@jbrowse/core 2.4.0 → 2.4.2

package/BaseFeatureWidget/BaseFeatureDetail.d.ts

@@ -3,9 +3,7 @@ import { IAnyStateTreeNode } from 'mobx-state-tree';
 import { BaseCardProps, BaseProps } from './types';
 import { SimpleFeatureSerializedNoId } from '../util/simpleFeature';
 export declare const useStyles: (params: void, styleOverrides?: {
-    props: {
-        classes?: Record<string, string> | undefined;
-    } & Record<string, unknown>;
+    props: any;
     ownerState?: Record<string, unknown> | undefined;
 } | undefined) => {
     classes: Record<"expansionPanelDetails" | "expandIcon" | "field" | "fieldDescription" | "fieldName" | "fieldValue" | "fieldSubvalue", string>;

package/BaseFeatureWidget/BaseFeatureDetail.js

@@ -169,7 +169,7 @@ function Position(props) {
         '1': '+',
     };
     const str = strandMap[strand] ? `(${strandMap[strand]})` : '';
-    // @ts-ignore
+    // @ts-expect-error
     const loc = (0, util_1.assembleLocString)(feature);
     return react_1.default.createElement(react_1.default.Fragment, null, `${loc} ${str}`);
 }
@@ -209,7 +209,11 @@ exports.UriLink = UriLink;
 function DataGridDetails({ value, prefix, name, }) {
     const keys = Object.keys(value[0]).sort();
     const unionKeys = new Set(keys);
-    value.forEach((val) => Object.keys(val).forEach(k => unionKeys.add(k)));
+    for (const val of value) {
+        for (const k of Object.keys(val)) {
+            unionKeys.add(k);
+        }
+    }
     if (unionKeys.size < keys.length + 5) {
         // avoids key 'id' from being used in row data
         const rows = Object.entries(value).map(([k, val]) => {
@@ -294,12 +298,12 @@ function UriAttribute({ value, prefix, name, }) {
 }
 function Attributes(props) {
     const { attributes, omit = [], omitSingleLevel = [], descriptions, formatter = val => val, hideUris, prefix = [], } = props;
-    const omits = [...omit, ...globalOmit, ...omitSingleLevel];
+    const omits = new Set([...omit, ...globalOmit, ...omitSingleLevel]);
     const { __jbrowsefmt, ...rest } = attributes;
     const formattedAttributes = { ...rest, ...__jbrowsefmt };
-    const maxLabelWidth = generateMaxWidth(Object.entries(formattedAttributes).filter(([k, v]) => v !== undefined && !omits.includes(k)), prefix);
+    const maxLabelWidth = generateMaxWidth(Object.entries(formattedAttributes).filter(([k, v]) => v !== undefined && !omits.has(k)), prefix);
     return (react_1.default.createElement(react_1.default.Fragment, null, Object.entries(formattedAttributes)
-        .filter(([k, v]) => v !== undefined && !omits.includes(k))
+        .filter(([k, v]) => v !== undefined && !omits.has(k))
         .map(([key, value]) => {
         const description = accessNested([...prefix, key], descriptions);
         if (Array.isArray(value)) {
@@ -333,7 +337,7 @@ function generateTitle(name, id, type) {
 }
 function FeatureDetails(props) {
     const { omit = [], model, feature, depth = 0 } = props;
-    const { name = '', id = '', type = '', subfeatures } = feature;
+    const { mate, name = '', id = '', type = '', subfeatures } = feature;
     const pm = (0, util_1.getEnv)(model).pluginManager;
     const session = (0, util_1.getSession)(model);
     const ExtraPanel = pm.evaluateExtensionPoint('Core-extraFeaturePanel', null, {
@@ -344,10 +348,10 @@ function FeatureDetails(props) {
     return (react_1.default.createElement(BaseCard, { title: generateTitle(name, id, type) },
         react_1.default.createElement(material_1.Typography, null, "Core details"),
         react_1.default.createElement(CoreDetails, { ...props }),
-        feature.mate ? (react_1.default.createElement(react_1.default.Fragment, null,
+        mate ? (react_1.default.createElement(react_1.default.Fragment, null,
             react_1.default.createElement(material_1.Divider, null),
             react_1.default.createElement(material_1.Typography, null, "Mate details"),
-            react_1.default.createElement(CoreDetails, { ...props, feature: feature.mate }))) : null,
+            react_1.default.createElement(CoreDetails, { ...props, feature: mate }))) : null,
         react_1.default.createElement(material_1.Divider, null),
         react_1.default.createElement(material_1.Typography, null, "Attributes"),
         react_1.default.createElement(Attributes, { attributes: feature, ...props, omit: omit, omitSingleLevel: coreDetails }),
@@ -369,6 +373,6 @@ exports.default = (0, mobx_react_1.observer)(function ({ model }) {
     // setting null is not allowed by jexl so we set it to undefined to hide. see
     // config guide. this replacement happens both here and when snapshotting the
     // featureData
-    const g = JSON.parse(JSON.stringify(featureData, (_, v) => typeof v === 'undefined' ? null : v));
+    const g = JSON.parse(JSON.stringify(featureData, (_, v) => (v === undefined ? null : v)));
     return isEmpty(g) ? null : react_1.default.createElement(FeatureDetails, { model: model, feature: g });
 });

