@jbrowse/plugin-circular-view 2.13.0 → 2.14.0

package/dist/BaseChordDisplay/components/Loading.js

@@ -73,8 +73,12 @@ const Loading = (0, mobx_react_1.observer)(function ({ model: { renderProps: { r
     // only show the loading message after 400ms to prevent excessive flickering
     const [shown, setShown] = (0, react_1.useState)(false);
     (0, react_1.useEffect)(() => {
-        const timeout = setTimeout(() => setShown(true), 400);
-        return () => clearTimeout(timeout);
+        const timeout = setTimeout(() => {
+            setShown(true);
+        }, 400);
+        return () => {
+            clearTimeout(timeout);
+        };
     });
     return !shown ? null : (react_1.default.createElement("g", null,
         react_1.default.createElement("defs", null,

package/dist/BaseChordDisplay/models/model.d.ts

@@ -42,7 +42,7 @@ export declare const BaseChordDisplayModel: import("mobx-state-tree").IModelType
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function;
+        onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: React.FC<{
@@ -103,10 +103,9 @@ export declare const BaseChordDisplayModel: import("mobx-state-tree").IModelType
     renderProps(): any;
     /**
      * #getter
-     * the pluggable element type object for this display's
-     * renderer
+     * the pluggable element type object for this display's renderer
      */
-    readonly rendererType: RendererType;
+    readonly rendererType: RendererType | undefined;
     /**
      * #method
      */
@@ -147,6 +146,6 @@ export declare const BaseChordDisplayModel: import("mobx-state-tree").IModelType
      * #method
      */
     renderSvg(opts: ExportSvgOptions & {
-        theme: ThemeOptions;
+        theme?: ThemeOptions;
     }): Promise<React.JSX.Element>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/BaseChordDisplay/models/model.js

@@ -93,7 +93,6 @@ exports.BaseChordDisplayModel = mobx_state_tree_1.types
         return {
             ...(0, tracks_1.getParentRenderProps)(self),
             rpcDriverName: self.rpcDriverName,
-            displayModel: self,
             bezierRadius: view.radiusPx * self.bezierRadiusRatio,
             radius: view.radiusPx,
             blockDefinitions: this.blockDefinitions,
@@ -102,20 +101,10 @@ exports.BaseChordDisplayModel = mobx_state_tree_1.types
     },
     /**
      * #getter
-     * the pluggable element type object for this display's
-     * renderer
+     * the pluggable element type object for this display's renderer
      */
     get rendererType() {
-        const display = self;
-        const { pluginManager } = (0, util_1.getEnv)(self);
-        const ThisRendererType = pluginManager.getRendererType(self.rendererTypeName);
-        if (!ThisRendererType) {
-            throw new Error(`renderer "${display.rendererTypeName}" not found`);
-        }
-        if (!ThisRendererType.ReactComponent) {
-            throw new Error(`renderer ${display.rendererTypeName} has no ReactComponent, it may not be completely implemented yet`);
-        }
-        return ThisRendererType;
+        return (0, util_1.getEnv)(self).pluginManager.getRendererType(self.rendererTypeName);
     },
     /**
      * #method
@@ -133,9 +122,6 @@ exports.BaseChordDisplayModel = mobx_state_tree_1.types
             return undefined;
         }
         const session = (0, util_1.getSession)(self);
-        if (!session) {
-            return undefined;
-        }
         const { selection } = session;
         // does it quack like a feature?
         if ((0, util_1.isFeature)(selection)) {
@@ -212,17 +198,16 @@ exports.BaseChordDisplayModel = mobx_state_tree_1.types
         }, self.renderStarted, self.renderSuccess, self.renderError);
         (0, util_1.makeAbortableReaction)(self, () => ({
             assemblyNames: (0, tracks_1.getTrackAssemblyNames)(self.parentTrack),
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
             adapter: (0, configuration_1.getConf)((0, mobx_state_tree_1.getParent)(self, 2), 'adapter'),
             assemblyManager: (0, util_1.getSession)(self).assemblyManager,
-        }), 
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        async ({ assemblyNames, adapter, assemblyManager }, signal) => {
+        }), async ({ assemblyNames, adapter, assemblyManager }, signal) => {
             return assemblyManager.getRefNameMapForAdapter(adapter, assemblyNames[0], { signal, sessionId: (0, tracks_1.getRpcSessionId)(self) });
         }, {
             name: `${self.type} ${self.id} getting refNames`,
             fireImmediately: true,
-        }, () => { }, refNameMap => self.setRefNameMap(refNameMap), error => {
+        }, () => { }, refNameMap => {
+            self.setRefNameMap(refNameMap);
+        }, error => {
             console.error(error);
             self.setError(error);
         });

