVal] = (0, react_1.useState)('MultiWiggle ' + Date.now());
     const allQuant = tracks.every(t => t.type === 'QuantitativeTrack');
-    return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: () => onClose(false) },
-        react_1.default.createElement(material_1.DialogTitle, null, "Confirm multi-wiggle track create"),
+    return (react_1.default.createElement(Dialog_1.default, { open: true, onClose: () => onClose(false), title: "Confirm multi-wiggle track create" },
         react_1.default.createElement(material_1.DialogContent, null,
             react_1.default.createElement(material_1.Typography, null,
                 !allQuant

package/dist/CreateMultiWiggleExtension/ConfirmDialog.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"ConfirmDialog.js","sourceRoot":"","sources":["../../src/CreateMultiWiggleExtension/ConfirmDialog.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,4CAMsB;AACtB,qEAA4C;AAC5C,+DAGoC;AAEpC,MAAM,aAAa,GAAG,CAAC,EACrB,MAAM,EACN,OAAO,GAIR,EAAE,EAAE;IACH,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,cAAc,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,CAAA;IAC3D,MAAM,QAAQ,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,mBAAmB,CAAC,CAAA;IAClE,OAAO,CACL,8BAAC,gBAAM,IACL,IAAI,QACJ,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC,EAC7B,KAAK,EAAC,mCAAmC;QAEzC,8BAAC,wBAAa;YACZ,8BAAC,qBAAU;gBACR,CAAC,QAAQ;oBACR,CAAC,CAAC,8GAA8G;oBAChH,CAAC,CAAC,IAAI;2BAEG;YACb,0CACG,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CACnB,sCAAI,GAAG,EAAE,KAAK,CAAC,OAAO;gBACnB,IAAA,8BAAc,EAAC,KAAK,EAAE,MAAM,CAAC;;gBAAK,KAAK,CAAC,IAAI,CAC1C,CACN,CAAC,CACC;YACL,8BAAC,oBAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,UAAU,EAAC,YAAY,GACvB;YACF,8BAAC,qBAAU,qCAAwC,CACrC;QAChB,8BAAC,wBAAa;YACZ,8BAAC,iBAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAC,SAAS,aAE7C;YACT,8BAAC,iBAAM,IACL,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC,EAC3C,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,SAAS,mBAGF,CACK,CACT,CACV,CAAA;AACH,CAAC,CAAA;AAED,kBAAe,aAAa,CAAA"}

package/dist/LinearWiggleDisplay/components/Tooltip.d.ts CHANGED Viewed

@@ -1,9 +1,10 @@
 import React from 'react';
 import { Feature } from '@jbrowse/core/util';
 import Tooltip, { TooltipContentsComponent } from '../../Tooltip';
-declare const TooltipContents: React.ForwardRefExoticComponent<{
+interface Props {
     feature: Feature;
-} & React.RefAttributes<HTMLDivElement>>;
+}
+declare const TooltipContents: React.ForwardRefExoticComponent<Props & React.RefAttributes<HTMLDivElement>>;
 type Coord = [number, number];
 declare const WiggleTooltip: (props: {
     model: {

package/dist/LinearWiggleDisplay/components/Tooltip.js CHANGED Viewed

@@ -11,7 +11,7 @@ const Tooltip_1 = __importDefault(require("../../Tooltip"));
 exports.Tooltip = Tooltip_1.default;
 const util_1 = require("../../util");
 const en = (n) => n.toLocaleString('en-US');
-const TooltipContents = react_1.default.forwardRef(({ feature }, ref) => {
+const TooltipContents = react_1.default.forwardRef(function ({ feature }, ref) {
     const start = feature.get('start');
     const end = feature.get('end');
     const name = feature.get('refName');
@@ -33,7 +33,7 @@ const TooltipContents = react_1.default.forwardRef(({ feature }, ref) => {
         react_1.default.createElement("br", null),
         `${(0, util_1.toP)(feature.get('score'))}`));
 });
-const WiggleTooltip = (0, mobx_react_1.observer)((props) => {
+const WiggleTooltip = (0, mobx_react_1.observer)(function (props) {
     return react_1.default.createElement(Tooltip_1.default, { TooltipContents: TooltipContents, ...props });
 });
 exports.default = WiggleTooltip;