package/BaseFeatureWidget/SequenceFeatureDetails.js

@@ -48,9 +48,6 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
     formControl: {
         margin: 0,
     },
-    container: {
-        margin: theme.spacing(1),
-    },
     container2: {
         marginTop: theme.spacing(1),
     },
@@ -60,14 +57,10 @@ const BPLIMIT = 500000;
 // sequence. this is a best effort and weird genomic phenomena could lead these
 // to not be 100% accurate
 function SequenceFeatureDetails({ model, feature }) {
-    var _a;
     const { classes } = useStyles();
-    const parentFeature = feature;
-    const hasCDS = !!((_a = parentFeature.subfeatures) === null || _a === void 0 ? void 0 : _a.find(sub => sub.type === 'CDS'));
-    const isGene = feature.type === 'gene';
     const [shown, setShown] = (0, react_1.useState)(false);
     const [helpShown, setHelpShown] = (0, react_1.useState)(false);
-    return (isGene && !hasCDS) || !model ? null : (react_1.default.createElement("div", { className: classes.container2 },
+    return !model ? null : (react_1.default.createElement("div", { className: classes.container2 },
         react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => setShown(!shown) }, shown ? 'Hide feature sequence' : 'Show feature sequence'),
         react_1.default.createElement(material_1.FormControl, { className: classes.formControl },
             react_1.default.createElement(material_1.IconButton, { onClick: () => setHelpShown(true) },
@@ -79,7 +72,7 @@ function SequenceFeatureDetails({ model, feature }) {
 }
 exports.default = SequenceFeatureDetails;
 function FeatureSequence({ model, feature }) {
-    var _a;
+    var _a, _b;
     const { classes } = useStyles();
     const parentFeature = feature;
     const hasCDS = !!((_a = parentFeature.subfeatures) === null || _a === void 0 ? void 0 : _a.find(sub => sub.type === 'CDS'));
@@ -166,7 +159,7 @@ function FeatureSequence({ model, feature }) {
     // only attempt fetching gene type sequence on a bare CDS if it has no parent
     const attemptGeneType = feature.type === 'CDS'
         ? sequenceTypes.includes('CDS') && !feature.parentId
-        : sequenceTypes.includes(feature.type);
+        : sequenceTypes.includes(feature.type) && ((_b = feature.subfeatures) === null || _b === void 0 ? void 0 : _b.length);
     const val = attemptGeneType ? (hasCDS ? 'cds' : 'cdna') : 'genomic';
     // this useEffect is needed to reset the mode/setMode useState because the
     // contents of the select box can completely change depending on whether we

