refactor!: switch to esm-only and update ml-gsd

.github/workflows/typedoc.yml

@@ -1,32 +1,15 @@
-name: Deploy TypeDoc on GitHub pages
+name: TypeDoc
 
 on:
   workflow_dispatch:
   release:
     types: [published]
 
-env:
-  NODE_VERSION: 16.x
-  ENTRY_FILE: 'src/index.ts'
-
 jobs:
-  deploy:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-node@v3
-        with:
-          node-version: ${{ env.NODE_VERSION }}
-      - name: Install dependencies
-        run: npm install
-      - name: Build documentation
-        uses: zakodium/typedoc-action@v2
-        with:
-          entry: ${{ env.ENTRY_FILE }}
-      - name: Deploy to GitHub pages
-        uses: JamesIves/github-pages-deploy-action@releases/v4
-        with:
-          token: ${{ secrets.BOT_TOKEN }}
-          branch: gh-pages
-          folder: docs
-          clean: true
+  typedoc:
+    # Documentation: https://github.com/zakodium/workflows#typedoc
+    uses: zakodium/workflows/.github/workflows/typedoc.yml@typedoc-v1
+    with:
+      entry: 'src/index.ts'
+    secrets:
+      github-token: ${{ secrets.BOT_TOKEN }}

.prettierignore

@@ -0,0 +1,5 @@
+CHANGELOG.md
+lib
+coverage
+FilterXYSchema.json
+FilterXYSchema.js

FilterXYSchema.d.ts

@@ -1,2 +1,2 @@
-declare const schema: typeof import('./FilterXYSchema.json')
+declare const schema: typeof import('./FilterXYSchema.json');
 export = schema;

eslint.config.mjs

@@ -1,9 +1,7 @@
+import { defineConfig, globalIgnores } from 'eslint/config';
 import cheminfo from 'eslint-config-cheminfo-typescript';
 
-export default [
-  ...cheminfo,
-  {
-    languageOptions: {},
-    rules: {},
-  },
-];
+export default defineConfig(
+  globalIgnores(['coverage', 'lib', 'FilterXYSchema.*']),
+  cheminfo,
+);

package.json

@@ -2,35 +2,32 @@
   "name": "ml-signal-processing",
   "version": "1.2.0",
   "description": "Process data in the form of {x:[], y:[]}",
-  "main": "./lib/index.js",
-  "module": "./lib-esm/index.js",
-  "types": "./lib/index.d.ts",
+  "type": "module",
+  "exports": "./lib/index.js",
   "keywords": [],
   "author": "Luc Patiny",
   "license": "MIT",
   "files": [
     "src",
     "lib",
-    "lib-esm",
     "FilterXYSchema.d.ts",
     "FilterXYSchema.js",
     "FilterXYSchema.json"
   ],
   "scripts": {
     "check-types": "tsc --noEmit",
-    "clean": "rimraf lib lib-esm",
+    "clean": "rimraf lib",
     "createSchema": "typescript-json-schema --refs false ./tsconfig.json FilterXYType > FilterXYSchema.json",
     "postcreateSchema": "node scripts/create_js_schema.mjs",
-    "eslint": "eslint src --cache",
-    "eslint-fix": "npm run eslint -- --fix",
+    "eslint": "eslint . --cache",
+    "eslint-fix": "node --run eslint -- --fix",
     "prepack": "npm run createSchema && npm run tsc",
-    "prettier": "prettier --check src",
-    "prettier-write": "prettier --write src",
+    "prettier": "prettier --check .",
+    "prettier-write": "prettier --write .",
     "test": "npm run test-only && npm run eslint && npm run prettier && npm run check-types",
     "test-only": "vitest run --coverage",
-    "tsc": "npm run clean && npm run tsc-cjs && npm run tsc-esm",
-    "tsc-cjs": "tsc --project tsconfig.cjs.json",
-    "tsc-esm": "tsc --project tsconfig.esm.json"
+    "tsc": "npm run clean && npm run tsc-build",
+    "tsc-build": "tsc --project tsconfig.build.json"
   },
   "repository": {
     "type": "git",
@@ -41,22 +38,22 @@
   },
   "homepage": "https://github.com/mljs/signal-processing#readme",
   "devDependencies": {
-    "@vitest/coverage-v8": "^2.1.4",
-    "eslint": "^9.14.0",
-    "eslint-config-cheminfo-typescript": "^16.0.0",
+    "@vitest/coverage-v8": "^3.2.3",
+    "@zakodium/tsconfig": "^1.0.1",
+    "eslint": "^9.29.0",
+    "eslint-config-cheminfo-typescript": "^18.0.1",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "prettier": "^3.3.3",
+    "prettier": "^3.5.3",
     "rimraf": "^6.0.1",
-    "ts-jest": "^29.2.5",
-    "typescript": "^5.6.3",
+    "typescript": "^5.8.3",
     "typescript-json-schema": "^0.65.1",
-    "vitest": "^2.1.4"
+    "vitest": "^3.2.3"
   },
   "dependencies": {
     "baselines": "^1.1.9",
     "cheminfo-types": "^1.8.1",
-    "ml-gsd": "^12.1.8",
+    "ml-gsd": "^13.0.1",
     "ml-savitzky-golay-generalized": "^4.2.0",
-    "ml-spectra-processing": "^14.6.2"
+    "ml-spectra-processing": "^14.12.0"
   }
 }

