update the library to modern standards

.github/workflows/ci.yml

@@ -0,0 +1,41 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  check-format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: oven-sh/setup-bun@v2
+      - run: bun install
+      - run: bun run check-format
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: oven-sh/setup-bun@v2
+      - run: bun install
+      - run: bun run lint
+
+  type-check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: oven-sh/setup-bun@v2
+      - run: bun install
+      - run: bun run type-check
+
+  build:
+    runs-on: ubuntu-latest
+    needs: [check-format, lint, type-check]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: oven-sh/setup-bun@v2
+      - run: bun install
+      - run: bun run build

.github/workflows/publish.yml

@@ -1,20 +1,24 @@
-name: Publish
+name: Publish Package to npmjs
 
 on:
-  push:
-    branches:
-      - main
+  release:
+    types: [published]
 
 jobs:
-  publish:
+  build:
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      id-token: write
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-node@v1
+      - uses: actions/checkout@v4
+      - uses: oven-sh/setup-bun@v2
+      - run: bun install
+      - run: bun run build
+      - uses: actions/setup-node@v4
         with:
-          node-version: 12
-      - run: yarn config delete proxy
-      - run: yarn
-      - uses: JS-DevTools/npm-publish@v1
-        with:
-          token: ${{ secrets.NPM_TOKEN }}
+          node-version: "22.x"
+          registry-url: "https://registry.npmjs.org"
+      - run: npm publish --provenance --access public
+        env:
+          NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }}

.gitignore

@@ -1,2 +1,3 @@
 node_modules/
 .vscode
+dist/

eslint.config.mjs

@@ -0,0 +1,11 @@
+import { defineConfig, globalIgnores } from "eslint/config";
+
+export default defineConfig([
+  globalIgnores([".github/workflows/**/*", "dist/**/*"]),
+  {
+    languageOptions: {
+      ecmaVersion: "latest",
+      sourceType: "module",
+    },
+  },
+]);

package.json

@@ -1,20 +1,57 @@
 {
   "name": "edam2json-js",
-  "version": "0.3.2",
+  "version": "0.4.0",
   "description": "Javascript library to convert EDAM to JSON/CSV/TSV",
-  "main": "index.js",
   "type": "module",
+  "main": "dist/index.cjs.js",
+  "module": "dist/index.esm.js",
+  "browser": "dist/index.umd.js",
+  "types": "dist/index.d.ts",
+  "files": [
+    "dist"
+  ],
+  "sideEffects": false,
+  "exports": {
+    ".": {
+      "import": "./dist/index.esm.js",
+      "require": "./dist/index.cjs.js",
+      "types": "./dist/index.d.ts"
+    },
+    "./browser": {
+      "import": "./dist/browser.umd.js",
+      "require": "./dist/browser.umd.js",
+      "types": "./dist/index.d.ts"
+    }
+  },
+  "scripts": {
+    "test": "echo \"Error: no test specified\" && exit 1",
+    "clean": "rimraf dist",
+    "lint": "eslint .",
+    "type-check": "tsc --noEmit",
+    "check-format": "prettier --check src/",
+    "check": "bun run check-format && bun run lint && bun run type-check",
+    "prepare": "npm run build",
+    "build": "rollup -c",
+    "prepublishOnly": "npm test"
+  },
   "dependencies": {
-    "axios": "^0.21.1",
     "commander": "^8.1.0",
-    "eslint": "^7.32.0",
-    "prettier": "^2.3.2",
-    "rdfxml-streaming-parser": "^1.4.0"
+    "rdfxml-streaming-parser": "^1.4.0",
+    "tslib": "^2.8.1"
   },
-  "browser": "browser.js",
-  "devDependencies": {},
-  "scripts": {
-    "test": "echo \"Error: no test specified\" && exit 1"
+  "devDependencies": {
+    "@rollup/plugin-commonjs": "^28.0.6",
+    "@rollup/plugin-node-resolve": "^16.0.1",
+    "@rollup/plugin-terser": "^0.4.4",
+    "@rollup/plugin-typescript": "^12.1.3",
+    "@types/node": "^24.0.3",
+    "eslint": "^9.29.0",
+    "prettier": "^3.5.3",
+    "rimraf": "^6.0.1",
+    "rollup": "^4.43.0",
+    "rollup-plugin-dts": "^6.2.1",
+    "rollup-plugin-polyfill-node": "^0.13.0",
+    "typescript": "^5.8.3"
   },
   "repository": {
     "type": "git",