package/BaseFeatureWidget/SequencePanel.js

@@ -68,7 +68,7 @@ const SeqPanel = react_1.default.forwardRef(function (props, ref) {
             } },
             react_1.default.createElement("span", { style: { background: 'white' } }, `>${feature.name ||
                 feature.id ||
-                feature.refName + ':' + (feature.start + 1) + '-' + feature.end}-${mode}\n`),
+                `${feature.refName}:${feature.start + 1}-${feature.end}`}-${mode}\n`),
             react_1.default.createElement("br", null),
             mode === 'genomic' ? (react_1.default.createElement(SequenceBox_1.Genomic, { sequence: seq })) : mode === 'genomic_sequence_updown' ? (react_1.default.createElement(SequenceBox_1.Genomic, { sequence: seq, upstream: upstream, downstream: downstream })) : mode === 'cds' ? (react_1.default.createElement(SequenceBox_1.GeneCDS, { cds: cds, sequence: seq })) : mode === 'cdna' ? (react_1.default.createElement(SequenceBox_1.GenecDNA, { exons: exons, cds: cds, utr: utr, sequence: seq, intronBp: intronBp })) : mode === 'protein' ? (react_1.default.createElement(SequenceBox_1.GeneProtein, { cds: cds, codonTable: codonTable, sequence: seq })) : mode === 'gene' ? (react_1.default.createElement(SequenceBox_1.GenecDNA, { exons: exons, cds: cds, utr: utr, sequence: seq, includeIntrons: true, intronBp: intronBp })) : mode === 'gene_collapsed_intron' ? (react_1.default.createElement(SequenceBox_1.GenecDNA, { exons: exons, cds: cds, sequence: seq, utr: utr, includeIntrons: true, collapseIntron: true, intronBp: intronBp })) : mode === 'gene_updownstream' ? (react_1.default.createElement(SequenceBox_1.GenecDNA, { exons: exons, cds: cds, sequence: seq, utr: utr, upstream: upstream, downstream: downstream, includeIntrons: true, intronBp: intronBp })) : mode === 'gene_updownstream_collapsed_intron' ? (react_1.default.createElement(SequenceBox_1.GenecDNA, { exons: exons, cds: cds, sequence: seq, utr: utr, upstream: upstream, downstream: downstream, includeIntrons: true, collapseIntron: true, intronBp: intronBp })) : (react_1.default.createElement("div", null, "Unknown type")))));
 });

package/BaseFeatureWidget/index.d.ts

@@ -28,8 +28,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 }>>, {
-    id: string;
     type: "BaseFeatureWidget";
+    id: string;
     track: import("mobx-state-tree").ReferenceIdentifier | undefined;
     view: import("mobx-state-tree").ReferenceIdentifier | undefined;
     trackId: string | undefined;

package/BaseFeatureWidget/index.js

@@ -60,20 +60,17 @@ function stateModelFactory(pluginManager) {
                 const session = (0, util_1.getSession)(self);
                 if (unformattedFeatureData) {
                     const feature = (0, clone_1.default)(unformattedFeatureData);
-                    const f = (obj, arg2) => (0, configuration_1.getConf)(obj, ['formatDetails', arg2], { feature });
+                    const combine = (arg2, feature) => ({
+                        ...(0, configuration_1.getConf)(session, ['formatDetails', arg2], { feature }),
+                        ...(0, configuration_1.getConf)(track, ['formatDetails', arg2], { feature }),
+                    });
                     if (track) {
                         // eslint-disable-next-line no-underscore-dangle
-                        feature.__jbrowsefmt = {
-                            ...f(session, 'feature'),
-                            ...f(track, 'feature'),
-                        };
+                        feature.__jbrowsefmt = combine('feature', feature);
                         const depth = (0, configuration_1.getConf)(track, ['formatDetails', 'depth']);
                         formatSubfeatures(feature, depth, sub => {
                             // eslint-disable-next-line no-underscore-dangle
-                            sub.__jbrowsefmt = {
-                                ...f(session, 'subfeature'),
-                                ...f(track, 'subfeature'),
-                            };
+                            sub.__jbrowsefmt = combine('subfeatures', sub);
                         });
                     }
                     self.setFormattedData(feature);
@@ -82,7 +79,7 @@ function stateModelFactory(pluginManager) {
         },
     }))
         .preProcessSnapshot(snap => {
-        // @ts-ignore
+        // @ts-expect-error
         const { featureData, finalizedFeatureData, ...rest } = snap;
         return {
             unformattedFeatureData: featureData,
@@ -100,7 +97,7 @@ function stateModelFactory(pluginManager) {
             // hidden, setting null is not allowed by jexl so we set it to
             // undefined to hide. see config guide. this replacement happens both
             // here and when displaying the featureData in base feature widget
-            finalizedFeatureData: JSON.parse(JSON.stringify(featureData, (_, v) => typeof v === 'undefined' ? null : v)),
+            finalizedFeatureData: JSON.parse(JSON.stringify(featureData, (_, v) => (v === undefined ? null : v))),
             ...rest,
         };
     });