package/dist/BaseChordDisplay/models/renderReaction.js

@@ -8,9 +8,7 @@ exports.renderReactionEffect = renderReactionEffect;
 const clone_1 = __importDefault(require("clone"));
 const tracks_1 = require("@jbrowse/core/util/tracks");
 const util_1 = require("@jbrowse/core/util");
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
 function renderReactionData(self) {
-    var _a;
     const view = (0, util_1.getContainingView)(self);
     const { rendererType } = self;
     const { rpcManager } = (0, util_1.getSession)(view);
@@ -19,7 +17,7 @@ function renderReactionData(self) {
         rpcManager,
         renderProps: self.renderProps(),
         renderArgs: {
-            assemblyName: (_a = view.displayedRegions[0]) === null || _a === void 0 ? void 0 : _a.assemblyName,
+            assemblyName: view.displayedRegions[0].assemblyName,
             adapterConfig: (0, clone_1.default)(self.adapterConfig),
             rendererType: rendererType.name,
             regions: (0, clone_1.default)(view.displayedRegions),
@@ -29,11 +27,7 @@ function renderReactionData(self) {
         },
     };
 }
-async function renderReactionEffect(
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-props, signal, 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-self) {
+async function renderReactionEffect(props, signal, self) {
     var _a;
     if (!props) {
         throw new Error('cannot render with no props');

package/dist/CircularView/components/Controls.js

@@ -67,7 +67,9 @@ const Controls = (0, mobx_react_1.observer)(function ({ model }) {
         react_1.default.createElement(material_1.IconButton, { onClick: model.toggleFitToWindowLock, title: model.lockedFitToWindow
                 ? 'locked model to window size'
                 : 'unlocked model to zoom further', disabled: model.tooSmallToLock }, model.lockedFitToWindow ? react_1.default.createElement(Lock_1.default, null) : react_1.default.createElement(LockOpen_1.default, null)),
-        react_1.default.createElement(material_1.IconButton, { onClick: event => setAnchorEl(event.currentTarget) },
+        react_1.default.createElement(material_1.IconButton, { onClick: event => {
+                setAnchorEl(event.currentTarget);
+            } },
             react_1.default.createElement(MoreVert_1.default, null)),
         model.hideTrackSelectorButton ? null : (react_1.default.createElement(material_1.IconButton, { onClick: model.activateTrackSelector, title: "Open track selector", "data-testid": "circular_track_select" },
             react_1.default.createElement(Icons_1.TrackSelector, null))),
@@ -85,6 +87,8 @@ const Controls = (0, mobx_react_1.observer)(function ({ model }) {
             ], onMenuItemClick: (_event, callback) => {
                 callback();
                 setAnchorEl(null);
-            }, open: Boolean(anchorEl), onClose: () => setAnchorEl(null) })) : null));
+            }, open: Boolean(anchorEl), onClose: () => {
+                setAnchorEl(null);
+            } })) : null));
 });
 exports.default = Controls;

package/dist/CircularView/components/ExportSvgDialog.js

@@ -38,7 +38,7 @@ function TextField2({ children, ...rest }) {
         react_1.default.createElement(material_1.TextField, { ...rest }, children)));
 }
 function useSvgLocal(key, val) {
-    return (0, util_1.useLocalStorage)('svg-' + key, val);
+    return (0, util_1.useLocalStorage)(`svg-${key}`, val);
 }
 function ExportSvgDialog({ model, handleClose, }) {
     const session = (0, util_1.getSession)(model);
@@ -51,13 +51,21 @@ function ExportSvgDialog({ model, handleClose, }) {
     return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Export SVG" },
         react_1.default.createElement(material_1.DialogContent, null,
             error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : loading ? (react_1.default.createElement(LoadingMessage, null)) : null,
-            react_1.default.createElement(TextField2, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
-            session.allThemes ? (react_1.default.createElement(TextField2, { select: true, label: "Theme", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (react_1.default.createElement(material_1.MenuItem, { key: key, value: key }, 
+            react_1.default.createElement(TextField2, { helperText: "filename", value: filename, onChange: event => {
+                    setFilename(event.target.value);
+                } }),
+            session.allThemes ? (react_1.default.createElement(TextField2, { select: true, label: "Theme", value: themeName, onChange: event => {
+                    setThemeName(event.target.value);
+                } }, Object.entries(session.allThemes()).map(([key, val]) => (react_1.default.createElement(material_1.MenuItem, { key: key, value: key }, 
             // @ts-expect-error
             val.name || '(Unknown name)'))))) : null,
-            offscreenCanvas ? (react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: rasterizeLayers, onChange: () => setRasterizeLayers(val => !val) }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (react_1.default.createElement(material_1.Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
+            offscreenCanvas ? (react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: rasterizeLayers, onChange: () => {
+                        setRasterizeLayers(val => !val);
+                    } }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (react_1.default.createElement(material_1.Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
         react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"),
+            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                    handleClose();
+                } }, "Cancel"),
             react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", onClick: async () => {
                     setLoading(true);
                     setError(undefined);

