@galaxyproject/jupyterlite 0.0.10 → 0.0.11
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/package.json +6 -5
- package/static/dist/_output/jupyter-lite.json +27 -23
- package/static/dist/_output/pypi/all.json +366 -0
- package/static/dist/_output/pypi/gxy-0.0.0-py3-none-any.whl +0 -0
- package/static/dist/_output/pypi/{narwhals-1.38.2-py3-none-any.whl → narwhals-1.39.0-py3-none-any.whl} +0 -0
- package/static/jupyterlite.xml +81 -0
- package/static/logo.svg +202 -0
package/package.json
CHANGED
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@@ -1,10 +1,8 @@
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{
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"name": "@galaxyproject/jupyterlite",
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-
"version": "0.0.
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"version": "0.0.11",
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"type": "module",
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"files": [
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"static/dist"
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],
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"files": ["static"],
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"scripts": {
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"build": "webpack && npm run build:jupyter && npm run build:gxy && npm run build:extension && npm run build:patch && npm run build:index",
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"build:extension": "node install-extension.js",
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@@ -13,11 +11,14 @@
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"build:jupyter": "jupyter lite build --output-dir static/dist/_output --config static/dist/_output/jupyter-lite.json",
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"build:patch": "node patch-config.js",
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"dev": "jupyter lite serve --output-dir static/dist/_output --config static/dist/_output/jupyter-lite.json",
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"prettier": "prettier --write 'package.json' '*.js' 'src/*.js' 'src/*.ts'"
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"prettier": "prettier --write 'package.json' '*.js' 'src/*.js' 'src/*.ts'",
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"test": "npx playwright test --headed"
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},
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"devDependencies": {
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"@playwright/test": "^1.52.0",
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"axios": "^1.9.0",
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"cpx": "^1.5.0",
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"playwright": "^1.52.0",
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"prettier": "^3.5.3",
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"ts-loader": "^9.5.0",
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"typescript": "^5.4.2",
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@@ -5,6 +5,21 @@
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"appVersion": "0.5.1",
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"baseUrl": "./",
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"defaultKernelName": "python",
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"disabledExtensions": [
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"@jupyterlab/filebrowser-extension",
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"@jupyterlab/launcher-extension",
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"@jupyterlab/running-extension",
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"@jupyterlab/toc-extension",
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"@jupyterlab/fileeditor-extension:plugin",
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"@jupyterlab/fileeditor-extension:cursor-position",
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"@jupyterlab/fileeditor-extension:completer",
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"@jupyterlab/fileeditor-extension:language-server",
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"@jupyterlab/fileeditor-extension:editor-syntax-status",
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"@jupyterlab/fileeditor-extension:tab-space-status",
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"@jupyterlab/notebook-extension:toc",
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"@jupyterlite/application-extension:share-file",
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"@jupyterlab/tooltip-extension:files"
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],
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"faviconUrl": "./lab/favicon.ico",
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"federated_extensions": [
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{
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@@ -13,17 +28,17 @@
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"load": "static/remoteEntry.3ac7f76fb22d01270496.js",
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"name": "@jupyterlite/pyodide-kernel-extension"
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},
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{
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"extension": "./extension",
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"load": "entry.js",
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"name": "jl-galaxy"
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},
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{
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"extension": "./extension",
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"liteExtension": false,
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"load": "static/remoteEntry.5cbb9d2323598fbda535.js",
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"name": "jupyterlab_pygments",
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"style": "./style"
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},
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{
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"name": "jl-galaxy",
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"load": "entry.js",
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"extension": "./extension"
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}
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],
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"fileTypes": {
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"../../../../pypi/jsonschema-4.23.0-py3-none-any.whl",
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"../../../../pypi/jsonschema_specifications-2025.4.1-py3-none-any.whl",
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"../../../../pypi/jupyter_core-5.7.2-py3-none-any.whl",
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"../../../../pypi/narwhals-1.
