@galaxyproject/jupyterlite 0.0.4 → 0.0.6

package/README.md

@@ -1,39 +1,47 @@
-# JupyterLite + Pyodide Setup
+# JupyterLite + Galaxy Integration
 
 This project integrates JupyterLite with the Pyodide kernel and custom extensions such as `jl-galaxy`.
 
+The `jl-galaxy` extension enables Jupyter users to interact seamlessly with their Galaxy history — including loading and saving notebooks — through a fully integrated browser-based interface.
+
 ## ⚙️ Requirements
 
-- Python 3.7+
-- Node.js 16+
-- npm 7+
+- Python **3.10.17+**
+- Node.js **20.19.1+**
+- npm **10.8.2+**
 
-## 📦 Installation
+---
 
-### 1. Set up Python dependencies
+## 📦 Setup Instructions
 
-Install JupyterLite and the Pyodide kernel plugin:
+### 1. Create and activate a virtual environment
 
 ```bash
-pip install jupyterlite
-pip install jupyterlite-pyodide-kernel
+python -m venv .venv
+source .venv/bin/activate
 ```
 
-> These packages provide the CLI and register the Pyodide kernel for bundling.
+### 2. Install Python dependencies
+
+```bash
+pip install -r requirements.txt
+```
 
-### 2. Set up Node dependencies
+This installs `jupyterlite`, `jupyterlite-pyodide-kernel`, and the `gxy` utility module for Galaxy integration.
 
-Install JavaScript dependencies (for building extensions):
+### 3. Install Node.js dependencies
 
 ```bash
 npm install
 ```
 
-This installs dependencies listed in `package.json`, such as custom JupyterLite extensions.
+This installs JavaScript dependencies listed in `package.json`, including custom JupyterLite extensions.
+
+---
 
 ## 🔨 Build
 
-Run the build to generate a standalone JupyterLite distribution:
+Run the full build to generate a standalone JupyterLite distribution:
 
 ```bash
 npm run build
@@ -42,29 +50,92 @@ npm run build
 This will:
 - Run `jupyter lite build`
 - Include the Pyodide kernel
-- Bundle your extensions (e.g., `jl-galaxy`)
-- Generate the final site in `./static/dist/_output`
+- Bundle federated extensions like `jl-galaxy`
+- Output the final static site to: `./static/dist/_output`
+
+---
 
-## 🚀 Launch
+## 🚀 Serve
 
-You can serve the output using any static file server. For quick testing:
+To serve the JupyterLite site locally:
 
 ```bash
-npx serve static/dist/_output
+npm run serve
 ```
 
-Or use Python:
+Then open [http://localhost:3000](http://localhost:3000) in your browser.
 
-```bash
-cd static/dist/_output
-python -m http.server
+---
+
+## 🧰 Galaxy Integration Utilities (`gxy`)
+
+The `gxy` module provides Python functions to interact with the Galaxy API directly from JupyterLite.
+
+### ✅ `api(endpoint, method="GET", data=None)`
+Makes an HTTP request to a Galaxy API endpoint and returns the parsed JSON response.
+
+```python
+await api("/api/histories")
+await api("/api/histories", method="POST", data={"name": "New History"})
 ```
 
-Then open [http://localhost:8000](http://localhost:8000) in your browser.
+---
+
+### ✅ `get(datasets_identifiers, identifier_type="hid", retrieve_datatype=False)`
+Downloads dataset(s) by HID, ID, or regex pattern. Saves them to Pyodide's virtual filesystem.
+
+```python
+await get(3)                          # by HID
+await get("some_id", identifier_type="id")
+await get("myfile.*", identifier_type="regex")
+```
 
 ---
 
-## 💡 Notes
+### ✅ `put(name, output=None, ext="auto", dbkey="?", history_id=None)`
+Uploads a file from the virtual filesystem to the current Galaxy history.
+
+```python
+await put("mydata.txt", "newname.txt", ext="txt")
+```
+
+---
+
+### ✅ `get_history(history_id=None)`
+Returns metadata for all visible datasets in the current history.
+
+```python
+await get_history()
+```
+
+---
+
+### ✅ `get_history_id()`
+Returns the current history ID based on the dataset context.
+
+```python
+await get_history_id()
+```
+
+---
+
+### ✅ `get_environment()`
+Returns the Galaxy environment injected into the session via `__gxy__`.
+
+```python
+get_environment()
+```
+
+---
+
+### ✅ `_find_matching_ids(history_datasets, list_of_regex_patterns, identifier_type='hid')`
+Used internally to resolve regex patterns to dataset identifiers.
+
+---
+
+## 📎 Notes
+
+- The `jl-galaxy` extension allows users to browse and manage Galaxy histories directly from the Jupyter UI.
+- All files must be placed within `static/dist/_output`; writing outside this directory breaks the build.
+- The upload helper uses `XMLHttpRequest` to work around Pyodide's limitations with `fetch`.
 
-- The build process automatically configures the Pyodide kernel and registers it as a federated extension.
-- If you're developing additional extensions, make sure to register them in `jupyter-lite.json` under `federated_extensions`.

package/package.json

@@ -1,12 +1,12 @@
 {
     "name": "@galaxyproject/jupyterlite",
-    "version": "0.0.4",
+    "version": "0.0.6",
     "type": "module",
     "files": [
         "static/dist"
     ],
     "scripts": {
-        "build": "webpack && npm run build:jupyter && npm run build:gxy && npm run build:extension && npm run build:patch && npm run build:index",
+        "build": "webpack && npm run build:jupyter && npm run build:extension && npm run build:gxy && npm run build:patch && npm run build:index",
         "build:extension": "node install-extension.js",
         "build:gxy": "cd gxy && python -m build --wheel",
         "build:index": "cpx src/index.js static/dist",
@@ -23,5 +23,8 @@
         "typescript": "^5.4.2",
         "webpack": "^5.89.0",
         "webpack-cli": "^5.1.4"
+    },
+    "dependencies": {
+        "node-fetch": "^3.3.2"
     }
 }

package/static/dist/_output/jupyter-lite.json

@@ -306,7 +306,22 @@
       "@jupyterlite/pyodide-kernel-extension:kernel": {
         "loadPyodideOptions": {
           "packages": [
-            "../../../../pypi/gxy-0.0.0-py3-none-any.whl"
+            "../../../../pypi/gxy-0.0.0-py3-none-any.whl",
+            "../../../../pypi/attrs-25.3.0-py3-none-any.whl",
+            "../../../../pypi/fastjsonschema-2.21.1-py3-none-any.whl",
+            "../../../../pypi/gxy-0.0.0-py3-none-any.whl",
+            "../../../../pypi/jsonschema-4.23.0-py3-none-any.whl",
+            "../../../../pypi/jsonschema_specifications-2025.4.1-py3-none-any.whl",
+            "../../../../pypi/jupyter_core-5.7.2-py3-none-any.whl",
+            "../../../../pypi/narwhals-1.38.2-py3-none-any.whl",
+            "../../../../pypi/nbformat-5.10.4-py3-none-any.whl",
+            "../../../../pypi/packaging-25.0-py3-none-any.whl",
+            "../../../../pypi/platformdirs-4.3.8-py3-none-any.whl",
+            "../../../../pypi/plotly-6.0.1-py3-none-any.whl",
+            "../../../../pypi/referencing-0.36.2-py3-none-any.whl",
+            "../../../../pypi/traitlets-5.14.3-py3-none-any.whl",
+            "../../../../pypi/typing_extensions-4.13.2-py3-none-any.whl",
+            "rpds-py"
           ]
         }
       }