package/dist/CircularView/components/ImportForm.d.ts

@@ -1,5 +1,6 @@
 import React from 'react';
+import { CircularViewModel } from '../models/model';
 declare const ImportForm: ({ model }: {
-    model: any;
+    model: CircularViewModel;
 }) => React.JSX.Element;
 export default ImportForm;

package/dist/CircularView/components/ImportForm.js

@@ -34,8 +34,7 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         padding: theme.spacing(6),
     },
 }));
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-const ImportForm = (0, mobx_react_1.observer)(({ model }) => {
+const ImportForm = (0, mobx_react_1.observer)(function ({ model }) {
     const { classes } = useStyles();
     const session = (0, util_1.getSession)(model);
     const { error } = model;
@@ -58,7 +57,7 @@ const ImportForm = (0, mobx_react_1.observer)(({ model }) => {
                         setSelectedAsm(val);
                     }, session: session, selected: selectedAsm })),
             react_1.default.createElement(material_1.Grid, { item: true },
-                react_1.default.createElement(material_1.Button, { disabled: !(regions === null || regions === void 0 ? void 0 : regions.length), onClick: () => {
+                react_1.default.createElement(material_1.Button, { disabled: !regions.length, onClick: () => {
                         model.setError(undefined);
                         model.setDisplayedRegions(regions);
                     }, variant: "contained", color: "primary" }, regions.length || err ? 'Open' : 'Loading...')))));

package/dist/CircularView/components/Ruler.js

@@ -99,11 +99,8 @@ const RegionRulerArc = (0, mobx_react_1.observer)(function ({ model, slice, regi
     const centerRadians = (endRadians + startRadians) / 2;
     const widthPx = (endRadians - startRadians) * radiusPx;
     const session = (0, util_1.getSession)(model);
-    let color;
     const assembly = session.assemblyManager.get(region.assemblyName);
-    if (assembly) {
-        color = assembly.getRefNameColor(region.refName);
-    }
+    let color = assembly ? assembly.getRefNameColor(region.refName) : undefined;
     if (color) {
         try {
             color = (0, color_1.makeContrasting)(color, theme.palette.background.paper);

package/dist/CircularView/models/model.d.ts

@@ -136,8 +136,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
     readonly figureHeight: number;
     /**
      * #getter
-     * this is displayedRegions, post-processed to
-     * elide regions that are too small to see reasonably
+     * this is displayedRegions, post-processed to elide regions that are too
+     * small to see reasonably
      */
     readonly elidedRegions: SliceRegion[];
     /**
@@ -207,10 +207,6 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
      * #action
      */
     setModelViewWhenAdjust(secondCondition: boolean): void;
-    /**
-     * #action
-     */
-    closeView(): void;
     /**
      * #action
      */

package/dist/CircularView/models/model.js

@@ -261,8 +261,8 @@ function stateModelFactory(pluginManager) {
         },
         /**
          * #getter
-         * this is displayedRegions, post-processed to
-         * elide regions that are too small to see reasonably
+         * this is displayedRegions, post-processed to elide regions that are too
+         * small to see reasonably
          */
         get elidedRegions() {
             const visible = [];
@@ -418,13 +418,6 @@ function stateModelFactory(pluginManager) {
                 this.setBpPerPx(self.minBpPerPx);
             }
         },
-        /**
-         * #action
-         */
-        closeView() {
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            (0, mobx_state_tree_1.getParent)(self, 2).removeView(self);
-        },
         /**
          * #action
          */
@@ -518,7 +511,9 @@ function stateModelFactory(pluginManager) {
             const schema = pluginManager.pluggableConfigSchemaType('track');
             const conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
             const t = self.tracks.filter(t => t.configuration === conf);
-            (0, mobx_1.transaction)(() => t.forEach(t => self.tracks.remove(t)));
+            (0, mobx_1.transaction)(() => {
+                t.forEach(t => self.tracks.remove(t));
+            });
             return t.length;
         },
         /**
@@ -551,7 +546,9 @@ function stateModelFactory(pluginManager) {
             return [
                 {
                     label: 'Return to import form',
-                    onClick: () => self.setDisplayedRegions([]),
+                    onClick: () => {
+                        self.setDisplayedRegions([]);
+                    },
                     icon: FolderOpen_1.default,
                 },
                 {

