[draft] refactor(core): move /track-def under /src

demo/App.tsx

@@ -16,10 +16,6 @@ import { compile } from '../src/compiler/compile';
 import { getTheme } from '../src/core/utils/theme';
 
 import './App.css';
-import { createTrackDefs, renderTrackDefs, showTrackInfoPositions } from './track-def/main';
-import type { TrackInfo } from 'src/compiler/bounding-box';
-import type { GoslingSpec } from 'gosling.js';
-import { getLinkedEncodings } from './linking/linkedEncoding';
 import { GoslingComponent } from './GoslingComponent';
 
 function App() {

demo/GoslingComponent.tsx

@@ -2,7 +2,7 @@ import React, { useState, useEffect } from 'react';
 import { PixiManager } from '@pixi-manager';
 import { compile, type UrlToFetchOptions } from '../src/compiler/compile';
 import { getTheme } from '../src/core/utils/theme';
-import { createTrackDefs } from './track-def/main';
+import { createTrackDefs } from '../src/track-def';
 import { renderTrackDefs } from './renderer/main';
 import type { TrackInfo } from 'src/compiler/bounding-box';
 import type { GoslingSpec } from 'gosling.js';

demo/linking/linkedEncoding.ts

@@ -1,9 +1,15 @@
-import { IsDummyTrack, IsMultipleViews, IsSingleView, type Assembly, type SingleView } from '@gosling-lang/gosling-schema';
+import {
+    IsDummyTrack,
+    IsMultipleViews,
+    IsSingleView,
+    type Assembly,
+    type SingleView
+} from '@gosling-lang/gosling-schema';
 import { GenomicPositionHelper, computeChromSizes } from '../../src/core/utils/assembly';
 import { signal, type Signal } from '@preact/signals-core';
 import type { GoslingSpec } from 'gosling.js';
-import { TrackType } from '../track-def/main';
-import { isHeatmapTrack } from '../track-def/heatmap';
+import { TrackType } from '../../src/track-def';
+import { isHeatmapTrack } from '../../src/track-def/heatmap';
 
 /**
  * This is the information needed to link tracks together

demo/renderer/main.ts

@@ -5,7 +5,7 @@ import { Signal } from '@preact/signals-core';
 import { TextTrack } from '@gosling-lang/text-track';
 
 import { panZoom, panZoomHeatmap } from '@gosling-lang/interactors';
-import { type TrackDefs, TrackType } from '../track-def/main';
+import { type TrackDefs, TrackType } from '../../src/track-def';
 import { getDataFetcher } from './dataFetcher';
 import type { LinkedEncoding } from '../linking/linkedEncoding';
 import { BrushCircularTrack } from '@gosling-lang/brush-circular';

editor/index.css

@@ -15,8 +15,17 @@ body {
 /* Common font styles */
 body,
 button {
-    font-family: 'Helvetica Neue', -apple-system, BlinkMacSystemFont, 'Segoe UI', 'Roboto', 'Oxygen', 'Ubuntu',
-        'Cantarell', 'Droid Sans', sans-serif;
+    font-family:
+        'Helvetica Neue',
+        -apple-system,
+        BlinkMacSystemFont,
+        'Segoe UI',
+        'Roboto',
+        'Oxygen',
+        'Ubuntu',
+        'Cantarell',
+        'Droid Sans',
+        sans-serif;
     font-size: 14px;
     text-align: left;
     line-height: 1.42857143;

src/compiler/bounding-box.ts

@@ -10,7 +10,7 @@ import {
 import { resolveSuperposedTracks } from '../core/utils/overlay';
 import { traverseTracksAndViews, traverseViewArrangements } from './spec-preprocess';
 import type { CompleteThemeDeep } from '../core/utils/theme';
-import type { ProcessedCircularTrack, ProcessedTrack } from '../../demo/track-def/types';
+import type { ProcessedCircularTrack, ProcessedTrack } from '../track-def/types';
 export interface Size {
     width: number;
     height: number;

src/compiler/compile.test.ts

@@ -6,7 +6,7 @@ import { convertToFlatTracks } from './spec-preprocess';
 import type { SingleView } from '@gosling-lang/gosling-schema';
 import { spreadTracksByData } from '../core/utils/overlay';
 import { getDataFetcher } from '../../demo/renderer/dataFetcher';
-import type { ProcessedTrack } from 'demo/track-def/types';
+import type { ProcessedTrack } from '../track-def/types';
 
 // TODO: Move this to dataFetcher.test.ts after we move the /demo/renderer under /src
 describe('Compiler with UrlToFetchOptions', () => {

src/compiler/views-and-tracks.ts

@@ -10,7 +10,7 @@ import type {
 import type { CompleteThemeDeep } from '../core/utils/theme';
 import { getViewApiData } from '../api/api-data';
 import { IsDummyTrack } from '@gosling-lang/gosling-schema';
-import type { ProcessedCircularTrack } from 'demo/track-def/types';
+import type { ProcessedCircularTrack } from '../track-def/types';
 