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"../../../../pypi/narwhals-1.39.0-py3-none-any.whl",
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"../../../../pypi/nbformat-5.10.4-py3-none-any.whl",
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"../../../../pypi/packaging-25.0-py3-none-any.whl",
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"../../../../pypi/platformdirs-4.3.8-py3-none-any.whl",
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@@ -325,24 +340,13 @@
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"pandas",
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"rpds-py"
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]
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}
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},
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"pipliteUrls": [
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"./pypi/all.json?sha256=4ab6b5fd089188d3d12e0a6d237883bfca6fb146a6693a20635befc7f0b86b4d",
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"./extensions/@jupyterlite/pyodide-kernel-extension/static/pypi/all.json?sha256=8410129b75a5560182e60e67735d1efad22cde00c42736ad5f8841351d33b617"
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]
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}
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}
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"disabledExtensions": [
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"@jupyterlab/filebrowser-extension",
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"@jupyterlab/launcher-extension",
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"@jupyterlab/running-extension",
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"@jupyterlab/toc-extension",
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"@jupyterlab/fileeditor-extension:plugin",
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"@jupyterlab/fileeditor-extension:cursor-position",
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"@jupyterlab/fileeditor-extension:completer",
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"@jupyterlab/fileeditor-extension:language-server",
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"@jupyterlab/fileeditor-extension:editor-syntax-status",
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"@jupyterlab/fileeditor-extension:tab-space-status",
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"@jupyterlab/notebook-extension:toc",
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"@jupyterlite/application-extension:share-file",
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"@jupyterlab/tooltip-extension:files"
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]
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}
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},
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"jupyter-lite-schema-version": 0
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}
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@@ -0,0 +1,366 @@
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"attrs": {
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"25.3.0": [
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"fastjsonschema": {
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},
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"gxy": {
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|
Binary file
|
|
Binary file
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|
@@ -0,0 +1,81 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="UTF-8"?>
|
|
2
|
+
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
|
|
3
|
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<visualization name="JupyterLite" embeddable="true">
|
|
4
|
+
<description>Pyodide-based Jupyter Notebooks</description>
|
|
5
|
+
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|
|
6
|
+
<data_source>
|
|
7
|
+
<model_class>HistoryDatasetAssociation</model_class>
|
|
8
|
+
<test test_attr="ext">ipynb</test>
|
|
9
|
+
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|
|
10
|
+
</data_sources>
|
|
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|
+
<params>
|
|
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|
+
<param required="true">dataset_id</param>
|
|
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|
+
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|
|
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|
+
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|
|
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|
+
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|
|
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|
+
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|
|
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|
+
<param name="dataset_id" value="http://cdn.jsdelivr.net/gh/galaxyproject/galaxy-test-data/1.ipynb" ftype="ipynb" />
|
|
18
|
+
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|
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|
+
</tests>
|
|
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|
+
<help format="markdown"><
|
|
44
|
+
|
|
45
|
+
---
|
|
46
|
+
|
|
47
|
+
## What is `gxy`?
|
|
48
|
+
|
|
49
|
+
The `gxy` Python module is available inside JupyterLite and provides helper functions to interact with your Galaxy history programmatically. It uses the Galaxy API in the background and supports operations like file upload, download, and metadata lookup—all within the browser.
|
|
50
|
+
|
|
51
|
+
### Examples
|
|
52
|
+
|
|
53
|
+
```python
|
|
54
|
+
# Preloaded in the kernel — no installation required
|
|
55
|
+
import gxy
|
|
56
|
+
|
|
57
|
+
# Perform arbitrary Galaxy API requests
|
|
58
|
+
await gxy.api("/api/histories", method="GET")
|
|
59
|
+
|
|
60
|
+
# Download a dataset by HID into the virtual filesystem
|
|
61
|
+
await gxy.get(3)
|
|
62
|
+
|
|
63
|
+
# Upload a local file to the associated Galaxy history (renamed to "newname.txt")
|
|
64
|
+
await gxy.put("output.txt", "newname.txt")
|
|
65
|
+
|
|
66
|
+
# List all datasets in the associated history
|
|
67
|
+
await gxy.get_history()
|
|
68
|
+
|
|
69
|
+
# Retrieve the associated history ID (auto-detected from the dataset context)
|
|
70
|
+
await gxy.get_history_id()
|
|
71
|
+
|
|
72
|
+
# Access the injected environment info (e.g., dataset ID and root URL)
|
|
73
|
+
gxy.get_environment()
|
|
74
|
+
```
|
|
75
|
+
|
|
76
|
+
This makes it easy to load, process, and save data inside Jupyter notebooks while fully integrated with Galaxy’s dataset system.
|
|
77
|
+
|
|
78
|
+
A complete reference of available functions is available at:
|
|
79
|
+
[https://www.npmjs.com/package/@galaxyproject/jupyterlite](https://www.npmjs.com/package/@galaxyproject/jupyterlite)
|
|
80
|
+
]]></help>
|
|
81
|
+
</visualization>
|
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