package/dist/CircularView/models/slices.d.ts

@@ -31,7 +31,7 @@ export declare class Slice {
     };
 }
 declare function calculateStaticSlices(self: {
-    elidedRegions: SliceRegion[];
+    elidedRegions: readonly SliceRegion[];
     bpPerRadian: number;
     spacingPx: number;
     pxPerRadian: number;

package/dist/CircularView/models/viewportVisibleRegion.d.ts

@@ -1,4 +1,4 @@
-export declare function cartesianToPolar(x: number, y: number): number[];
+export declare function cartesianToPolar(x: number, y: number): readonly [number, number];
 export declare function thetaRangesOverlap(r1start: number, r1length: number, r2start: number, r2length: number): boolean;
 export declare function viewportVisibleSection(viewSides: [number, number, number, number], circleCenter: [number, number], circleRadius: number): {
     rho: [number, number];

package/dist/CircularView/models/viewportVisibleRegion.js

@@ -85,7 +85,7 @@ function viewportVisibleSection(viewSides, circleCenter, circleRadius) {
             [viewL, viewB],
             [viewR, viewB],
         ];
-        let maxRho = -Infinity;
+        let maxRho = Number.NEGATIVE_INFINITY;
         for (const [x, y] of vertices) {
             const rho = Math.sqrt(x * x + y * y);
             if (rho > maxRho) {
@@ -182,10 +182,10 @@ function viewportVisibleSection(viewSides, circleCenter, circleRadius) {
     // viewportCenterTheta < Math.PI / 2 || viewportCenterTheta > 1.5 * Math.PI
     //   ? -1
     //   : 1
-    let rhoMin = Infinity;
-    let rhoMax = -Infinity;
-    let thetaMin = Infinity;
-    let thetaMax = -Infinity;
+    let rhoMin = Number.POSITIVE_INFINITY;
+    let rhoMax = Number.NEGATIVE_INFINITY;
+    let thetaMin = Number.POSITIVE_INFINITY;
+    let thetaMax = Number.NEGATIVE_INFINITY;
     for (const [vx, vy] of vertices) {
         // ignore vertex if outside the viewport
         if (vx >= viewL && vx <= viewR && vy >= viewT && vy <= viewB) {

package/dist/CircularView/svgcomponents/SVGCircularView.js

@@ -18,7 +18,6 @@ async function renderToSvg(model, opts) {
     const { themeName = 'default', Wrapper = ({ children }) => children } = opts;
     const session = (0, util_1.getSession)(model);
     const theme = (_a = session.allThemes) === null || _a === void 0 ? void 0 : _a.call(session)[themeName];
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const { createRootFn } = (0, mobx_state_tree_1.getRoot)(model);
     const { width, tracks, height } = model;
     const shift = 50;
@@ -35,6 +34,10 @@ async function renderToSvg(model, opts) {
             react_1.default.createElement("svg", { width: width, height: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, width + shift * 2, height].toString() },
                 react_1.default.createElement(SVGBackground_1.default, { width: width, height: height, shift: shift }),
                 react_1.default.createElement("g", { transform: `translate(${centerXY}) rotate(${deg})` },
-                    staticSlices.map((slice, i) => (react_1.default.createElement(Ruler_1.default, { key: i, model: model, slice: slice }))),
-                    displayResults.map(({ result }, i) => (react_1.default.createElement(react_1.default.Fragment, { key: i }, result))))))), createRootFn);
+                    staticSlices.map((slice, i) => (
+                    /* biome-ignore lint/suspicious/noArrayIndexKey: */
+                    react_1.default.createElement(Ruler_1.default, { key: i, model: model, slice: slice }))),
+                    displayResults.map(({ result }, i) => (
+                    /* biome-ignore lint/suspicious/noArrayIndexKey: */
+                    react_1.default.createElement(react_1.default.Fragment, { key: i }, result))))))), createRootFn);
 }

package/dist/LaunchCircularView/index.js

@@ -17,6 +17,8 @@ function LaunchCircularViewF(pluginManager) {
             throw new Error(`Assembly "${assembly}" not found when launching circular genome view`);
         }
         view.setDisplayedRegions(asm.regions || []);
-        tracks.forEach(track => view.showTrack(track));
+        tracks.forEach(track => {
+            view.showTrack(track);
+        });
     });
 }

