refactor: file structure; separate folder for compiler, tracks, api, …

…and schema (gosling-lang#959)

* refactor: file structure; separate folder for compiler, tracks, api, and schema

* fix: fix build and test

* chore: more import adjust

* chore: more import clean up

* fix: fix import of schema

* chore: more refactor

editor/Editor.tsx

@@ -14,14 +14,14 @@ import 'allotment/dist/style.css';
 import { debounce, isEqual } from 'lodash-es';
 import stripJsonComments from 'strip-json-comments';
 import JSONCrush from 'jsoncrush';
-import type { HiGlassSpec } from '@higlass.schema';
-import type { Datum } from '@gosling.schema';
+import type { HiGlassSpec } from '@gosling-lang/higlass-schema';
+import type { Datum } from '@gosling-lang/gosling-schema';
 import { Themes } from 'gosling-theme';
 
 import { ICONS, type ICON_INFO } from './icon';
 import { getHtmlTemplate } from './html-template';
 import ErrorBoundary from './error-boundary';
-import { traverseTracksAndViews } from '../src/core/utils/spec-preprocess';
+import { traverseTracksAndViews } from '../src/compiler/spec-preprocess';
 import { examples, type Example } from './example';
 import EditorPanel, { type EditorLangauge } from './EditorPanel';
 import EditorExamples from './EditorExamples';

editor/EditorPanel.tsx

@@ -3,7 +3,7 @@ import MonacoEditor from 'react-monaco-editor';
 
 import ReactResizeDetector from 'react-resize-detector';
 import { GoslingSchema } from 'gosling.js';
-import goslingSpec from '../src/core/gosling.schema?raw';
+import goslingSpec from '../src/gosling-schema/gosling.schema?raw';
 
 export * from './monaco_worker';
 import * as Monaco from 'monaco-editor';

editor/example/doc-examples/single-mark.ts

@@ -1,4 +1,4 @@
-import type { GoslingSpec, Mark, DataDeep } from '@gosling.schema';
+import type { GoslingSpec, Mark, DataDeep } from '@gosling-lang/gosling-schema';
 
 export const data: DataDeep = {
     url: 'https://resgen.io/api/v1/tileset_info/?d=UvVPeLHuRDiYA3qwFlm7xQ',

editor/example/doc-examples/triangle.ts

@@ -1,4 +1,4 @@
-import type { GoslingSpec, SingleTrack } from '@gosling.schema';
+import type { GoslingSpec, SingleTrack } from '@gosling-lang/gosling-schema';
 
 import { HiGlass } from '../json-spec/gene-annotation';
 

editor/example/index.test.ts

@@ -1,6 +1,6 @@
-import { GoslingTrackModel } from '../../src/core/gosling-track-model';
+import { GoslingTrackModel } from '../../src/tracks/gosling-track/gosling-track-model';
 import { resolveSuperposedTracks } from '../../src/core/utils/overlay';
-import { convertToFlatTracks } from '../../src/core/utils/spec-preprocess';
+import { convertToFlatTracks } from '../../src/compiler/spec-preprocess';
 import { getTheme } from '../../src/core/utils/theme';
 import { EX_TRACK_SEMANTIC_ZOOM } from './json-spec/semantic-zoom';
 

editor/example/json-spec/circos.ts

@@ -1,4 +1,4 @@
-import type { GoslingSpec } from '@gosling.schema';
+import type { GoslingSpec } from '@gosling-lang/gosling-schema';
 import { GOSLING_PUBLIC_DATA } from './gosling-data';
 
 export const EX_SPEC_CIRCULR_RANGE: GoslingSpec = {

editor/example/json-spec/gene-annotation.ts

@@ -1,4 +1,4 @@
-import type { DataDeep, GoslingSpec, OverlaidTracks } from '@gosling.schema';
+import type { DataDeep, GoslingSpec, OverlaidTracks } from '@gosling-lang/gosling-schema';
 import { GOSLING_PUBLIC_DATA } from './gosling-data';
 
 const width = 350;

editor/example/json-spec/glyph.ts

@@ -1,4 +1,4 @@
-import type { Mark } from '@gosling.schema';
+import type { Mark } from '@gosling-lang/gosling-schema';
 