package/dist/LinearWiggleDisplay/components/Tooltip.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"Tooltip.js","sourceRoot":"","sources":["../../../src/LinearWiggleDisplay/components/Tooltip.tsx"],"names":[],"mappings":";;;;;;AAAA,kDAAyB;AACzB,2CAAqC;AAGrC,SAAS;AACT,4DAAiE;AAoDxD,kBApDF,iBAAO,CAoDE;AAnDhB,qCAAgC;AAEhC,MAAM,EAAE,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,CAAC,cAAc,CAAC,OAAO,CAAC,CAAA;AAMnD,MAAM,eAAe,GAAG,eAAK,CAAC,UAAU,CAAwB,UAC9D,EAAE,OAAO,EAAE,EACX,GAAG;IAEH,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IAClC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC9B,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;IACnC,MAAM,GAAG,GAAG,CAAC,IAAI,EAAE,KAAK,KAAK,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;SACvE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,IAAI,CAAC,GAAG,CAAC,CAAA;IAEZ,OAAO,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,CAC5C,uCAAK,GAAG,EAAE,GAAG;QACV,GAAG;QACJ,yCAAM;;QACA,IAAA,UAAG,EAAC,OAAO,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC;QAClC,yCAAM;;QACA,IAAA,UAAG,EAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;QAC/B,yCAAM;;QACA,IAAA,UAAG,EAAC,OAAO,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC,CAC9B,CACP,CAAC,CAAC,CAAC,CACF,uCAAK,GAAG,EAAE,GAAG;QACV,GAAG;QACJ,yCAAM;QACL,GAAG,IAAA,UAAG,EAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,EAAE,CAC3B,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAIF,MAAM,aAAa,GAAG,IAAA,qBAAQ,EAAC,UAAU,KAOxC;IACC,OAAO,8BAAC,iBAAO,IAAC,eAAe,EAAE,eAAe,KAAM,KAAK,GAAI,CAAA;AACjE,CAAC,CAAC,CAAA;AACF,kBAAe,aAAa,CAAA"}

package/dist/LinearWiggleDisplay/models/model.d.ts CHANGED Viewed

@@ -41,20 +41,14 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         status: string;
         error: unknown;
         message: string | undefined;
-        maxHeightReached: boolean; /**
-         * #property
-         */
+        maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any; /**
-             * #property
-             */
+            model: any;
         }) => any;
         renderProps: any;
     } & {
         doReload(): void;
-        afterAttach(): void; /**
-         * #property
-         */
+        afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;

package/dist/MultiWiggleAdapter/MultiWiggleAdapter.js CHANGED Viewed

@@ -49,8 +49,8 @@ class MultiWiggleAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const stats = (await Promise.all(
         // @ts-ignore
         adapters.map(adp => { var _a, _b; return (_b = (_a = adp.dataAdapter).getGlobalStats) === null || _b === void 0 ? void 0 : _b.call(_a, opts); }))).filter(f => !!f);
-        const scoreMin = Math.min(...stats.map(s => s.scoreMin));
-        const scoreMax = Math.max(...stats.map(s => s.scoreMax));
+        const scoreMin = (0, util_1.min)(stats.map(s => s.scoreMin));
+        const scoreMax = (0, util_1.max)(stats.map(s => s.scoreMax));
         return { scoreMin, scoreMax };
     }
     getFeatures(region, opts = {}) {

package/dist/MultiWiggleAdapter/MultiWiggleAdapter.js.map CHANGED Viewed

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package/dist/drawxy.js CHANGED Viewed

@@ -3,6 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.drawDensity = exports.drawLine = exports.drawXY = void 0;
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
+// locals
 const util_2 = require("./util");
 // avoid drawing negative width features for SVG exports
 function fillRectCtx(x, y, width, height, ctx, color) {

package/dist/drawxy.js.map CHANGED Viewed

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package/dist/util.d.ts CHANGED Viewed