package/esm/BaseChordDisplay/components/Loading.js

@@ -48,8 +48,12 @@ const Loading = observer(function ({ model: { renderProps: { radius }, }, }) {
     // only show the loading message after 400ms to prevent excessive flickering
     const [shown, setShown] = useState(false);
     useEffect(() => {
-        const timeout = setTimeout(() => setShown(true), 400);
-        return () => clearTimeout(timeout);
+        const timeout = setTimeout(() => {
+            setShown(true);
+        }, 400);
+        return () => {
+            clearTimeout(timeout);
+        };
     });
     return !shown ? null : (React.createElement("g", null,
         React.createElement("defs", null,

package/esm/BaseChordDisplay/models/model.d.ts

@@ -42,7 +42,7 @@ export declare const BaseChordDisplayModel: import("mobx-state-tree").IModelType
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function;
+        onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: React.FC<{
@@ -103,10 +103,9 @@ export declare const BaseChordDisplayModel: import("mobx-state-tree").IModelType
     renderProps(): any;
     /**
      * #getter
-     * the pluggable element type object for this display's
-     * renderer
+     * the pluggable element type object for this display's renderer
      */
-    readonly rendererType: RendererType;
+    readonly rendererType: RendererType | undefined;
     /**
      * #method
      */
@@ -147,6 +146,6 @@ export declare const BaseChordDisplayModel: import("mobx-state-tree").IModelType
      * #method
      */
     renderSvg(opts: ExportSvgOptions & {
-        theme: ThemeOptions;
+        theme?: ThemeOptions;
     }): Promise<React.JSX.Element>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/BaseChordDisplay/models/model.js

@@ -87,7 +87,6 @@ export const BaseChordDisplayModel = types
         return {
             ...getParentRenderProps(self),
             rpcDriverName: self.rpcDriverName,
-            displayModel: self,
             bezierRadius: view.radiusPx * self.bezierRadiusRatio,
             radius: view.radiusPx,
             blockDefinitions: this.blockDefinitions,
@@ -96,20 +95,10 @@ export const BaseChordDisplayModel = types
     },
     /**
      * #getter
-     * the pluggable element type object for this display's
-     * renderer
+     * the pluggable element type object for this display's renderer
      */
     get rendererType() {
-        const display = self;
-        const { pluginManager } = getEnv(self);
-        const ThisRendererType = pluginManager.getRendererType(self.rendererTypeName);
-        if (!ThisRendererType) {
-            throw new Error(`renderer "${display.rendererTypeName}" not found`);
-        }
-        if (!ThisRendererType.ReactComponent) {
-            throw new Error(`renderer ${display.rendererTypeName} has no ReactComponent, it may not be completely implemented yet`);
-        }
-        return ThisRendererType;
+        return getEnv(self).pluginManager.getRendererType(self.rendererTypeName);
     },
     /**
      * #method
@@ -127,9 +116,6 @@ export const BaseChordDisplayModel = types
             return undefined;
         }
         const session = getSession(self);
-        if (!session) {
-            return undefined;
-        }
         const { selection } = session;
         // does it quack like a feature?
         if (isFeature(selection)) {
@@ -206,17 +192,16 @@ export const BaseChordDisplayModel = types
         }, self.renderStarted, self.renderSuccess, self.renderError);
         makeAbortableReaction(self, () => ({
             assemblyNames: getTrackAssemblyNames(self.parentTrack),
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
             adapter: getConf(getParent(self, 2), 'adapter'),
             assemblyManager: getSession(self).assemblyManager,
-        }), 
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        async ({ assemblyNames, adapter, assemblyManager }, signal) => {
+        }), async ({ assemblyNames, adapter, assemblyManager }, signal) => {
             return assemblyManager.getRefNameMapForAdapter(adapter, assemblyNames[0], { signal, sessionId: getRpcSessionId(self) });
         }, {
             name: `${self.type} ${self.id} getting refNames`,
             fireImmediately: true,
-        }, () => { }, refNameMap => self.setRefNameMap(refNameMap), error => {
+        }, () => { }, refNameMap => {
+            self.setRefNameMap(refNameMap);
+        }, error => {
             console.error(error);
             self.setError(error);
         });