 export const GLYPH_PRESETS: {
     name: GLYPH_LOCAL_PRESET_TYPE;

editor/example/json-spec/ideograms.ts

@@ -1,4 +1,4 @@
-import type { GoslingSpec, OverlaidTracks, Track } from '@gosling.schema';
+import type { GoslingSpec, OverlaidTracks, Track } from '@gosling-lang/gosling-schema';
 import { GOSLING_PUBLIC_DATA } from './gosling-data';
 
 export const CytoBands: OverlaidTracks = {

editor/example/json-spec/layout-and-arrangement.ts

@@ -1,6 +1,6 @@
 import type { GoslingSpec } from 'gosling.js';
-import type { SingleView } from '@gosling.schema';
-import { DEFAULT_VIEW_SPACING } from '../../../src/core/defaults';
+import type { SingleView } from '@gosling-lang/gosling-schema';
+import { DEFAULT_VIEW_SPACING } from '../../../src/compiler/defaults';
 import { GOSLING_PUBLIC_DATA } from './gosling-data';
 
 const COLORS = ['#D45E00', '#029F73', '#0072B2', '#CB7AA7', '#E79F00'];

editor/example/json-spec/matrix.ts

@@ -1,4 +1,4 @@
-import type { PredefinedColors, SingleTrack } from '@gosling.schema';
+import type { PredefinedColors, SingleTrack } from '@gosling-lang/gosling-schema';
 import type { GoslingSpec } from 'gosling.js';
 import { random } from 'lodash-es';
 import { GOSLING_PUBLIC_DATA } from './gosling-data';

editor/example/json-spec/mouse-event.ts

@@ -1,4 +1,4 @@
-import type { GoslingSpec, SingleTrack } from '@gosling.schema';
+import type { GoslingSpec, SingleTrack } from '@gosling-lang/gosling-schema';
 import { GOSLING_PUBLIC_DATA } from './gosling-data';
 import { CytoBands } from './ideograms';
 

editor/example/json-spec/pileup.ts

@@ -1,4 +1,4 @@
-import type { Domain, GoslingSpec, View } from '@gosling.schema';
+import type { Domain, GoslingSpec, View } from '@gosling-lang/gosling-schema';
 
 export function EX_SPEC_VIEW_PILEUP(
     id: string,

editor/example/json-spec/responsive-alignment.ts

@@ -1,4 +1,4 @@
-import type { OverlaidTracks, SingleTrack, SingleView } from '@gosling.schema';
+import type { OverlaidTracks, SingleTrack, SingleView } from '@gosling-lang/gosling-schema';
 import type { GoslingSpec } from 'gosling.js';
 import { CHANNEL_DEFAULTS } from '../../../src/core/channel';
 

editor/example/json-spec/responsive-track-wise-comparison.ts

@@ -1,4 +1,4 @@
-import type { DomainChrInterval, GoslingSpec, OverlaidTracks, SingleTrack, TemplateTrack } from '@gosling.schema';
+import type { DomainChrInterval, GoslingSpec, OverlaidTracks, SingleTrack, TemplateTrack } from '@gosling-lang/gosling-schema';
 import { GOSLING_PUBLIC_DATA } from './gosling-data';
 
 const trackColor = {

editor/example/json-spec/responsive.ts

@@ -1,4 +1,4 @@
-import type { GoslingSpec } from '@gosling.schema';
+import type { GoslingSpec } from '@gosling-lang/gosling-schema';
 
 export const EX_SPEC_RESPONSIVE_SEGREGATED_AREA_CHART: GoslingSpec = {
     // title: 'Responsive Visualization',

editor/example/json-spec/sars-cov-2.ts

@@ -1,4 +1,4 @@
-import type { GoslingSpec, MultivecData, OverlaidTracks } from '@gosling.schema';
+import type { GoslingSpec, MultivecData, OverlaidTracks } from '@gosling-lang/gosling-schema';
 import { EX_TRACK_SEMANTIC_ZOOM } from './semantic-zoom';
 
