refactor!: migrate to TypeScript (#26)

Signed-off-by: Adithya Krishna <adikrish@redhat.com>

.eslintrc.yml

@@ -1,3 +1 @@
-extends: cheminfo
-parserOptions:
-  sourceType: module
+extends: cheminfo-typescript

.github/workflows/nodejs.yml

@@ -10,3 +10,5 @@ jobs:
   nodejs:
     # Documentation: https://github.com/zakodium/workflows#nodejs-ci
     uses: zakodium/workflows/.github/workflows/nodejs.yml@nodejs-v1
+    with:
+      lint-check-types: true

.github/workflows/typedoc.yml

@@ -0,0 +1,32 @@
+name: Deploy TypeDoc on GitHub pages
+
+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@v2
+      - uses: actions/setup-node@v2
+        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

.gitignore

@@ -7,3 +7,5 @@ dist/
 .vscode
 docs
 lib
+lib-esm
+.eslintcache

.prettierrc.json

@@ -0,0 +1,7 @@
+{
+  "arrowParens": "always",
+  "semi": true,
+  "singleQuote": true,
+  "tabWidth": 2,
+  "trailingComma": "all"
+}

README.md

@@ -1,8 +1,8 @@
 # netcdfjs
 
 [![NPM version][npm-image]][npm-url]
-[![build status][travis-image]][travis-url]
-[![Test coverage][coveralls-image]][coveralls-url]
+[![build status][ci-image]][ci-url]
+[![Test coverage][codecov-image]][codecov-url]
 [![npm download][download-image]][download-url]
 
 Read and explore NetCDF v3 files.
@@ -32,9 +32,10 @@ reader.getDataVariable("wmoId"); // go to offset and read it
 
 [MIT](./LICENSE)
 
-[npm-image]: https://img.shields.io/npm/v/netcdfjs.svg?style=flat-square
+[npm-image]: https://img.shields.io/npm/v/netcdfjs.svg
 [npm-url]: https://www.npmjs.com/package/netcdfjs
-[coveralls-image]: https://img.shields.io/coveralls/cheminfo/netcdfjs.svg?style=flat-square
-[coveralls-url]: https://coveralls.io/github/cheminfo/netcdfjs
-[download-image]: https://img.shields.io/npm/dm/netcdfjs.svg?style=flat-square
-[download-url]: https://www.npmjs.com/package/netcdfjs
+[ci-image]: https://github.com/cheminfo/netcdfjs/workflows/Node.js%20CI/badge.svg?branch=main
+[ci-url]: https://github.com/cheminfo/netcdfjs/actions?query=workflow%3A%22Node.js+CI%22
+[codecov-image]: https://img.shields.io/codecov/c/github/cheminfo/netcdfjs.svg
+[codecov-url]: https://codecov.io/gh/cheminfo/netcdfjs
+[download-image]: https://img.shields.io/npm/dm/netcdfjs.svg

demo/agilent.ts

@@ -0,0 +1,20 @@
+import { readFileSync as rfs } from 'node:fs';
+import { join } from 'node:path';
+
+import { NetCDFReader } from '../src/index';
+
+const data = rfs(join(__dirname, '../src/__tests__/files/agilent_hplc.cdf'));
+
+let reader = new NetCDFReader(data);
+
+let selectedVariable = reader.variables[4];
+
+reader.getDataVariable(selectedVariable);
+
+for (let variable of reader.variables) {
+  console.log(variable.name, reader.getDataVariable(variable));
+}
+
+let ordinates = reader.getDataVariable(reader.variables[5]);
+console.log(Math.max(...(ordinates as number[])));
+console.log(Math.min(...(ordinates as number[])));

jest.config.js

@@ -0,0 +1,4 @@
+module.exports = {
+    preset: 'ts-jest/presets/js-with-ts',
+    testEnvironment: 'node',
+};