scripts/create_js_schema.mjs

@@ -1,6 +1,9 @@
 import fs from 'node:fs';
 
-const schema = fs.readFileSync(new URL('../FilterXYSchema.json', import.meta.url), 'utf8');
+const schema = fs.readFileSync(
+  new URL('../FilterXYSchema.json', import.meta.url),
+  'utf8',
+);
 
 const schemaJs = `'use strict';
 

src/FilterMatrixType.ts

@@ -1,6 +1,6 @@
-import { MatrixCenterZMeanFilter } from './matrixFilters/centerZMean';
-import { PQNFilter } from './matrixFilters/pqn';
-import { MatrixZRescaleFilter } from './matrixFilters/zRescale';
+import type { MatrixCenterZMeanFilter } from './matrixFilters/centerZMean.ts';
+import type { PQNFilter } from './matrixFilters/pqn.ts';
+import type { MatrixZRescaleFilter } from './matrixFilters/zRescale.ts';
 
 export type FilterMatrixType =
   | MatrixCenterZMeanFilter

src/FilterXYType.ts

@@ -1,4 +1,4 @@
-import {
+import type {
   AirPLSBaselineFilter,
   CenterMeanFilter,
   CenterMedianFilter,
@@ -21,8 +21,8 @@ import {
   YFunctionFilter,
   CalibrateFilter,
   ParetoNormalizationFilter,
-} from './filters/filters';
-import { ReverseIfNeededFilter } from './filters/x/reverseIfNeeded';
+} from './filters/filters.ts';
+import type { ReverseIfNeededFilter } from './filters/x/reverseIfNeeded.ts';
 
 export type FilterXYType =
   | AirPLSBaselineFilter

src/__tests__/filterMatrix.test.ts

@@ -1,7 +1,7 @@
 import { test, expect } from 'vitest';
 
-import { filterMatrix } from '..';
-import { FilterMatrixType } from '../FilterMatrixType';
+import type { FilterMatrixType } from '../FilterMatrixType.ts';
+import { filterMatrix } from '../index.ts';
 
 test('filterMatrix', () => {
   const filters: FilterMatrixType[] = [

src/__tests__/filterXY.test.ts

@@ -1,8 +1,8 @@
 import { describe, it, expect } from 'vitest';
 
-import { filterXY } from '..';
-import { FilterXYType } from '../FilterXYType';
-import linear from '../filters/__tests__/data/linear';
+import type { FilterXYType } from '../FilterXYType.ts';
+import linear from '../filters/__tests__/data/linear.ts';
+import { filterXY } from '../index.ts';
 
 describe('filterXY', () => {
   it('filters', () => {

src/filterMatrix.ts

@@ -1,8 +1,8 @@
-import { DoubleMatrix } from 'ml-spectra-processing';
+import type { DoubleMatrix } from 'ml-spectra-processing';
 
-import { FilterMatrixType } from './FilterMatrixType';
-//import * as Filters from './matrixFilters/matrixFilters';
+import type { FilterMatrixType } from './FilterMatrixType.ts';
 
+// eslint-disable-next-line jsdoc/require-jsdoc
 export function filterMatrix(
   matrix: DoubleMatrix,
   // eslint-disable-next-line @typescript-eslint/no-unused-vars
@@ -12,7 +12,7 @@
     data: matrix,
   };
 
   const logs: any = [];
 
   /**
    * todo

src/filterXY.ts

@@ -1,13 +1,13 @@
-import { DataXY } from 'cheminfo-types';
+import type { DataXY } from 'cheminfo-types';
 import { xEnsureFloat64, xyGrowingX } from 'ml-spectra-processing';
 