 export const EX_TRACK_SARS_COV_2_GENES: OverlaidTracks = {

editor/example/json-spec/sashimi.ts

@@ -1,4 +1,4 @@
-import type { GoslingSpec } from '@gosling.schema';
+import type { GoslingSpec } from '@gosling-lang/gosling-schema';
 
 export const EX_SPEC_SASHIMI: GoslingSpec = {
     title: 'Sashimi Plot',

editor/example/json-spec/semantic-zoom.ts

@@ -1,4 +1,4 @@
-import type { GoslingSpec, OverlaidTracks } from '@gosling.schema';
+import type { GoslingSpec, OverlaidTracks } from '@gosling-lang/gosling-schema';
 import { GOSLING_PUBLIC_DATA } from './gosling-data';
 import { EX_SPEC_PATHOGENIC } from './pathogenic';
 

editor/example/json-spec/theme.ts

@@ -1,4 +1,4 @@
-import type { GoslingSpec } from '@gosling.schema';
+import type { GoslingSpec } from '@gosling-lang/gosling-schema';
 import { GOSLING_PUBLIC_DATA } from './gosling-data';
 
 export const EX_SPEC_CUSTOM_THEME: GoslingSpec = {

editor/example/json-spec/visual-encoding.ts

@@ -1,4 +1,4 @@
-import type { GoslingSpec } from '@gosling.schema';
+import type { GoslingSpec } from '@gosling-lang/gosling-schema';
 import { GOSLING_PUBLIC_DATA } from './gosling-data';
 
 export const EX_SPEC_VISUAL_ENCODING: GoslingSpec = {

editor/example/json-spec/visual-linking.ts

@@ -1,4 +1,4 @@
-import type { GoslingSpec } from '@gosling.schema';
+import type { GoslingSpec } from '@gosling-lang/gosling-schema';
 import { GOSLING_PUBLIC_DATA } from './gosling-data';
 
 export const EX_SPEC_LINKING: GoslingSpec = {

editor/example/spec/basic-semantic-zoom.ts

@@ -1,4 +1,4 @@
-import type { GoslingSpec, VisibilityCondition, MultivecData } from '@gosling.schema';
+import type { GoslingSpec, VisibilityCondition, MultivecData } from '@gosling-lang/gosling-schema';
 
 const data: MultivecData = {
     type: 'multivec',

editor/example/spec/corces.ts

@@ -1,4 +1,4 @@
-import type { GoslingSpec, PartialTrack, View, BigWigData, BeddbData } from '@gosling.schema';
+import type { GoslingSpec, PartialTrack, View, BigWigData, BeddbData } from '@gosling-lang/gosling-schema';
 
 const width = 400;
 

editor/example/spec/islandviewer.ts

@@ -1,4 +1,4 @@
-import type { GoslingSpec } from '@gosling.schema';
+import type { GoslingSpec } from '@gosling-lang/gosling-schema';
 
 const circularRadius = 250;
 const centerRadius = 0.5;

editor/example/spec/rule.ts

@@ -1,4 +1,4 @@
-import type { PartialTrack, GoslingSpec, JsonData } from '@gosling.schema';
+import type { PartialTrack, GoslingSpec, JsonData } from '@gosling-lang/gosling-schema';
 
 const barTrack: PartialTrack = {
     data: {

editor/example/spec/sashimi.ts

@@ -1,4 +1,4 @@
-import type { BamData, GoslingSpec } from '@gosling.schema';
+import type { BamData, GoslingSpec } from '@gosling-lang/gosling-schema';
 
 const bamData: BamData = {
     type: 'bam',

editor/example/spec/vertical-band.ts

@@ -1,4 +1,4 @@
-import type { GoslingSpec, CsvData, Track } from '@gosling.schema';
+import type { GoslingSpec, CsvData, Track } from '@gosling-lang/gosling-schema';
 const data: CsvData = {
     type: 'csv',
     url: 'https://raw.githubusercontent.com/sehilyi/gemini-datasets/master/data/circos-segdup-edited.txt',