package/esm/BaseChordDisplay/models/renderReaction.js

@@ -1,9 +1,7 @@
 import clone from 'clone';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
 import { getSession, getContainingView } from '@jbrowse/core/util';
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
 export function renderReactionData(self) {
-    var _a;
     const view = getContainingView(self);
     const { rendererType } = self;
     const { rpcManager } = getSession(view);
@@ -12,7 +10,7 @@ export function renderReactionData(self) {
         rpcManager,
         renderProps: self.renderProps(),
         renderArgs: {
-            assemblyName: (_a = view.displayedRegions[0]) === null || _a === void 0 ? void 0 : _a.assemblyName,
+            assemblyName: view.displayedRegions[0].assemblyName,
             adapterConfig: clone(self.adapterConfig),
             rendererType: rendererType.name,
             regions: clone(view.displayedRegions),
@@ -22,11 +20,7 @@ export function renderReactionData(self) {
         },
     };
 }
-export async function renderReactionEffect(
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-props, signal, 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-self) {
+export async function renderReactionEffect(props, signal, self) {
     var _a;
     if (!props) {
         throw new Error('cannot render with no props');

package/esm/CircularView/components/Controls.js

@@ -39,7 +39,9 @@ const Controls = observer(function ({ model }) {
         React.createElement(IconButton, { onClick: model.toggleFitToWindowLock, title: model.lockedFitToWindow
                 ? 'locked model to window size'
                 : 'unlocked model to zoom further', disabled: model.tooSmallToLock }, model.lockedFitToWindow ? React.createElement(LockIcon, null) : React.createElement(LockOpenIcon, null)),
-        React.createElement(IconButton, { onClick: event => setAnchorEl(event.currentTarget) },
+        React.createElement(IconButton, { onClick: event => {
+                setAnchorEl(event.currentTarget);
+            } },
             React.createElement(MoreVert, null)),
         model.hideTrackSelectorButton ? null : (React.createElement(IconButton, { onClick: model.activateTrackSelector, title: "Open track selector", "data-testid": "circular_track_select" },
             React.createElement(TrackSelectorIcon, null))),
@@ -57,6 +59,8 @@ const Controls = observer(function ({ model }) {
             ], onMenuItemClick: (_event, callback) => {
                 callback();
                 setAnchorEl(null);
-            }, open: Boolean(anchorEl), onClose: () => setAnchorEl(null) })) : null));
+            }, open: Boolean(anchorEl), onClose: () => {
+                setAnchorEl(null);
+            } })) : null));
 });
 export default Controls;

package/esm/CircularView/components/ExportSvgDialog.js

@@ -12,7 +12,7 @@ function TextField2({ children, ...rest }) {
         React.createElement(TextField, { ...rest }, children)));
 }
 function useSvgLocal(key, val) {
-    return useLocalStorage('svg-' + key, val);
+    return useLocalStorage(`svg-${key}`, val);
 }
 export default function ExportSvgDialog({ model, handleClose, }) {
     const session = getSession(model);
@@ -25,13 +25,21 @@ export default function ExportSvgDialog({ model, handleClose, }) {
     return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Export SVG" },
         React.createElement(DialogContent, null,
             error ? (React.createElement(ErrorMessage, { error: error })) : loading ? (React.createElement(LoadingMessage, null)) : null,
-            React.createElement(TextField2, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
-            session.allThemes ? (React.createElement(TextField2, { select: true, label: "Theme", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (React.createElement(MenuItem, { key: key, value: key }, 
+            React.createElement(TextField2, { helperText: "filename", value: filename, onChange: event => {
+                    setFilename(event.target.value);
+                } }),
+            session.allThemes ? (React.createElement(TextField2, { select: true, label: "Theme", value: themeName, onChange: event => {
+                    setThemeName(event.target.value);
+                } }, Object.entries(session.allThemes()).map(([key, val]) => (React.createElement(MenuItem, { key: key, value: key }, 
             // @ts-expect-error
             val.name || '(Unknown name)'))))) : null,
-            offscreenCanvas ? (React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: rasterizeLayers, onChange: () => setRasterizeLayers(val => !val) }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (React.createElement(Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
+            offscreenCanvas ? (React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: rasterizeLayers, onChange: () => {
+                        setRasterizeLayers(val => !val);
+                    } }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (React.createElement(Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
         React.createElement(DialogActions, null,
-            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"),
+            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
+                    handleClose();
+                } }, "Cancel"),
             React.createElement(Button, { variant: "contained", color: "primary", type: "submit", onClick: async () => {
                     setLoading(true);
                     setError(undefined);

package/esm/CircularView/components/ImportForm.d.ts

@@ -1,5 +1,6 @@
 import React from 'react';
+import { CircularViewModel } from '../models/model';
 declare const ImportForm: ({ model }: {
-    model: any;
+    model: CircularViewModel;
 }) => React.JSX.Element;
 export default ImportForm;

