Upgrade webR, jupyterlite and expose baseUrl & repoUrl in configuration

README.md

@@ -28,6 +28,26 @@ Then build your JupyterLite site:
 jupyter lite build
 ```
 
+## Configuration
+
+The file `jypyter-lite.json` may be modified to set the webR base URL `baseUrl` and default package repository `repoUrl`. For example:
+
+```json
+{
+  "jupyter-lite-schema-version": 0,
+  "jupyter-config-data": {
+    "litePluginSettings": {
+      "@r-wasm/webr-kernel-extension:kernel": {
+        "baseUrl": "https://webr.r-wasm.org/latest/",
+        "repoUrl": "https://repo.r-wasm.org/"
+      }
+    }
+  }
+}
+```
+
+See the Jupyterlite documentation on [configuration files](https://jupyterlite.readthedocs.io/en/latest/howto/configure/config_files.html#jupyter-lite-json) for more information.
+
 ## Limitations
 
 ### Headers
@@ -51,7 +71,7 @@ While webR supports interrupting long running computations, interrupting cell ex
 
 ### Development install
 
-Note: You will need NodeJS and Python 3.8+ to build the extension package. There is an environment.yml file for conda/mamba/micromamba users to create a conda environment with the required dependencies.
+Note: You will need NodeJS and Python 3.9+ to build the extension package. There is an environment.yml file for conda/mamba/micromamba users to create a conda environment with the required dependencies.
 
 The `jlpm` command is JupyterLab's pinned version of [yarn](https://yarnpkg.com/) that is installed with JupyterLab. You may use `yarn` or `npm` in lieu of `jlpm` below.
 

environment.yml

@@ -12,4 +12,4 @@ dependencies:
   - nodejs=20
   # deps
   - jupyterlab >=4.0,<5
-  - jupyterlite-core >=0.3.0rc1
+  - jupyterlite-core >=0.5.0

jupyter-lite.json.example

@@ -0,0 +1,11 @@
+{
+  "jupyter-lite-schema-version": 0,
+  "jupyter-config-data": {
+    "litePluginSettings": {
+      "@r-wasm/webr-kernel-extension:kernel": {
+        "baseUrl": "https://webr.r-wasm.org/latest/",
+        "repoUrl": "https://repo.r-wasm.org/"
+      }
+    }
+  }
+}

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@r-wasm/jupyterlite-webr-kernel",
-  "version": "0.3.0",
+  "version": "0.5.0",
   "description": "An R kernel for JupyterLite, powered by webR",
   "keywords": [
     "jupyter",
@@ -60,13 +60,14 @@
     "watch:labextension": "jupyter labextension watch ."
   },
   "dependencies": {
-    "@jupyterlite/kernel": "^0.3.0-rc.1",
-    "@jupyterlite/server": "^0.3.0-rc.1",
+    "@jupyterlite/kernel": "^0.5.0",
+    "@jupyterlite/server": "^0.5.0",
     "hash.js": "^1.1.7",
-    "webr": "^0.3.0"
+    "webr": "^0.4.2"
   },
   "devDependencies": {
-    "@jupyterlab/builder": "^4.1.5",
+    "@jupyterlab/builder": "^4.4.1",
+    "@jupyterlab/coreutils": "^6.4.0",
     "@types/uuid": "^9.0.0",
     "@typescript-eslint/eslint-plugin": "^4.8.1",
     "@typescript-eslint/parser": "^4.8.1",
@@ -111,7 +112,7 @@
     ],
     "hooks": {
       "before-build-npm": [
-        "python -m pip install 'jupyterlab>=4.0.0,<5'",
+        "python -m pip install 'jupyterlab>=4.3.0,<5'",
         "jlpm"
       ]
     }

pyproject.toml

@@ -1,12 +1,12 @@
 [build-system]
-requires = ["hatchling>=1.5.0", "jupyterlab>=4.1.0,<5", "hatch-nodejs-version>=0.3.2"]
+requires = ["hatchling>=1.5.0", "jupyterlab>=4.3.0,<4.4", "hatch-nodejs-version>=0.3.2"]
 build-backend = "hatchling.build"
 
 [project]
 name = "jupyterlite-webr"
 readme = "README.md"
 license = { file = "LICENSE" }
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 classifiers = [
   "Framework :: Jupyter",
   "Framework :: Jupyter :: JupyterLab",
@@ -16,19 +16,21 @@ classifiers = [