@@ -6,7 +6,7 @@ export interface ScaleOpts {
     range: number[];
     scaleType: string;
     pivotValue?: number;
-    inverted: boolean;
+    inverted?: boolean;
 }
 export interface Source {
     name: string;
@@ -44,8 +44,8 @@ export declare function getOrigin(scaleType: string): 1 | 0;
  */
 export declare function getNiceDomain({ scaleType, domain, bounds, }: {
     scaleType: string;
-    domain: number[];
-    bounds: number[];
+    domain: readonly [number, number];
+    bounds: readonly [number | undefined, number | undefined];
 }): [number, number];
 export declare function groupBy<T>(array: T[], predicate: (v: T) => string): {
     [key: string]: T[];

package/esm/CreateMultiWiggleExtension/ConfirmDialog.js CHANGED Viewed

@@ -1,11 +1,11 @@
 import React, { useState } from 'react';
-import { Button, Dialog, DialogActions, DialogContent, DialogTitle, TextField, Typography, } from '@mui/material';
+import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
+import Dialog from '@jbrowse/core/ui/Dialog';
 import { readConfObject, } from '@jbrowse/core/configuration';
 const ConfirmDialog = ({ tracks, onClose, }) => {
     const [val, setVal] = useState('MultiWiggle ' + Date.now());
     const allQuant = tracks.every(t => t.type === 'QuantitativeTrack');
-    return (React.createElement(Dialog, { open: true, onClose: () => onClose(false) },
-        React.createElement(DialogTitle, null, "Confirm multi-wiggle track create"),
+    return (React.createElement(Dialog, { open: true, onClose: () => onClose(false), title: "Confirm multi-wiggle track create" },
         React.createElement(DialogContent, null,
             React.createElement(Typography, null,
                 !allQuant

package/esm/CreateMultiWiggleExtension/ConfirmDialog.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"ConfirmDialog.js","sourceRoot":"","sources":["../../src/CreateMultiWiggleExtension/ConfirmDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,MAAM,MAAM,yBAAyB,CAAA;AAC5C,OAAO,EAEL,cAAc,GACf,MAAM,6BAA6B,CAAA;AAEpC,MAAM,aAAa,GAAG,CAAC,EACrB,MAAM,EACN,OAAO,GAIR,EAAE,EAAE;IACH,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,cAAc,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,CAAA;IAC3D,MAAM,QAAQ,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,mBAAmB,CAAC,CAAA;IAClE,OAAO,CACL,oBAAC,MAAM,IACL,IAAI,QACJ,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC,EAC7B,KAAK,EAAC,mCAAmC;QAEzC,oBAAC,aAAa;YACZ,oBAAC,UAAU;gBACR,CAAC,QAAQ;oBACR,CAAC,CAAC,8GAA8G;oBAChH,CAAC,CAAC,IAAI;2BAEG;YACb,gCACG,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CACnB,4BAAI,GAAG,EAAE,KAAK,CAAC,OAAO;gBACnB,cAAc,CAAC,KAAK,EAAE,MAAM,CAAC;;gBAAK,KAAK,CAAC,IAAI,CAC1C,CACN,CAAC,CACC;YACL,oBAAC,SAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,UAAU,EAAC,YAAY,GACvB;YACF,oBAAC,UAAU,qCAAwC,CACrC;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAC,SAAS,aAE7C;YACT,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC,EAC3C,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,SAAS,mBAGF,CACK,CACT,CACV,CAAA;AACH,CAAC,CAAA;AAED,eAAe,aAAa,CAAA"}