package/esm/CircularView/components/ImportForm.js

@@ -9,8 +9,7 @@ const useStyles = makeStyles()(theme => ({
         padding: theme.spacing(6),
     },
 }));
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-const ImportForm = observer(({ model }) => {
+const ImportForm = observer(function ({ model }) {
     const { classes } = useStyles();
     const session = getSession(model);
     const { error } = model;
@@ -33,7 +32,7 @@ const ImportForm = observer(({ model }) => {
                         setSelectedAsm(val);
                     }, session: session, selected: selectedAsm })),
             React.createElement(Grid, { item: true },
-                React.createElement(Button, { disabled: !(regions === null || regions === void 0 ? void 0 : regions.length), onClick: () => {
+                React.createElement(Button, { disabled: !regions.length, onClick: () => {
                         model.setError(undefined);
                         model.setDisplayedRegions(regions);
                     }, variant: "contained", color: "primary" }, regions.length || err ? 'Open' : 'Loading...')))));

package/esm/CircularView/components/Ruler.js

@@ -94,11 +94,8 @@ const RegionRulerArc = observer(function ({ model, slice, region, }) {
     const centerRadians = (endRadians + startRadians) / 2;
     const widthPx = (endRadians - startRadians) * radiusPx;
     const session = getSession(model);
-    let color;
     const assembly = session.assemblyManager.get(region.assemblyName);
-    if (assembly) {
-        color = assembly.getRefNameColor(region.refName);
-    }
+    let color = assembly ? assembly.getRefNameColor(region.refName) : undefined;
     if (color) {
         try {
             color = makeContrasting(color, theme.palette.background.paper);

package/esm/CircularView/models/model.d.ts

@@ -136,8 +136,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
     readonly figureHeight: number;
     /**
      * #getter
-     * this is displayedRegions, post-processed to
-     * elide regions that are too small to see reasonably
+     * this is displayedRegions, post-processed to elide regions that are too
+     * small to see reasonably
      */
     readonly elidedRegions: SliceRegion[];
     /**
@@ -207,10 +207,6 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
      * #action
      */
     setModelViewWhenAdjust(secondCondition: boolean): void;
-    /**
-     * #action
-     */
-    closeView(): void;
     /**
      * #action
      */

package/esm/CircularView/models/model.js

@@ -1,5 +1,5 @@
 import { lazy } from 'react';
-import { cast, getParent, getRoot, resolveIdentifier, types, } from 'mobx-state-tree';
+import { cast, getRoot, resolveIdentifier, types, } from 'mobx-state-tree';
 import { Region } from '@jbrowse/core/util/types/mst';
 import { transaction } from 'mobx';
 import { saveAs } from 'file-saver';
@@ -233,8 +233,8 @@ function stateModelFactory(pluginManager) {
         },
         /**
          * #getter
-         * this is displayedRegions, post-processed to
-         * elide regions that are too small to see reasonably
+         * this is displayedRegions, post-processed to elide regions that are too
+         * small to see reasonably
          */
         get elidedRegions() {
             const visible = [];
@@ -390,13 +390,6 @@ function stateModelFactory(pluginManager) {
                 this.setBpPerPx(self.minBpPerPx);
             }
         },
-        /**
-         * #action
-         */
-        closeView() {
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            getParent(self, 2).removeView(self);
-        },
         /**
          * #action
          */
@@ -490,7 +483,9 @@ function stateModelFactory(pluginManager) {
             const schema = pluginManager.pluggableConfigSchemaType('track');
             const conf = resolveIdentifier(schema, getRoot(self), trackId);
             const t = self.tracks.filter(t => t.configuration === conf);
-            transaction(() => t.forEach(t => self.tracks.remove(t)));
+            transaction(() => {
+                t.forEach(t => self.tracks.remove(t));
+            });
             return t.length;
         },
         /**
@@ -523,7 +518,9 @@ function stateModelFactory(pluginManager) {
             return [
                 {
                     label: 'Return to import form',
-                    onClick: () => self.setDisplayedRegions([]),
+                    onClick: () => {
+                        self.setDisplayedRegions([]);
+                    },
                     icon: FolderOpenIcon,
                 },
                 {

package/esm/CircularView/models/slices.d.ts

@@ -31,7 +31,7 @@ export declare class Slice {
     };
 }
 declare function calculateStaticSlices(self: {
-    elidedRegions: SliceRegion[];
+    elidedRegions: readonly SliceRegion[];
     bpPerRadian: number;
     spacingPx: number;
     pxPerRadian: number;