package/PluginLoader.js

@@ -39,9 +39,9 @@ class PluginLoader {
         if (!isInWebWorker()) {
             return (0, load_script2_1.default)(scriptUrl);
         }
-        // @ts-ignore
+        // @ts-expect-error
         if (globalThis === null || globalThis === void 0 ? void 0 : globalThis.importScripts) {
-            // @ts-ignore
+            // @ts-expect-error
             await globalThis.importScripts(scriptUrl);
             return;
         }
@@ -84,14 +84,14 @@ class PluginLoader {
         }
         const moduleName = def.name;
         const umdName = `JBrowsePlugin${moduleName}`;
-        if (typeof jest !== 'undefined') {
-            // @ts-ignore
-            globalThis[umdName] = { default: Plugin_1.default };
+        if (typeof jest === 'undefined') {
+            await this.loadScript(parsedUrl.href);
         }
         else {
-            await this.loadScript(parsedUrl.href);
+            // @ts-expect-error
+            globalThis[umdName] = { default: Plugin_1.default };
         }
-        // @ts-ignore
+        // @ts-expect-error
         const plugin = globalThis[umdName];
         if (!plugin) {
             throw new Error(`Failed to load UMD bundle for ${moduleName}, ${umdName} is undefined`);
@@ -118,7 +118,7 @@ class PluginLoader {
         return plugin.default;
     }
     installGlobalReExports(target) {
-        // @ts-ignore
+        // @ts-expect-error
         target.JBrowseExports = Object.fromEntries(Object.entries(ReExports_1.default).map(([moduleName, module]) => {
             return [moduleName, module];
         }));

package/PluginManager.d.ts

@@ -195,7 +195,7 @@ export default class PluginManager {
             showAllRegions(): void;
             zoomOut(): void;
             zoomIn(): void;
-            zoomTo(newBpPerPx: number, offset?: number): number;
+            zoomTo(bpPerPx: number, offset?: number): number;
             scrollTo(offsetPx: number): number;
             centerAt(coord: number, refName: string | undefined, regionNumber: number): void;
             scroll(distance: number): number;
@@ -228,9 +228,7 @@ export default class PluginManager {
                 name?: string | Record<string, unknown> | undefined;
                 uniqId?: string | undefined;
             } | undefined) => <RuleName extends string>(cssObjectByRuleNameOrGetCssObjectByRuleName: Record<RuleName, import("tss-react").CSSObject> | ((theme: import("@mui/material").Theme, params: Params, classes: Record<RuleNameSubsetReferencableInNestedSelectors, string>) => Record<RuleNameSubsetReferencableInNestedSelectors | RuleName, import("tss-react").CSSObject>)) => (params: Params, styleOverrides?: {
-                props: {
-                    classes?: Record<string, string> | undefined;
-                } & Record<string, unknown>;
+                props: any;
                 ownerState?: Record<string, unknown> | undefined;
             } | undefined) => {
                 classes: Record<RuleName, string>;

package/PluginManager.js

@@ -149,7 +149,6 @@ class PluginManager {
         }
         this.pluginMetadata[plugin.name] = metadata;
         if ('definition' in load) {
-            // @ts-ignore
             this.runtimePluginDefinitions.push(load.definition);
         }
         plugin.install(this);
@@ -253,7 +252,7 @@ class PluginManager {
     pluggableMstType(groupName, fieldName, fallback = mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.null)) {
         const pluggableTypes = this.getElementTypeRecord(groupName)
             .all()
-            // @ts-ignore
+            // @ts-expect-error
             .map(t => t[fieldName])
             .filter(t => (0, mobx_state_tree_1.isType)(t) && (0, mobx_state_tree_1.isModelType)(t));
         // try to smooth over the case when no types are registered, mostly
@@ -268,7 +267,7 @@ class PluginManager {
     pluggableConfigSchemaType(typeGroup, fieldName = 'configSchema') {
         const pluggableTypes = this.getElementTypeRecord(typeGroup)
             .all()
-            // @ts-ignore
+            // @ts-expect-error
             .map(t => t[fieldName])
             .filter(t => (0, configuration_1.isBareConfigurationSchemaType)(t));
         if (pluggableTypes.length === 0) {