package/esm/LinearWiggleDisplay/components/Tooltip.d.ts CHANGED Viewed

@@ -1,9 +1,10 @@
 import React from 'react';
 import { Feature } from '@jbrowse/core/util';
 import Tooltip, { TooltipContentsComponent } from '../../Tooltip';
-declare const TooltipContents: React.ForwardRefExoticComponent<{
+interface Props {
     feature: Feature;
-} & React.RefAttributes<HTMLDivElement>>;
+}
+declare const TooltipContents: React.ForwardRefExoticComponent<Props & React.RefAttributes<HTMLDivElement>>;
 type Coord = [number, number];
 declare const WiggleTooltip: (props: {
     model: {

package/esm/LinearWiggleDisplay/components/Tooltip.js CHANGED Viewed

@@ -4,7 +4,7 @@ import { observer } from 'mobx-react';
 import Tooltip from '../../Tooltip';
 import { toP } from '../../util';
 const en = (n) => n.toLocaleString('en-US');
-const TooltipContents = React.forwardRef(({ feature }, ref) => {
+const TooltipContents = React.forwardRef(function ({ feature }, ref) {
     const start = feature.get('start');
     const end = feature.get('end');
     const name = feature.get('refName');
@@ -26,7 +26,7 @@ const TooltipContents = React.forwardRef(({ feature }, ref) => {
         React.createElement("br", null),
         `${toP(feature.get('score'))}`));
 });
-const WiggleTooltip = observer((props) => {
+const WiggleTooltip = observer(function (props) {
     return React.createElement(Tooltip, { TooltipContents: TooltipContents, ...props });
 });
 export default WiggleTooltip;

package/esm/LinearWiggleDisplay/components/Tooltip.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/LinearWiggleDisplay/models/model.d.ts CHANGED Viewed

@@ -41,20 +41,14 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         status: string;
         error: unknown;
         message: string | undefined;
-        maxHeightReached: boolean; /**
-         * #property
-         */
+        maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any; /**
-             * #property
-             */
+            model: any;
         }) => any;
         renderProps: any;
     } & {
         doReload(): void;
-        afterAttach(): void; /**
-         * #property
-         */
+        afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;

package/esm/MultiWiggleAdapter/MultiWiggleAdapter.js CHANGED Viewed

@@ -1,6 +1,6 @@
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { SimpleFeature } from '@jbrowse/core/util';
+import { SimpleFeature, min, max } from '@jbrowse/core/util';
 import { merge } from 'rxjs';
 import { map } from 'rxjs/operators';
 function getFilename(uri) {
@@ -47,8 +47,8 @@ export default class MultiWiggleAdapter extends BaseFeatureDataAdapter {
         const stats = (await Promise.all(
         // @ts-ignore
         adapters.map(adp => { var _a, _b; return (_b = (_a = adp.dataAdapter).getGlobalStats) === null || _b === void 0 ? void 0 : _b.call(_a, opts); }))).filter(f => !!f);
-        const scoreMin = Math.min(...stats.map(s => s.scoreMin));
-        const scoreMax = Math.max(...stats.map(s => s.scoreMax));
+        const scoreMin = min(stats.map(s => s.scoreMin));
+        const scoreMax = max(stats.map(s => s.scoreMax));
         return { scoreMin, scoreMax };
     }
     getFeatures(region, opts = {}) {

package/esm/MultiWiggleAdapter/MultiWiggleAdapter.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/drawxy.js CHANGED Viewed

@@ -1,5 +1,6 @@
 import { readConfObject, } from '@jbrowse/core/configuration';
 import { clamp, featureSpanPx } from '@jbrowse/core/util';
+// locals
 import { getOrigin, getScale } from './util';
 // avoid drawing negative width features for SVG exports
 function fillRectCtx(x, y, width, height, ctx, color) {

package/esm/drawxy.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/util.d.ts CHANGED Viewed

@@ -6,7 +6,7 @@ export interface ScaleOpts {
     range: number[];
     scaleType: string;
     pivotValue?: number;
-    inverted: boolean;
+    inverted?: boolean;
 }
 export interface Source {
     name: string;
@@ -44,8 +44,8 @@ export declare function getOrigin(scaleType: string): 1 | 0;
  */
 export declare function getNiceDomain({ scaleType, domain, bounds, }: {
     scaleType: string;
-    domain: number[];
-    bounds: number[];
+    domain: readonly [number, number];
+    bounds: readonly [number | undefined, number | undefined];
 }): [number, number];
 export declare function groupBy<T>(array: T[], predicate: (v: T) => string): {
     [key: string]: T[];