package.json

@@ -2,18 +2,20 @@
   "name": "netcdfjs",
   "version": "2.0.2",
   "description": "Read and explore NetCDF files",
-  "main": "lib/index.js",
-  "module": "src/index.js",
+  "main": "./lib/index.js",
+  "module": "./lib-esm/index.js",
+  "types": "./lib/index.d.ts",
+  "files": [
+    "src",
+    "lib",
+    "lib-esm"
+  ],
   "keywords": [
     "netcdf",
     "nc",
     "data",
     "format"
   ],
-  "files": [
-    "src",
-    "lib"
-  ],
   "author": "Miguel Asencio <maasencioh@gmail.com> (https://github.com/maasencioh)",
   "repository": "cheminfo/netcdfjs",
   "bugs": {
@@ -22,24 +24,30 @@
   "homepage": "https://github.com/cheminfo/netcdfjs",
   "license": "MIT",
   "scripts": {
-    "build": "cheminfo-build --entry src/index.js --root NetCDF",
-    "eslint": "eslint src",
-    "eslint-fix": "npm run eslint -- --fix",
-    "prepack": "rollup -c",
+    "check-types": "tsc --noEmit",
+    "clean": "rimraf lib lib-esm",
+    "eslint": "eslint src --cache",
+    "eslint:fix": "npm run eslint -- --fix",
+    "prepack": "npm run tsc",
     "prettier": "prettier --check src",
-    "prettier-write": "prettier --write src",
-    "test": "npm run test-only && npm run eslint && npm run prettier",
-    "test-only": "jest --coverage"
+    "prettier:fix": "prettier --write src",
+    "test": "npm run test-only && npm run eslint && npm run prettier && npm run check-types",
+    "test-only": "jest --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"
   },
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.19.6",
-    "@types/jest": "^29.2.0",
+    "@types/jest": "^29.2.3",
     "cheminfo-build": "^1.1.11",
+    "cheminfo-types": "^1.4.0",
     "eslint": "^8.25.0",
-    "eslint-config-cheminfo": "^8.0.2",
-    "jest": "^29.2.1",
+    "eslint-config-cheminfo-typescript": "^11.2.2",
+    "eslint-plugin-import": "^2.28.0",
+    "jest": "^29.3.1",
     "prettier": "^2.7.1",
-    "rollup": "^3.2.3"
+    "ts-jest": "^29.0.3",
+    "typescript": "^4.9.3"
   },
   "dependencies": {
     "iobuffer": "^5.2.1"

src/__tests__/attributeExists.test.ts

@@ -0,0 +1,13 @@
+import { readFileSync } from 'fs';
+
+import { NetCDFReader } from '../parser';
+
+const pathFiles = `${__dirname}/files/`;
+
+test('attributeExists', () => {
+  const data = readFileSync(`${pathFiles}P071.CDF`);
+
+  let reader = new NetCDFReader(data);
+  expect(reader.attributeExists('operator_name')).toBe(true);
+  expect(reader.attributeExists('operator_nameXX')).toBe(false);
+});

src/__tests__/dataVariableExists.test.ts

@@ -0,0 +1,13 @@
+import { readFileSync } from 'fs';
+
+import { NetCDFReader } from '../parser';
+
+const pathFiles = `${__dirname}/files/`;
+
+test('dataVariableExists', () => {
+  const data = readFileSync(`${pathFiles}P071.CDF`);
+
+  let reader = new NetCDFReader(data);
+  expect(reader.dataVariableExists('instrument_name')).toBe(true);
+  expect(reader.dataVariableExists('instrument_nameXX')).toBe(false);
+});

src/__tests__/getAttribute.test.ts

@@ -0,0 +1,12 @@
+import { readFileSync } from 'fs';
+
+import { NetCDFReader } from '../parser';
+
+const pathFiles = `${__dirname}/files/`;
+
+test('getAttribute', () => {
+  const data = readFileSync(`${pathFiles}P071.CDF`);
+
+  let reader = new NetCDFReader(data);
+  expect(reader.getAttribute('operator_name')).toBe('SC');
+});

src/__tests__/getDataVariableAsString.test.ts

@@ -0,0 +1,14 @@
+import { readFileSync } from 'fs';
+
+import { NetCDFReader } from '../parser';
+
+const pathFiles = `${__dirname}/files/`;
+
+test('getDataVariableAsString', () => {
+  const data = readFileSync(`${pathFiles}P071.CDF`);
+
+  let reader = new NetCDFReader(data);
+  expect(reader.getDataVariableAsString('instrument_name')).toBe(
+    'Gas Chromatograph',
+  );
+});