package/ReExports/Attributes.d.ts

@@ -1,2 +1 @@
-import { Attributes } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
-export default Attributes;
+export { Attributes as default } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';

package/ReExports/Attributes.js

@@ -1,5 +1,6 @@
 "use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
 // convert named export to default for lazy react
-const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
-exports.default = BaseFeatureDetail_1.Attributes;
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = void 0;
+var BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+Object.defineProperty(exports, "default", { enumerable: true, get: function () { return BaseFeatureDetail_1.Attributes; } });

package/ReExports/BaseCard.d.ts

@@ -1,2 +1 @@
-import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
-export default BaseCard;
+export { BaseCard as default } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';

package/ReExports/BaseCard.js

@@ -1,5 +1,6 @@
 "use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
 // convert named export to default for lazy react
-const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
-exports.default = BaseFeatureDetail_1.BaseCard;
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = void 0;
+var BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+Object.defineProperty(exports, "default", { enumerable: true, get: function () { return BaseFeatureDetail_1.BaseCard; } });

package/ReExports/DataGrid.d.ts

@@ -1,2 +1 @@
-import { DataGrid } from '@mui/x-data-grid';
-export { DataGrid as default };
+export { DataGrid as default } from '@mui/x-data-grid';

package/ReExports/DataGrid.js

@@ -1,6 +1,6 @@
 "use strict";
+// convert named export to default for lazy react
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = void 0;
-// convert named export to default for lazy react
-const x_data_grid_1 = require("@mui/x-data-grid");
+var x_data_grid_1 = require("@mui/x-data-grid");
 Object.defineProperty(exports, "default", { enumerable: true, get: function () { return x_data_grid_1.DataGrid; } });

package/ReExports/FeatureDetails.d.ts

@@ -1,2 +1 @@
-import { FeatureDetails } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
-export default FeatureDetails;
+export { FeatureDetails as default } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';

package/ReExports/FeatureDetails.js

@@ -1,5 +1,6 @@
 "use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
 // convert named export to default for lazy react
-const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
-exports.default = BaseFeatureDetail_1.FeatureDetails;
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = void 0;
+var BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+Object.defineProperty(exports, "default", { enumerable: true, get: function () { return BaseFeatureDetail_1.FeatureDetails; } });

package/ReExports/index.d.ts

@@ -1,2 +1 @@
-import modules from './modules';
-export default modules;
+export { default } from './modules';

package/ReExports/index.js

@@ -3,5 +3,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const modules_1 = __importDefault(require("./modules"));
-exports.default = modules_1.default;
+exports.default = void 0;
+var modules_1 = require("./modules");
+Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(modules_1).default; } });

package/ReExports/modules.d.ts

@@ -112,7 +112,7 @@ declare const libs: {
         showAllRegions(): void;
         zoomOut(): void;
         zoomIn(): void;
-        zoomTo(newBpPerPx: number, offset?: number): number;
+        zoomTo(bpPerPx: number, offset?: number): number;
         scrollTo(offsetPx: number): number;
         centerAt(coord: number, refName: string | undefined, regionNumber: number): void;
         scroll(distance: number): number;
@@ -145,9 +145,7 @@ declare const libs: {
             name?: string | Record<string, unknown> | undefined;
             uniqId?: string | undefined;
         } | undefined) => <RuleName extends string>(cssObjectByRuleNameOrGetCssObjectByRuleName: Record<RuleName, import("tss-react").CSSObject> | ((theme: MUIStyles.Theme, params: Params, classes: Record<RuleNameSubsetReferencableInNestedSelectors, string>) => Record<RuleNameSubsetReferencableInNestedSelectors | RuleName, import("tss-react").CSSObject>)) => (params: Params, styleOverrides?: {
-            props: {
-                classes?: Record<string, string> | undefined;
-            } & Record<string, unknown>;
+            props: any;
             ownerState?: Record<string, unknown> | undefined;
         } | undefined) => {
             classes: Record<RuleName, string>;