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-wiggle",
-  "version": "2.3.1",
+  "version": "2.3.3",
   "description": "JBrowse 2 wiggle adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -37,7 +37,7 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@gmod/bbi": "^2.0.3",
+    "@gmod/bbi": "^3.0.0",
     "@mui/icons-material": "^5.0.2",
     "@popperjs/core": "^2.11.0",
     "clone": "^2.1.2",
@@ -60,7 +60,7 @@
     "mobx-react": "^7.0.0",
     "mobx-state-tree": "^5.0.0",
     "react": ">=16.8.0",
-    "rxjs": "^6.0.0",
+    "rxjs": "^7.0.0",
     "tss-react": "^4.0.0"
   },
   "publishConfig": {
@@ -69,5 +69,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "75c4cba2f50c626c62881abd5851dbf2435c2401"
+  "gitHead": "283e0387ccd5acc9f092cf00804d1fcac212e68d"
 }

package/src/BigWigAdapter/BigWigAdapter.test.ts CHANGED Viewed

@@ -1,4 +1,5 @@
 import { toArray } from 'rxjs/operators'
+import { firstValueFrom } from 'rxjs'
 import BigWigAdapter from './BigWigAdapter'
 import configSchema from './configSchema'
@@ -26,7 +27,7 @@ describe('adapter can fetch features from volvox.bw', () => {
     expect(await adapter.hasDataForRefName('ctgA')).toBe(true)
     expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
-    const featuresArray = await features.pipe(toArray()).toPromise()
+    const featuresArray = await firstValueFrom(features.pipe(toArray()))
     const featuresJsonArray = featuresArray.map(f => f.toJSON())
     expect(featuresJsonArray.slice(1000, 1010)).toMatchSnapshot()
   })

package/src/CreateMultiWiggleExtension/ConfirmDialog.tsx CHANGED Viewed

@@ -1,13 +1,12 @@
 import React, { useState } from 'react'
 import {
   Button,
-  Dialog,
   DialogActions,
   DialogContent,
-  DialogTitle,
   TextField,
   Typography,
 } from '@mui/material'
+import Dialog from '@jbrowse/core/ui/Dialog'
 import {
   AnyConfigurationModel,
   readConfObject,
@@ -23,8 +22,11 @@ const ConfirmDialog = ({
   const [val, setVal] = useState('MultiWiggle ' + Date.now())
   const allQuant = tracks.every(t => t.type === 'QuantitativeTrack')
   return (
-    <Dialog open onClose={() => onClose(false)}>
-      <DialogTitle>Confirm multi-wiggle track create</DialogTitle>
+    <Dialog
+      open
+      onClose={() => onClose(false)}
+      title="Confirm multi-wiggle track create"
+    >
       <DialogContent>
         <Typography>
           {!allQuant

package/src/DensityRenderer/{DensityRenderer.test.js → DensityRenderer.test.ts} RENAMED Viewed

@@ -6,10 +6,15 @@ import ReactComponent from '../WiggleRendering'
 import { Image, createCanvas } from 'canvas'
+// @ts-ignore
 global.nodeImage = Image
+// @ts-ignore
 global.nodeCreateCanvas = createCanvas
-const pluginManager = {}
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+const pluginManager = {} as any
 const renderer = new DensityRenderer({
   name: 'DensityRenderer',
   ReactComponent,
@@ -48,6 +53,7 @@ test('inverted mode and reversed', async () => {
   }
   const res = await renderToAbstractCanvas(1000, 200, renderProps, ctx =>
+    // @ts-ignore
     renderer.draw(ctx, renderProps),
   )
   expect(res).toMatchSnapshot({

package/src/DensityRenderer/__snapshots__/{DensityRenderer.test.js.snap → DensityRenderer.test.ts.snap} RENAMED Viewed