-import { FilterXYType } from './FilterXYType';
-import * as Filters from './filters/filters';
+import type { FilterXYType } from './FilterXYType.ts';
+import * as Filters from './filters/filters.ts';
 
 /**
  * Apply filters on {x:[], y:[]}
  * @param data
  * @param filters
  * @returns A very important number
  */
 export function filterXY(data: DataXY, filters: FilterXYType[]) {

src/filters/baseline/__tests__/airPLSBaseline.test.ts

@@ -1,10 +1,7 @@
-import { toBeDeepCloseTo, toMatchCloseTo } from 'jest-matcher-deep-close-to';
 import { test, expect } from 'vitest';
 
-import baseline from '../../__tests__/data/baseline';
-import { airPLSBaseline } from '../airPLSBaseline';
-
-expect.extend({ toBeDeepCloseTo, toMatchCloseTo });
+import baseline from '../../__tests__/data/baseline.ts';
+import { airPLSBaseline } from '../airPLSBaseline.ts';
 
 test('airPLSBaseline', () => {
   const result = airPLSBaseline(baseline);

src/filters/baseline/__tests__/iterativePolynomialBaseline.test.ts

@@ -1,10 +1,7 @@
-import { toBeDeepCloseTo, toMatchCloseTo } from 'jest-matcher-deep-close-to';
 import { test, expect } from 'vitest';
 
-import baseline from '../../__tests__/data/baseline';
-import { iterativePolynomialBaseline } from '../iterativePolynomialBaseline';
-
-expect.extend({ toBeDeepCloseTo, toMatchCloseTo });
+import baseline from '../../__tests__/data/baseline.ts';
+import { iterativePolynomialBaseline } from '../iterativePolynomialBaseline.ts';
 
 test('iterativePolynomialBaseline', () => {
   const result = iterativePolynomialBaseline(baseline);

src/filters/baseline/__tests__/rollingAverageBaseline.test.ts

@@ -1,10 +1,7 @@
-import { toBeDeepCloseTo, toMatchCloseTo } from 'jest-matcher-deep-close-to';
 import { test, expect } from 'vitest';
 
-import baseline from '../../__tests__/data/baseline';
-import { rollingAverageBaseline } from '../rollingAverageBaseline';
-
-expect.extend({ toBeDeepCloseTo, toMatchCloseTo });
+import baseline from '../../__tests__/data/baseline.ts';
+import { rollingAverageBaseline } from '../rollingAverageBaseline.ts';
 
 test('rollingAverageBaseline', () => {
   const result = rollingAverageBaseline(baseline);

src/filters/baseline/__tests__/rollingBallBaseline.test.ts

@@ -1,10 +1,7 @@
-import { toBeDeepCloseTo, toMatchCloseTo } from 'jest-matcher-deep-close-to';
 import { test, expect } from 'vitest';
 
-import baseline from '../../__tests__/data/baseline';
-import { rollingBallBaseline } from '../rollingBallBaseline';
-
-expect.extend({ toBeDeepCloseTo, toMatchCloseTo });
+import baseline from '../../__tests__/data/baseline.ts';
+import { rollingBallBaseline } from '../rollingBallBaseline.ts';
 
 test('rollingBallBaseline', () => {
   const result = rollingBallBaseline(baseline);

src/filters/baseline/__tests__/rollingMedianBaseline.test.ts

@@ -1,10 +1,7 @@
-import { toBeDeepCloseTo, toMatchCloseTo } from 'jest-matcher-deep-close-to';
 import { test, expect } from 'vitest';
 
-import baseline from '../../__tests__/data/baseline';
-import { rollingMedianBaseline } from '../rollingMedianBaseline';
-
-expect.extend({ toBeDeepCloseTo, toMatchCloseTo });
+import baseline from '../../__tests__/data/baseline.ts';
+import { rollingMedianBaseline } from '../rollingMedianBaseline.ts';
 
 test('rollingMedianBaseline', () => {
   const result = rollingMedianBaseline(baseline);

src/filters/baseline/airPLSBaseline.ts

@@ -1,13 +1,13 @@
 //@ts-expect-error no type definition for baselines
 import { airPLSBaseline as baselineFct } from 'baselines';
-import { DataXY } from 'cheminfo-types';
+import type { DataXY } from 'cheminfo-types';
 
 export interface AirPLSBaselineFilter {
   name: 'airPLSBaseline';
 }
 
 /**
  * @param data
  */
 export function airPLSBaseline(data: DataXY<Float64Array>) {
   data.y = baselineFct(data.y).correctedSpectrum;

src/filters/baseline/iterativePolynomialBaseline.ts

@@ -1,13 +1,13 @@
 //@ts-expect-error no type definition for baselines
 import { iterativePolynomialBaseline as baselineFct } from 'baselines';
-import { DataXY } from 'cheminfo-types';
+import type { DataXY } from 'cheminfo-types';
 
 export interface IterativePolynomialBaselineFilter {
   name: 'iterativePolynomialBaseline';
 }
 