   "License :: OSI Approved :: MIT License",
   "Programming Language :: Python",
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
 ]
-dependencies = ["jupyterlite-core>=0.3.0rc1"]
+dependencies = ["jupyterlite-core>=0.5,<0.6"]
 dynamic = ["version", "description", "authors", "urls", "keywords"]
 
 [project.optional-dependencies]
 dev = [
-  "jupyterlab>=4.1.0,<5",
+  "jupyterlab>=4.3.0,<4.4",
   "ruff==0.1.5",
-  "jupyterlite-pyodide-kernel>=0.3.0a0"
+  "jupyterlite-pyodide-kernel>=0.5.2",
+  "pkginfo>=1.10.0",
 ]
 
 [tool.hatch.version]
@@ -77,7 +79,7 @@ version_cmd = "hatch version"
 
 [tool.jupyter-releaser.hooks]
 before-build-npm = [
-    "python -m pip install 'jupyterlab>=4.1.0,<5'",
+    "python -m pip install 'jupyterlab>=4.3.0,<4.4'",
     "jlpm",
     "jlpm build:prod"
 ]

src/index.ts

@@ -1,14 +1,39 @@
 import { JupyterLiteServer, JupyterLiteServerPlugin } from '@jupyterlite/server';
 import { IKernel, IKernelSpecs } from '@jupyterlite/kernel';
+import { PageConfig, URLExt } from '@jupyterlab/coreutils';
 import { WebRKernel } from './webr_kernel';
 import logo32 from '!!file-loader?context=.!../style/logos/r-logo-32x32.png';
 import logo64 from '!!file-loader?context=.!../style/logos/r-logo-64x64.png';
+import type { WebROptions } from 'webr';
+
+const PLUGIN_ID = '@r-wasm/webr-kernel-extension:kernel';
 
 const server_kernel: JupyterLiteServerPlugin<void> = {
-  id: '@jupyterlite/webr-kernel-extension:kernel',
+  id: PLUGIN_ID,
   autoStart: true,
   requires: [IKernelSpecs],
   activate: (app: JupyterLiteServer, kernelspecs: IKernelSpecs) => {
+    console.log(PageConfig.getOption('litePluginSettings'));
+    const config = JSON.parse(
+      PageConfig.getOption('litePluginSettings') || '{}'
+    )[PLUGIN_ID] || {};
+
+    const webROptions: WebROptions = {
+      REnv: {
+          R_HOME: '/usr/lib/R',
+          FONTCONFIG_PATH: '/etc/fonts',
+          R_ENABLE_JIT: '0',
+      },
+    };
+
+    if (config.baseUrl) {
+      webROptions.baseUrl = URLExt.parse(config.baseUrl).href;
+    }
+
+    if (config.repoUrl) {
+      webROptions.repoUrl = URLExt.parse(config.repoUrl).href;
+    }
+
     kernelspecs.register({
       spec: {
         name: 'webR',
@@ -29,7 +54,7 @@ const server_kernel: JupyterLiteServerPlugin<void> = {
         },
       },
       create: async (options: IKernel.IOptions): Promise<IKernel> => {
-        return new WebRKernel({ ...options });
+        return new WebRKernel({ ...options }, webROptions);
       },
     });
   },

src/webr_kernel.ts

@@ -2,7 +2,7 @@ import { BaseKernel } from '@jupyterlite/kernel';
 import { KernelMessage } from '@jupyterlab/services';
 import { IKernel } from '@jupyterlite/kernel';
 
-import { Console, WebR, Shelter} from 'webr';
+import { Console, WebR, Shelter, WebROptions } from 'webr';
 import { RList, RCharacter, RLogical } from 'webr';
 
 const webRVersion = "0.3.0";
@@ -17,13 +17,13 @@ export class WebRKernel extends BaseKernel {
   #bitmapCanvas: HTMLCanvasElement;
   #lastPlot: string | null = null;
 
-  constructor(options: IKernel.IOptions) {
+  constructor(options: IKernel.IOptions, webROptions: WebROptions) {
     super(options);
     this.#webRConsole = new Console({
       stdout: (line: string) => console.log(line),
       stderr: (line: string) => console.error(line),
       prompt: (prompt: string) => this.inputRequest({ prompt, password: false }),
-    });
+    }, webROptions);
     this.webR = this.#webRConsole.webR;
     this.init = this.setupEnvironment();
     this.#bitmapCanvas = document.createElement('canvas');