editor/example/spec/visual-encoding-circular.ts

@@ -1,4 +1,4 @@
-import type { GoslingSpec, View, MultivecData, Tooltip } from '@gosling.schema';
+import type { GoslingSpec, View, MultivecData, Tooltip } from '@gosling-lang/gosling-schema';
 
 const size = { width: 350, height: 130 };
 const data: MultivecData = {

editor/example/spec/visual-encoding.ts

@@ -1,4 +1,4 @@
-import type { GoslingSpec, MultivecData, View, Tooltip } from '@gosling.schema';
+import type { GoslingSpec, MultivecData, View, Tooltip } from '@gosling-lang/gosling-schema';
 
 const size = { width: 600, height: 130 };
 

embed/index.ts

@@ -1,5 +1,5 @@
 import { embed as goslingEmbed } from 'gosling.js';
-import type { GoslingSpec } from '@gosling.schema';
+import type { GoslingSpec } from '@gosling-lang/gosling-schema';
 import 'higlass/dist/hglib.css';
 
 // https://github.com/vega/vega-embed/blob/master/src/container.ts

scripts/generate-schemas.mjs

@@ -12,10 +12,10 @@ import stableStringify from "safe-stable-stringify";
 const __dirname = path.dirname(url.fileURLToPath(import.meta.url));
 
 const SCHEMAS = [
-  ["GoslingSpec", "gosling.schema.json"],
-  ["HiGlassSpec", "higlass.schema.json"],
-  ["Theme", "theme.schema.json"],
-  ["TemplateTrackDef", "template.schema.json"],
+  ["GoslingSpec", "gosling.schema.json", "../src/gosling-schema/"],
+  ["HiGlassSpec", "higlass.schema.json", "../src/higlass-schema/"],
+  ["Theme", "theme.schema.json", "../src/gosling-schema/"],
+  ["TemplateTrackDef", "template.schema.json", "../src/gosling-schema/"],
 ];
 
 const generator = tsj.createGenerator({
@@ -25,10 +25,10 @@ const generator = tsj.createGenerator({
   encodeRefs: false,
 });
 
-for (const [type, filename] of SCHEMAS) {
+for (const [type, filename, dir] of SCHEMAS) {
   const schema = generator.createSchema(type);
   fs.promises.writeFile(
-      path.resolve(__dirname, `../schema/${filename}`),
+      path.resolve(__dirname, `${dir}/${filename}`),
       stableStringify(schema, null, 2) + "\n",
   );
 }

src/api/README.md

@@ -0,0 +1,3 @@
+# @gosling-lang/gosling-api
+
+Code related to JavaScript API.

src/core/api-data.ts → src/api/api-data.ts

@@ -1,5 +1,5 @@
-import type { GoslingSpec, PartialTrack, TrackApiData, View } from '@gosling.schema';
-import { getInternalSpecById, getTrackIds, getViewIds } from './track-and-view-ids';
+import type { GoslingSpec, PartialTrack, TrackApiData, View } from '@gosling-lang/gosling-schema';
+import { getInternalSpecById, getTrackIds, getViewIds } from '../api/track-and-view-ids';
 
 /**
  * This collect information of views by referring to the track information.

src/core/api.ts → src/api/api.ts

@@ -1,10 +1,10 @@
 import * as PIXI from 'pixi.js';
-import type { TrackApiData, VisUnitApiData, ViewApiData } from '@gosling.schema';
-import type { HiGlassApi } from './higlass-component-wrapper';
-import type { HiGlassSpec } from '@higlass.schema';
+import type { TrackApiData, VisUnitApiData, ViewApiData } from '@gosling-lang/gosling-schema';
+import type { HiGlassSpec } from '@gosling-lang/higlass-schema';
+import type { HiGlassApi } from '../core/higlass-component-wrapper';
 import { subscribe, unsubscribe } from './pubsub';
-import { computeChromSizes, GenomicPositionHelper } from './utils/assembly';
-import type { CompleteThemeDeep } from './utils/theme';
+import { computeChromSizes, GenomicPositionHelper } from '../core/utils/assembly';
+import type { CompleteThemeDeep } from '../core/utils/theme';
 import type { IdTable } from './track-and-view-ids';
 