 /**
  * @param data
  */
 export function iterativePolynomialBaseline(data: DataXY<Float64Array>) {
   data.y = baselineFct(data.y).correctedSpectrum;

src/filters/baseline/rollingAverageBaseline.ts

@@ -1,12 +1,12 @@
 //@ts-expect-error no type definition for baselines
 import { rollingAverageBaseline as baselineFct } from 'baselines';
-import { DataXY } from 'cheminfo-types';
+import type { DataXY } from 'cheminfo-types';
 
 export interface RollingAverageBaselineFilter {
   name: 'rollingAverageBaseline';
 }
 
 /**
  * @param data
  */
 export function rollingAverageBaseline(data: DataXY<Float64Array>) {

src/filters/baseline/rollingBallBaseline.ts

@@ -1,6 +1,6 @@
 //@ts-expect-error no type definition for baselines
 import { rollingBallBaseline as baselineFct } from 'baselines';
-import { DataXY } from 'cheminfo-types';
+import type { DataXY } from 'cheminfo-types';
 
 export interface RollingBallBaselineFilter {
   name: 'rollingBallBaseline';

src/filters/baseline/rollingMedianBaseline.ts

@@ -1,6 +1,6 @@
 //@ts-expect-error no type definition for baselines
 import { rollingMedianBaseline as baselineFct } from 'baselines';
-import { DataXY } from 'cheminfo-types';
+import type { DataXY } from 'cheminfo-types';
 
 export interface RollingMedianBaselineFilter {
   name: 'rollingMedianBaseline';

src/filters/filters.ts

@@ -1,31 +1,31 @@
-export * from './scaling/centerMean';
-export * from './scaling/centerMedian';
-export * from './x/fromTo';
-export * from './scaling/normed';
-export * from './scaling/divideBySD';
-export * from './scaling/rescale';
-export * from './scaling/paretoNormalization';
+export * from './scaling/centerMean.ts';
+export * from './scaling/centerMedian.ts';
+export * from './x/fromTo.ts';
+export * from './scaling/normed.ts';
+export * from './scaling/divideBySD.ts';
+export * from './scaling/rescale.ts';
+export * from './scaling/paretoNormalization.ts';
 
-export * from './baseline/airPLSBaseline';
-export * from './baseline/iterativePolynomialBaseline';
-export * from './baseline/rollingAverageBaseline';
-export * from './baseline/rollingBallBaseline';
-export * from './baseline/rollingMedianBaseline';
+export * from './baseline/airPLSBaseline.ts';
+export * from './baseline/iterativePolynomialBaseline.ts';
+export * from './baseline/rollingAverageBaseline.ts';
+export * from './baseline/rollingBallBaseline.ts';
+export * from './baseline/rollingMedianBaseline.ts';
 
-export * from './sg/firstDerivative';
-export * from './sg/secondDerivative';
-export * from './sg/thirdDerivative';
-export * from './sg/savitzkyGolay';
+export * from './sg/firstDerivative.ts';
+export * from './sg/secondDerivative.ts';
+export * from './sg/thirdDerivative.ts';
+export * from './sg/savitzkyGolay.ts';
 
-export * from './x/ensureGrowing';
-export * from './x/reverseIfNeeded';
-export * from './x/equallySpaced';
-export * from './x/filterX';
-export * from './x/setMaxX';
-export * from './x/setMinX';
-export * from './x/calibrateX';
-export * from './x/xFunction';
+export * from './x/ensureGrowing.ts';
+export * from './x/reverseIfNeeded.ts';
+export * from './x/equallySpaced.ts';
+export * from './x/filterX.ts';
+export * from './x/setMaxX.ts';
+export * from './x/setMinX.ts';
+export * from './x/calibrateX.ts';
+export * from './x/xFunction.ts';
 
-export * from './scaling/yFunction';
-export * from './y/setMaxY';
-export * from './y/setMinY';
+export * from './scaling/yFunction.ts';
+export * from './y/setMaxY.ts';
+export * from './y/setMinY.ts';