 export function collectViewsAndTracks(spec: GoslingSpec, trackInfos: TrackInfo[], theme: Required<CompleteThemeDeep>) {
     if (trackInfos.length === 0) {
@@ -32,14 +32,14 @@ export function collectViewsAndTracks(spec: GoslingSpec, trackInfos: TrackInfo[]
             shape: isLinear
                 ? d.boundingBox
                 : {
-                    ...d.boundingBox,
-                    cx: d.boundingBox.x + d.boundingBox.width / 2.0,
-                    cy: d.boundingBox.y + d.boundingBox.height / 2.0,
-                    innerRadius: (d.track as ProcessedCircularTrack).innerRadius!,
-                    outerRadius: (d.track as ProcessedCircularTrack).outerRadius!,
-                    startAngle: (d.track as ProcessedCircularTrack).startAngle!,
-                    endAngle: (d.track as ProcessedCircularTrack).endAngle!
-                }
+                      ...d.boundingBox,
+                      cx: d.boundingBox.x + d.boundingBox.width / 2.0,
+                      cy: d.boundingBox.y + d.boundingBox.height / 2.0,
+                      innerRadius: (d.track as ProcessedCircularTrack).innerRadius!,
+                      outerRadius: (d.track as ProcessedCircularTrack).outerRadius!,
+                      startAngle: (d.track as ProcessedCircularTrack).startAngle!,
+                      endAngle: (d.track as ProcessedCircularTrack).endAngle!
+                  }
         };
     });
 

src/core/utils/assembly.ts

@@ -213,7 +213,11 @@ export function parseGenomicPosition(position: string): { chromosome: string; st
  * A class that consistently manage and convert genomics positions.
  */
 export class GenomicPositionHelper {
-    constructor(public chromosome: string, public start?: number, public end?: number) {}
+    constructor(
+        public chromosome: string,
+        public start?: number,
+        public end?: number
+    ) {}
     static fromString(str: string) {
         const result = parseGenomicPosition(str);
         return new GenomicPositionHelper(result.chromosome, result.start, result.end);

src/core/utils/overlay.ts

@@ -126,8 +126,8 @@ export function spreadTracksByData(tracks: Track[]): Track[] {
                     IsSingleTrack(track) && IsChannelDeep(track.y) && !track.y.axis && overlayOnPreviousTrack
                         ? ({ ...track.y, axis: i === 1 ? 'right' : 'none' } as ChannelDeep)
                         : IsSingleTrack(track)
-                        ? track.y
-                        : undefined;
+                          ? track.y
+                          : undefined;
 
                 if (track.title && i !== arr.length - 1 && arr.length !== 1) {
                     delete track.title; // remove `title` except the last one

src/data-fetchers/bam/bam-data-fetcher.ts

@@ -17,8 +17,8 @@ const DEBOUNCE_TIME = 200;
 type InferTileType<Config extends BamData> = Config['extractJunction'] extends true
     ? Junction
     : Config['loadMates'] extends true
-    ? SegmentWithMate
-    : Segment;
+      ? SegmentWithMate
+      : Segment;
 
 class BamDataFetcher<Config extends BamData> implements TabularDataFetcher<InferTileType<Config>> {
     static config = { type: 'bam' };

src/data-fetchers/bed/bed-worker.ts

@@ -51,7 +51,10 @@ class BedFile {
     #customFields?: string[];
     #uid: string;
 
-    constructor(public tbi: TabixIndexedFile, uid: string) {
+    constructor(
+        public tbi: TabixIndexedFile,
+        uid: string
+    ) {
         this.#uid = uid;
     }
     /**

src/data-fetchers/utils.ts

@@ -17,7 +17,11 @@ export class DataSource<File, Options> {
     chromInfo: ExtendedChromInfo;
     tilesetInfo: ReturnType<typeof tilesetInfoFromChromInfo>;
 
-    constructor(public file: File, chromSizes: ChromSizes, public options: Options) {
+    constructor(
+        public file: File,
+        chromSizes: ChromSizes,
+        public options: Options
+    ) {
         this.chromInfo = sizesToChromInfo(chromSizes);
         this.tilesetInfo = tilesetInfoFromChromInfo(this.chromInfo);
     }

src/data-fetchers/vcf/vcf-worker.ts

@@ -29,7 +29,10 @@ type VcfFileOptions = {
 class VcfFile {
     #parser?: VCF;
     #uid: string;
-    constructor(public tbi: TabixIndexedFile, uid: string) {
+    constructor(
+        public tbi: TabixIndexedFile,
+        uid: string
+    ) {
         this.#uid = uid;
     }
     /**

src/gosling-schema/gosling.schema.guards.ts

@@ -49,7 +49,7 @@ import {
 } from 'd3-scale-chromatic';
 import { resolveSuperposedTracks } from '../core/utils/overlay';
 import type { TabularDataFetcher } from '@data-fetchers';
-import type { ProcessedDummyTrack, ProcessedTrack } from 'demo/track-def/types';
+import type { ProcessedDummyTrack, ProcessedTrack } from '../track-def/types';
 
 export const PREDEFINED_COLOR_STR_MAP: { [k: string]: (t: number) => string } = {
     viridis: interpolateViridis,

src/gosling-schema/validate.ts

@@ -3,6 +3,7 @@ import type { SingleTrack, ChannelDeep, ChannelTypes, OverlaidTrack, Track } fro
 import { IsChannelDeep } from './gosling.schema.guards';
 import { resolveSuperposedTracks } from '../core/utils/overlay';
 import GoslingSchema from './gosling.schema.json';
+import type { ProcessedTrack } from 'src/track-def/types';
 
 export interface Validity {
     message: string;
@@ -37,10 +38,11 @@ export function validateSpec(schema: any, spec: any, silence = false): Validity
     return { state: valid ? 'success' : 'warn', message, details };
 }
 
-export function validateTrack(track: Track) {
+export function validateProcessedTrack(track: ProcessedTrack) {
     let valid = true;
     const errorMessages: string[] = [];
 
+    // @ts-expect-error This function should be re-written
     const resolvedTrack = resolveSuperposedTracks(track);
 
     resolvedTrack.forEach(spec => {