package/esm/CircularView/models/viewportVisibleRegion.d.ts

@@ -1,4 +1,4 @@
-export declare function cartesianToPolar(x: number, y: number): number[];
+export declare function cartesianToPolar(x: number, y: number): readonly [number, number];
 export declare function thetaRangesOverlap(r1start: number, r1length: number, r2start: number, r2length: number): boolean;
 export declare function viewportVisibleSection(viewSides: [number, number, number, number], circleCenter: [number, number], circleRadius: number): {
     rho: [number, number];

package/esm/CircularView/models/viewportVisibleRegion.js

@@ -80,7 +80,7 @@ export function viewportVisibleSection(viewSides, circleCenter, circleRadius) {
             [viewL, viewB],
             [viewR, viewB],
         ];
-        let maxRho = -Infinity;
+        let maxRho = Number.NEGATIVE_INFINITY;
         for (const [x, y] of vertices) {
             const rho = Math.sqrt(x * x + y * y);
             if (rho > maxRho) {
@@ -177,10 +177,10 @@ export function viewportVisibleSection(viewSides, circleCenter, circleRadius) {
     // viewportCenterTheta < Math.PI / 2 || viewportCenterTheta > 1.5 * Math.PI
     //   ? -1
     //   : 1
-    let rhoMin = Infinity;
-    let rhoMax = -Infinity;
-    let thetaMin = Infinity;
-    let thetaMax = -Infinity;
+    let rhoMin = Number.POSITIVE_INFINITY;
+    let rhoMax = Number.NEGATIVE_INFINITY;
+    let thetaMin = Number.POSITIVE_INFINITY;
+    let thetaMax = Number.NEGATIVE_INFINITY;
     for (const [vx, vy] of vertices) {
         // ignore vertex if outside the viewport
         if (vx >= viewL && vx <= viewR && vy >= viewT && vy <= viewB) {

package/esm/CircularView/svgcomponents/SVGCircularView.js

@@ -12,7 +12,6 @@ export async function renderToSvg(model, opts) {
     const { themeName = 'default', Wrapper = ({ children }) => children } = opts;
     const session = getSession(model);
     const theme = (_a = session.allThemes) === null || _a === void 0 ? void 0 : _a.call(session)[themeName];
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const { createRootFn } = getRoot(model);
     const { width, tracks, height } = model;
     const shift = 50;
@@ -29,6 +28,10 @@ export async function renderToSvg(model, opts) {
             React.createElement("svg", { width: width, height: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, width + shift * 2, height].toString() },
                 React.createElement(SVGBackground, { width: width, height: height, shift: shift }),
                 React.createElement("g", { transform: `translate(${centerXY}) rotate(${deg})` },
-                    staticSlices.map((slice, i) => (React.createElement(Ruler, { key: i, model: model, slice: slice }))),
-                    displayResults.map(({ result }, i) => (React.createElement(React.Fragment, { key: i }, result))))))), createRootFn);
+                    staticSlices.map((slice, i) => (
+                    /* biome-ignore lint/suspicious/noArrayIndexKey: */
+                    React.createElement(Ruler, { key: i, model: model, slice: slice }))),
+                    displayResults.map(({ result }, i) => (
+                    /* biome-ignore lint/suspicious/noArrayIndexKey: */
+                    React.createElement(React.Fragment, { key: i }, result))))))), createRootFn);
 }

package/esm/LaunchCircularView/index.js

@@ -14,6 +14,8 @@ export default function LaunchCircularViewF(pluginManager) {
             throw new Error(`Assembly "${assembly}" not found when launching circular genome view`);
         }
         view.setDisplayedRegions(asm.regions || []);
-        tracks.forEach(track => view.showTrack(track));
+        tracks.forEach(track => {
+            view.showTrack(track);
+        });
     });
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-circular-view",
-  "version": "2.13.0",
+  "version": "2.14.0",
   "description": "JBrowse 2 circular view",
   "keywords": [
     "jbrowse",
@@ -24,7 +24,7 @@
   ],
   "scripts": {
     "build": "npm-run-all build:*",
-    "test": "cd ../..; jest plugins/circular-view",
+    "test": "cd ../..; jest --passWithNoTests plugins/circular-view",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build && yarn useDist",
     "postpack": "yarn useSrc",
@@ -57,5 +57,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "efe02fb9616e20e929cceeed46eb96420c1b6923"
+  "gitHead": "9fb8231d932db40adf0a283081765431756c66ff"
 }