rollup.config.js

@@ -0,0 +1,83 @@
+import resolve from "@rollup/plugin-node-resolve";
+import commonjs from "@rollup/plugin-commonjs";
+import typescript from "@rollup/plugin-typescript";
+import dts from "rollup-plugin-dts";
+import terser from "@rollup/plugin-terser";
+import polyfillNode from "rollup-plugin-polyfill-node";
+
+// suppress rollup warnings we know are benign
+const onwarn = (warning, defaultHandler) => {
+  // polyfill-node circular deps
+  if (
+    warning.code === "CIRCULAR_DEPENDENCY" &&
+    /polyfill-node/.test(warning.importer)
+  ) {
+    return;
+  }
+  if (
+    warning.code === "THIS_IS_UNDEFINED" &&
+    warning.message.includes("sax.js")
+  ) {
+    return;
+  }
+  // suppress empty chunk warning for d.ts rollup
+  if (warning.code === "EMPTY_CHUNK") {
+    return;
+  }
+  defaultHandler(warning);
+};
+
+const sharedPlugins = [
+  resolve(),
+  commonjs(),
+  typescript({ tsconfig: "./tsconfig.json" }),
+];
+
+const browserPlugins = [
+  polyfillNode(),
+  resolve({ browser: true, preferBuiltins: false }),
+  commonjs(),
+  typescript({ tsconfig: "./tsconfig.json" }),
+];
+
+export default [
+  // 1) Node/CJS + ESM build
+  {
+    input: "src/index.ts",
+    onwarn,
+    output: [
+      { file: "dist/index.cjs.js", format: "cjs", sourcemap: true },
+      { file: "dist/index.esm.js", format: "es", sourcemap: true },
+    ],
+    plugins: sharedPlugins,
+  },
+  // 2) Browser UMD build (with polyfills)
+  {
+    input: "src/browser.ts",
+    onwarn,
+    plugins: browserPlugins,
+    context: "window", // Moved to the correct top-level position
+    output: [
+      {
+        file: "dist/browser.umd.js",
+        format: "umd",
+        name: "Edam2JSON",
+        sourcemap: true,
+      },
+      {
+        file: "dist/browser.umd.min.js",
+        format: "umd",
+        name: "Edam2JSON",
+        sourcemap: true,
+        plugins: [terser()],
+      },
+    ],
+  },
+  // 3) Roll up d.ts
+  {
+    input: "dist/index.d.ts",
+    onwarn, // Added onwarn here to suppress the empty chunk warning
+    output: [{ file: "dist/index.d.ts", format: "es" }],
+    plugins: [dts()],
+  },
+];

browser.js → src/browser.ts

@@ -1,30 +1,34 @@
-import { parseToJSON } from "./src/parser.js";
-import axios from "axios";
+import { parseToJSON } from "./parser";
 
 /**
  * Parses an OWL file to a json tree of nodes
  * @param {string} url The URL of the owl file in raw format e.g "https://raw.githubusercontent.com/edamontology/edamontology/main/releases/EDAM_1.25.owl"
  * @param {function} onSuccess The callback function to be executed after the tree is ready e.g (tree) => {console.log(tree)}
  * @param {function} onError The callback function to be executed in case of an error
  */
-const jsonTreeFromURL = (url, onSuccess, onError) => {
-  axios
-    .get(url)
-    .then((resp) => {
-      parseToJSON(resp.data, onSuccess);
-    })
-    .catch((err) => {
-      onError(err);
-    });
-};
+async function jsonTreeFromURL(
+  url: string,
+  onSuccess: () => void,
+  onError: (err: Error) => void,
+) {
+  try {
+    const response = await fetch(url);
+    if (!response.ok) throw new Error("Fetch call failed");
+
+    const data = await response.json();
+    parseToJSON(data, onSuccess);
+  } catch (err) {
+    onError(err);
+  }
+}
 
 /**
  * Parses an OWL file to a json tree of nodes
  * @param {string} text the string containing the OWL file content
  * @param {function} onSuccess The callback function to be executed after the tree is ready e.g (tree) => {console.log(tree)}
  */
-const jsonTreeFromString = (text, onSuccess) => {
+function jsonTreeFromString(text: string, onSuccess: () => void) {
   parseToJSON(text, onSuccess);
-};
+}
 
 export { jsonTreeFromURL, jsonTreeFromString };