File without changes

package/src/LinearWiggleDisplay/components/Tooltip.tsx CHANGED Viewed

@@ -8,48 +8,51 @@ import { toP } from '../../util'
 const en = (n: number) => n.toLocaleString('en-US')
-const TooltipContents = React.forwardRef<HTMLDivElement, { feature: Feature }>(
-  ({ feature }, ref) => {
-    const start = feature.get('start')
-    const end = feature.get('end')
-    const name = feature.get('refName')
-    const loc = [name, start === end ? en(start) : `${en(start)}..${en(end)}`]
-      .filter(f => !!f)
-      .join(':')
+interface Props {
+  feature: Feature
+}
-    return feature.get('summary') !== undefined ? (
-      <div ref={ref}>
-        {loc}
-        <br />
-        Max: {toP(feature.get('maxScore'))}
-        <br />
-        Avg: {toP(feature.get('score'))}
-        <br />
-        Min: {toP(feature.get('minScore'))}
-      </div>
-    ) : (
-      <div ref={ref}>
-        {loc}
-        <br />
-        {`${toP(feature.get('score'))}`}
-      </div>
-    )
-  },
-)
+const TooltipContents = React.forwardRef<HTMLDivElement, Props>(function (
+  { feature },
+  ref,
+) {
+  const start = feature.get('start')
+  const end = feature.get('end')
+  const name = feature.get('refName')
+  const loc = [name, start === end ? en(start) : `${en(start)}..${en(end)}`]
+    .filter(f => !!f)
+    .join(':')
+  return feature.get('summary') !== undefined ? (
+    <div ref={ref}>
+      {loc}
+      <br />
+      Max: {toP(feature.get('maxScore'))}
+      <br />
+      Avg: {toP(feature.get('score'))}
+      <br />
+      Min: {toP(feature.get('minScore'))}
+    </div>
+  ) : (
+    <div ref={ref}>
+      {loc}
+      <br />
+      {`${toP(feature.get('score'))}`}
+    </div>
+  )
+})
 type Coord = [number, number]
-const WiggleTooltip = observer(
-  (props: {
-    model: { featureUnderMouse: Feature }
-    height: number
-    offsetMouseCoord: Coord
-    clientMouseCoord: Coord
-    clientRect?: DOMRect
-    TooltipContents?: TooltipContentsComponent
-  }) => {
-    return <Tooltip TooltipContents={TooltipContents} {...props} />
-  },
-)
+const WiggleTooltip = observer(function (props: {
+  model: { featureUnderMouse: Feature }
+  height: number
+  offsetMouseCoord: Coord
+  clientMouseCoord: Coord
+  clientRect?: DOMRect
+  TooltipContents?: TooltipContentsComponent
+}) {
+  return <Tooltip TooltipContents={TooltipContents} {...props} />
+})
 export default WiggleTooltip
 export { Tooltip }

package/src/MultiWiggleAdapter/MultiWiggleAdapter.ts CHANGED Viewed

@@ -4,7 +4,7 @@ import {
 } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { AugmentedRegion as Region } from '@jbrowse/core/util/types'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { SimpleFeature, Feature } from '@jbrowse/core/util'
+import { SimpleFeature, Feature, min, max } from '@jbrowse/core/util'
 import { merge } from 'rxjs'
 import { map } from 'rxjs/operators'
@@ -77,8 +77,8 @@ export default class MultiWiggleAdapter extends BaseFeatureDataAdapter {
         adapters.map(adp => adp.dataAdapter.getGlobalStats?.(opts)),
       )
     ).filter(f => !!f)
-    const scoreMin = Math.min(...stats.map(s => s.scoreMin))
-    const scoreMax = Math.max(...stats.map(s => s.scoreMax))
+    const scoreMin = min(stats.map(s => s.scoreMin))
+    const scoreMax = max(stats.map(s => s.scoreMax))
     return { scoreMin, scoreMax }
   }

package/src/XYPlotRenderer/{XYPlotRenderer.test.js → XYPlotRenderer.test.ts} RENAMED Viewed