 /**

src/core/pubsub.ts → src/api/pubsub.ts

@@ -1,4 +1,4 @@
-import type { _EventMap } from './gosling.schema';
+import type { _EventMap } from '@gosling-lang/gosling-schema';
 import PubSub from 'pubsub-js';
 
 type EventName = keyof _EventMap;

src/core/track-and-view-ids.test.ts → src/api/track-and-view-ids.test.ts

@@ -1,4 +1,4 @@
-import type { GoslingSpec } from '@gosling.schema';
+import type { GoslingSpec } from '@gosling-lang/gosling-schema';
 import { getInternalSpecById, getTrackIds, getViewIds } from './track-and-view-ids';
 
 describe('Retrieve IDs and Sub-spec', () => {

src/core/track-and-view-ids.ts → src/api/track-and-view-ids.ts

@@ -1,5 +1,5 @@
-import type { CommonTrackDef, CommonViewDef, GoslingSpec, PartialTrack, View } from '@gosling.schema';
-import { traverseTracksAndViews } from './utils/spec-preprocess';
+import type { CommonTrackDef, CommonViewDef, GoslingSpec, PartialTrack, View } from '@gosling-lang/gosling-schema';
+import { traverseTracksAndViews } from '../compiler/spec-preprocess';
 
 /**
  * A table that maps Gosling track IDs to HiGlass view IDs.

src/compiler/README.md

@@ -0,0 +1,3 @@
+# @gosling-lang/compiler
+
+Related to spec processing and converting a gosling spec into HiGlass spec.

src/core/utils/bounding-box.test.ts → src/compiler/bounding-box.test.ts

@@ -1,8 +1,8 @@
-import type { GoslingSpec, Track } from '../gosling.schema';
-import { DEFAULT_CIRCULAR_VIEW_PADDING, DEFAULT_VIEW_SPACING } from '../defaults';
+import type { GoslingSpec, Track } from '@gosling-lang/gosling-schema';
+import { DEFAULT_CIRCULAR_VIEW_PADDING, DEFAULT_VIEW_SPACING } from './defaults';
 import { getBoundingBox, getRelativeTrackInfo } from './bounding-box';
-import { traverseToFixSpecDownstream } from './spec-preprocess';
-import { getTheme } from './theme';
+import { traverseToFixSpecDownstream } from '../compiler/spec-preprocess';
+import { getTheme } from '../core/utils/theme';
 
 describe('Arrangement', () => {
     it('1 View, 1 Track', () => {

src/core/utils/bounding-box.ts → src/compiler/bounding-box.ts

@@ -1,15 +1,15 @@
-import type { MultipleViews, CommonViewDef, GoslingSpec, Track, SingleView } from '@gosling.schema';
-import { Is2DTrack, IsDummyTrack, IsOverlaidTrack, IsXAxis, IsYAxis } from '../gosling.schema.guards';
-import { HIGLASS_AXIS_SIZE } from '../higlass-model';
+import type { MultipleViews, CommonViewDef, GoslingSpec, Track, SingleView } from '@gosling-lang/gosling-schema';
+import { Is2DTrack, IsDummyTrack, IsOverlaidTrack, IsXAxis, IsYAxis } from '@gosling-lang/gosling-schema';
+import { HIGLASS_AXIS_SIZE } from './higlass-model';
 import {
     DEFAULT_CIRCULAR_VIEW_PADDING,
     DEFAULT_INNER_RADIUS_PROP,
     DEFAULT_VIEW_SPACING,
     DEWFAULT_TITLE_PADDING_ON_TOP_AND_BOTTOM
-} from '../defaults';
-import { resolveSuperposedTracks } from './overlay';
+} from './defaults';
+import { resolveSuperposedTracks } from '../core/utils/overlay';
 import { traverseTracksAndViews, traverseViewArrangements } from './spec-preprocess';
-import type { CompleteThemeDeep } from './theme';
+import type { CompleteThemeDeep } from '../core/utils/theme';
 
 export interface Size {
     width: number;