package/ReExports/modules.js

@@ -445,11 +445,11 @@ const libs = {
     },
     '@jbrowse/core/data_adapters/BaseAdapter': BaseAdapterExports,
 };
-const libsList = Array.from(Object.keys(libs));
+const libsList = Object.keys(libs);
 // make sure that all the items in the ReExports/list array (used by build
 // systems and such) are included here, and vice versa
 const inLibsOnly = libsList.filter(mod => !list_1.default.includes(mod));
-if (inLibsOnly.length) {
+if (inLibsOnly.length > 0) {
     throw new Error(`The following modules are in the re-exports list, but not the modules libs: ${inLibsOnly.join(', ')}`);
 }
 const inReExportsOnly = list_1.default.filter(mod => !libsList.includes(mod));

package/assemblyManager/assembly.js

@@ -74,7 +74,7 @@ async function loadRefNameMap(assembly, adapterConfig, options, signal) {
 }
 // Valid refName pattern from https://samtools.github.io/hts-specs/SAMv1.pdf
 function checkRefName(refName) {
-    if (!refName.match(refNameRegex)) {
+    if (!refNameRegex.test(refName)) {
         throw new Error(`Encountered invalid refName: "${refName}"`);
     }
 }
@@ -104,7 +104,7 @@ function assemblyFactory(assemblyConfigType, pm) {
     }))
         .views(self => ({
         get initialized() {
-            // @ts-ignore
+            // @ts-expect-error
             self.load();
             return !!self.refNameAliases;
         },
@@ -112,7 +112,7 @@ function assemblyFactory(assemblyConfigType, pm) {
             return (0, configuration_1.getConf)(self, 'name');
         },
         get regions() {
-            // @ts-ignore
+            // @ts-expect-error
             self.load();
             return self.volatileRegions;
         },
@@ -172,7 +172,7 @@ function assemblyFactory(assemblyConfigType, pm) {
             if (!self.refNames) {
                 return undefined;
             }
-            const idx = self.refNames.findIndex(r => r === refName);
+            const idx = self.refNames.indexOf(refName);
             if (idx === -1) {
                 return undefined;
             }
@@ -301,7 +301,7 @@ async function getCytobands(config, pm) {
     const type = pm.getAdapterType(config.type);
     const CLASS = await type.getAdapterClass();
     const adapter = new CLASS(config, undefined, pm);
-    // @ts-ignore
+    // @ts-expect-error
     return adapter.getData();
 }
 async function getAssemblyRegions(config, pm, signal) {

package/assemblyManager/assemblyConfigSchema.js

@@ -42,7 +42,7 @@ function assemblyConfigSchema(pluginManager) {
         }, {
             preProcessSnapshot: snap => {
                 // allow refNameAliases to be unspecified
-                // @ts-ignore
+                // @ts-expect-error
                 if (!snap.adapter) {
                     return { adapter: { type: 'RefNameAliasAdapter' } };
                 }
@@ -59,7 +59,7 @@ function assemblyConfigSchema(pluginManager) {
         }, {
             preProcessSnapshot: snap => {
                 // allow cytoBand to be unspecified
-                // @ts-ignore
+                // @ts-expect-error
                 if (!snap.adapter) {
                     return { adapter: { type: 'CytobandAdapter' } };
                 }