@@ -1,16 +1,19 @@
-import SimpleFeature from '@jbrowse/core/util/simpleFeature'
-import { renderToAbstractCanvas } from '@jbrowse/core/util/offscreenCanvasUtils'
+import { SimpleFeature, renderToAbstractCanvas } from '@jbrowse/core/util'
+import { Image, createCanvas } from 'canvas'
+// locals
 import configSchema from './configSchema'
 import XYPlotRenderer from './XYPlotRenderer'
 import ReactComponent from '../WiggleRendering'
-import { Image, createCanvas } from 'canvas'
+// @ts-ignore
 global.nodeImage = Image
+// @ts-ignore
 global.nodeCreateCanvas = createCanvas
 test('several features', async () => {
-  const pluginManager = {}
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  const pluginManager = {} as any
   const renderer = new XYPlotRenderer({
     name: 'XYPlotRenderer',
     ReactComponent,
@@ -40,6 +43,7 @@ test('several features', async () => {
   }
   const res = await renderToAbstractCanvas(1000, 200, renderProps, ctx =>
+    // @ts-ignore
     renderer.draw(ctx, renderProps),
   )
   expect(res).toMatchSnapshot({

package/src/XYPlotRenderer/__snapshots__/{XYPlotRenderer.test.js.snap → XYPlotRenderer.test.ts.snap} RENAMED Viewed

File without changes

package/src/__snapshots__/{index.test.js.snap → index.test.ts.snap} RENAMED Viewed

File without changes

package/src/drawxy.ts CHANGED Viewed

@@ -3,6 +3,8 @@ import {
   readConfObject,
 } from '@jbrowse/core/configuration'
 import { clamp, featureSpanPx, Feature, Region } from '@jbrowse/core/util'
+// locals
 import { getOrigin, getScale, ScaleOpts } from './util'
 // avoid drawing negative width features for SVG exports

package/src/{index.test.js → index.test.ts} RENAMED Viewed

@@ -3,7 +3,6 @@ import { getSnapshot } from 'mobx-state-tree'
 import ThisPlugin from '.'
 test('plugin in a stock JBrowse', () => {
-  console.warn = jest.fn()
   const pluginManager = new PluginManager([new ThisPlugin()])
   pluginManager.createPluggableElements()
   pluginManager.configure()

package/src/{util.test.js → util.test.ts} RENAMED Viewed

@@ -28,18 +28,16 @@ test('test inverted', () => {
 test('test minScore', () => {
   const scaleType = 'linear'
-  const domain = [0, 100]
-  const range = [0, 100]
-  const bounds = [50, undefined]
-  const ret = getNiceDomain({ scaleType, domain, range, bounds })
+  const domain = [0, 100] as const
+  const bounds = [50, undefined] as const
+  const ret = getNiceDomain({ scaleType, domain, bounds })
   expect(ret).toEqual([50, 100])
 })
 test('test min and max score', () => {
   const scaleType = 'linear'
-  const domain = [1, 100]
-  const range = [0, 100]
-  const bounds = [undefined, 70]
-  const ret = getNiceDomain({ scaleType, domain, range, bounds })
+  const domain = [1, 100] as const
+  const bounds = [undefined, 70] as const
+  const ret = getNiceDomain({ scaleType, domain, bounds })
   expect(ret).toEqual([0, 70])
 })

package/src/util.ts CHANGED Viewed

@@ -21,7 +21,7 @@ export interface ScaleOpts {
   range: number[]
   scaleType: string
   pivotValue?: number
-  inverted: boolean
+  inverted?: boolean
 }
 export interface Source {
@@ -114,8 +114,8 @@ export function getNiceDomain({
   bounds,
 }: {
   scaleType: string
-  domain: number[]
-  bounds: number[]
+  domain: readonly [number, number]
+  bounds: readonly [number | undefined, number | undefined]
 }) {
   const [minScore, maxScore] = bounds
   let [min, max] = domain