src/core/compile.test.ts → src/compiler/compile.test.ts

@@ -1,6 +1,6 @@
 import { EX_SPEC_VISUAL_ENCODING } from '../../editor/example/json-spec/visual-encoding';
 import { compile } from './compile';
-import { getTheme } from './utils/theme';
+import { getTheme } from '../core/utils/theme';
 import type { GoslingSpec } from '../index';
 
 describe('compile', () => {

src/core/compile.ts → src/compiler/compile.ts

@@ -1,12 +1,12 @@
-import type { GoslingSpec, TemplateTrackDef, VisUnitApiData } from './gosling.schema';
-import type { HiGlassSpec } from './higlass.schema';
-import { traverseToFixSpecDownstream, overrideDataTemplates } from './utils/spec-preprocess';
-import { replaceTrackTemplates } from './utils/template';
-import { getRelativeTrackInfo, type Size } from './utils/bounding-box';
-import type { CompleteThemeDeep } from './utils/theme';
+import type { GoslingSpec, TemplateTrackDef, VisUnitApiData } from '@gosling-lang/gosling-schema';
+import type { HiGlassSpec } from '@gosling-lang/higlass-schema';
+import { traverseToFixSpecDownstream, overrideDataTemplates } from './spec-preprocess';
+import { replaceTrackTemplates } from '../core/utils/template';
+import { getRelativeTrackInfo, type Size } from './bounding-box';
+import type { CompleteThemeDeep } from '../core/utils/theme';
 import { renderHiGlass as createHiGlassModels } from './create-higlass-models';
 import { manageResponsiveSpecs } from './responsive';
-import type { IdTable } from './track-and-view-ids';
+import type { IdTable } from '../api/track-and-view-ids';
 
 /** The callback function called everytime after the spec has been compiled */
 export type CompileCallback = (

src/core/create-higlass-models.ts → src/compiler/create-higlass-models.ts

@@ -1,20 +1,20 @@
-import { getBoundingBox, type TrackInfo } from './utils/bounding-box';
+import { getBoundingBox, type TrackInfo } from './bounding-box';
 import { goslingToHiGlass } from './gosling-to-higlass';
 import { HiGlassModel } from './higlass-model';
-import { getLinkingInfo } from './utils/linking';
+import { getLinkingInfo } from '../core/utils/linking';
 import type {
     GoslingSpec,
     OverlaidTrack,
     SingleTrack,
     TrackApiData,
     VisUnitApiData,
     ViewApiData
-} from '@gosling.schema';
-import type { CompleteThemeDeep } from './utils/theme';
+} from '@gosling-lang/gosling-schema';
+import type { CompleteThemeDeep } from '../core/utils/theme';
 import type { CompileCallback } from './compile';
-import { getViewApiData } from './api-data';
-import { GoslingToHiGlassIdMapper } from './track-and-view-ids';
-import { IsDummyTrack } from './gosling.schema.guards';
+import { getViewApiData } from '../api/api-data';
+import { GoslingToHiGlassIdMapper } from '../api/track-and-view-ids';
+import { IsDummyTrack } from '@gosling-lang/gosling-schema';
 
 export function renderHiGlass(
     spec: GoslingSpec,

src/core/gosling-to-higlass.test.ts → src/compiler/gosling-to-higlass.test.ts

@@ -1,11 +1,11 @@
 import { goslingToHiGlass } from './gosling-to-higlass';
 import { HiGlassModel } from './higlass-model';
 import { EX_TRACK_SEMANTIC_ZOOM } from '../../editor/example/json-spec/semantic-zoom';
-import { convertToFlatTracks } from './utils/spec-preprocess';
-import { getTheme } from './utils/theme';
+import { convertToFlatTracks } from './spec-preprocess';
+import { getTheme } from '../core/utils/theme';
 
-import type { SingleTrack } from './gosling.schema';
-import { GoslingToHiGlassIdMapper } from './track-and-view-ids';
+import type { SingleTrack } from '@gosling-lang/gosling-schema';
+import { GoslingToHiGlassIdMapper } from '../api/track-and-view-ids';
 
 describe('Should convert gosling spec to higlass view config.', () => {
     it('Should return a generated higlass view config correctly', () => {