package/configuration/configurationSchema.d.ts

@@ -1,5 +1,5 @@
 import { Instance, IAnyType } from 'mobx-state-tree';
-import { ConfigSlotDefinition } from './configurationSlot';
+import ConfigSlot, { ConfigSlotDefinition } from './configurationSlot';
 export interface ConfigurationSchemaDefinition {
     [n: string]: ConfigSlotDefinition | ConfigurationSchemaDefinition | string | number | IAnyType;
 }
@@ -23,6 +23,8 @@ export interface AnyConfigurationSchemaType extends ReturnType<typeof makeConfig
     type: string;
 }
 export type AnyConfigurationModel = Instance<AnyConfigurationSchemaType>;
+export type AnyConfigurationSlotType = ReturnType<typeof ConfigSlot>;
+export type AnyConfigurationSlot = Instance<AnyConfigurationSlotType>;
 export type ConfigurationModel<SCHEMA extends AnyConfigurationSchemaType> = Instance<SCHEMA>;
 export declare function ConfigurationSchema<DEFINITION extends ConfigurationSchemaDefinition, OPTIONS extends ConfigurationSchemaOptions>(modelName: string, inputSchemaDefinition: DEFINITION, inputOptions?: OPTIONS): AnyConfigurationSchemaType;
 export declare function ConfigurationReference(schemaType: IAnyType): import("mobx-state-tree").ITypeUnion<any, any, any>;

package/configuration/configurationSchema.js

@@ -32,7 +32,7 @@ function preprocessConfigurationSchemaArguments(modelName, inputSchemaDefinition
             ...schemaDefinition,
         };
         options = {
-            ...(inputOptions.baseConfiguration.jbrowseSchemaOptions || {}),
+            ...inputOptions.baseConfiguration.jbrowseSchemaOptions,
             ...inputOptions,
         };
         delete options.baseConfiguration;

package/configuration/configurationSlot.d.ts

@@ -1,5 +1,6 @@
 import { IAnyModelType, IAnyComplexType } from 'mobx-state-tree';
 export interface ConfigSlotDefinition {
+    /** human-readable description of the slot's meaning */
     description?: string;
     /** custom base MST model for the slot's value */
     model?: IAnyModelType | IAnyComplexType;

package/configuration/util.js

@@ -100,7 +100,7 @@ exports.getConf = getConf;
 function getTypeNamesFromExplicitlyTypedUnion(maybeUnionType) {
     if ((0, mobx_state_tree_1.isType)(maybeUnionType)) {
         maybeUnionType = (0, mst_reflection_1.resolveLateType)(maybeUnionType);
-        // @ts-ignore
+        // @ts-expect-error
         if ((0, mobx_state_tree_1.isUnionType)(maybeUnionType)) {
             const typeNames = [];
             (0, mst_reflection_1.getUnionSubTypes)(maybeUnionType).forEach(type => {

package/data_adapters/BaseAdapter.js

@@ -169,7 +169,7 @@ class BaseFeatureDataAdapter extends BaseAdapter {
             }
             else {
                 console.warn("Stats estimation reached timeout, or didn't get enough features");
-                return { featureDensity: Infinity };
+                return { featureDensity: Number.POSITIVE_INFINITY };
             }
         };
         return statsFromInterval(1000, 0);

package/data_adapters/CytobandAdapter/CytobandAdapter.js

@@ -17,7 +17,7 @@ class CytobandAdapter extends BaseAdapter_1.BaseAdapter {
         if (loc.uri === '' || loc.uri === '/path/to/cytoband.txt.gz') {
             return [];
         }
-        const buffer = (await (0, io_1.openLocation)(loc, pm).readFile());
+        const buffer = await (0, io_1.openLocation)(loc, pm).readFile();
         const buf = isGzip(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer;
         const text = new TextDecoder('utf8', { fatal: true }).decode(buf);
         return text

package/data_adapters/dataAdapterCache.d.ts

@@ -1,7 +1,8 @@
 import { SnapshotIn } from 'mobx-state-tree';
 import PluginManager from '../PluginManager';
-import { AnyConfigurationSchemaType } from '../configuration/configurationSchema';
+import { AnyConfigurationSchemaType } from '../configuration';
 import { AnyDataAdapter } from './BaseAdapter';
+type ConfigSnap = SnapshotIn<AnyConfigurationSchemaType>;
 interface AdapterCacheEntry {
     dataAdapter: AnyDataAdapter;
     sessionIds: Set<string>;
@@ -21,7 +22,7 @@ export declare function getAdapter(pluginManager: PluginManager, sessionId: stri
  * allows them to get any sub-adapters that they need
  * internally, staying with the same worker session ID
  */
-export type getSubAdapterType = (adapterConfigSnapshot: SnapshotIn<AnyConfigurationSchemaType>) => ReturnType<typeof getAdapter>;
+export type getSubAdapterType = (adapterConfigSnap: ConfigSnap) => ReturnType<typeof getAdapter>;
 export declare function freeAdapterResources(specification: Record<string, any>): number;
 export declare function clearAdapterCache(): void;
 export {};

package/data_adapters/dataAdapterCache.js

@@ -39,7 +39,6 @@ async function getAdapter(pluginManager, sessionId, adapterConfigSnapshot) {
         // (such as sequence adapters or wrapped subadapters) that it needs
         //
         const { AdapterClass, getAdapterClass } = dataAdapterType;
-        // @ts-ignore
         const CLASS = AdapterClass || (await getAdapterClass());
         if (!CLASS) {
             throw new Error('Failed to get adapter');
@@ -81,11 +80,11 @@ function freeAdapterResources(specification) {
             else {
                 const regions = specification.regions ||
                     (specification.region ? [specification.region] : []);
-                regions.forEach((region) => {
+                for (const region of regions) {
                     if (region.refName !== undefined) {
                         cacheEntry.dataAdapter.freeResources(region);
                     }
-                });
+                }
             }
         });
     }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.4.0",
+  "version": "2.4.2",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -54,7 +54,6 @@
     "material-ui-popup-state": "^5.0.0",
     "rbush": "^3.0.1",
     "react-error-boundary": "^3.0.0",
-    "react-use-measure": "^2.1.1",
     "serialize-error": "^8.0.0",
     "shortid": "^2.2.13",
     "svg-path-generator": "^1.1.0"
@@ -75,5 +74,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "78707a2bc3ba8489f26a590ef83f62ede945d048"
+  "gitHead": "36e382a70e7d220343b873e7e6aba5c83e5342c8"
 }

package/pluggableElementTypes/RpcMethodType.js

@@ -55,7 +55,7 @@ class RpcMethodType extends PluggableElementBase_1.default {
         catch (error) {
             if ((0, types_1.isAuthNeededException)(error)) {
                 const retryAccount = 
-                // @ts-ignore
+                // @ts-expect-error
                 (_a = this.pluginManager.rootModel) === null || _a === void 0 ? void 0 : _a.createEphemeralInternetAccount(`HTTPBasicInternetAccount-${new URL(error.url).origin}`, {}, error.url);
                 throw new types_1.RetryError('Retrying with created internet account', retryAccount.internetAccountId);
             }

package/pluggableElementTypes/index.d.ts

@@ -11,6 +11,16 @@ import TextSearchAdapterType from './TextSearchAdapterType';
 import AddTrackWorkflowType from './AddTrackWorkflowType';
 export * from './renderers';
 export * from './models';
-export { AdapterType, ConnectionType, RendererType, WidgetType, TrackType, DisplayType, ViewType, RpcMethodType, InternetAccountType, TextSearchAdapterType, AddTrackWorkflowType, };
 export type PluggableElementType = AdapterType | ConnectionType | RendererType | WidgetType | TrackType | DisplayType | ViewType | RpcMethodType | InternetAccountType | TextSearchAdapterType | AddTrackWorkflowType;
 export type PluggableElementMember = keyof AdapterType | keyof ConnectionType | keyof RendererType | keyof WidgetType | keyof TrackType | keyof DisplayType | keyof ViewType | keyof RpcMethodType | keyof InternetAccountType | keyof TextSearchAdapterType | keyof AddTrackWorkflowType;
+export { default as AdapterType } from './AdapterType';
+export { default as RendererType } from './renderers/RendererType';
+export { default as ConnectionType } from './ConnectionType';
+export { default as TrackType } from './TrackType';
+export { default as WidgetType } from './WidgetType';
+export { default as ViewType } from './ViewType';
+export { default as DisplayType } from './DisplayType';
+export { default as InternetAccountType } from './InternetAccountType';
+export { default as RpcMethodType } from './RpcMethodType';
+export { default as AddTrackWorkflowType } from './AddTrackWorkflowType';
+export { default as TextSearchAdapterType } from './TextSearchAdapterType';