xcube JupyterLab integration
Project description
xcube_jl_ext
xcube JupyterLab integration
This extension is composed of a Python package named xcube_jl_ext
for the JupyterLab server extension and a NPM package named xcube-jl-ext
for the JupyterLab frontend extension.
The extension adds the following features to JupyterLab:
- Allows running a configurable xcube Viewer as widget in the JupyterLab.
- Allows using xcube Server and Viewer from within Jupyter Notebooks, even if JupyterLab is running remotely, i.e., spawned by JupyterHub.
NOTE
This extension is still experimental and has neither been packaged nor deployed. Refer to the section Development below for dev installs.
Requirements
- JupyterLab >= 3.0
- xcube >= 0.13
Install
To install the extension, execute:
pip install xcube_jl_ext
Uninstall
To remove the extension, execute:
pip uninstall xcube_jl_ext
Troubleshoot
If you are seeing the frontend extension, but it is not working, check that the server extension is enabled:
jupyter server extension list
If the server extension is installed and enabled, but you are not seeing the frontend extension, check the frontend extension is installed:
jupyter labextension list
Development
Setup environment
Build xcube Viewer resources
from sources. Note you'll need yarn
to be installed on your system.
cd ${projects}
git clone https://github.com/dcs4cop/xcube-viewer.git
cd xcube-viewer
yarn install
yarn build
Now set environment variable XCUBE_VIEWER_PATH
to point
to the xcube Viewer build directory:
export XCUBE_VIEWER_PATH=${projects}/xcube-viewer/build
Make sure to have a source installation of xcube in a dedicated xcube Python environment.
cd ${projects}
git clone https://github.com/dcs4cop/xcube.git
cd xcube
mamba env create
Activate xcube
environment and install xcube in editable (development) mode:
conda activate xcube
pip install -ve .
Update environment with required packages for building and running the JupyterLab extension.
Note, the version of the jupyterlab
in our development environment
should match the version of the target system. We also install
jupyter-server-proxy
.
mamba install -c conda-forge -c nodefaults jupyterlab=3.4.0 jupyter-server-proxy
Also install some packaging and build tools:
mamba install -c conda-forge -c nodefaults nodejs jupyter-packaging
pip install build
Refer also to the JupyterLab Extension Tutorial for the use these tools.
Install extension from sources
Make sure, xcube
environment is active:
conda activate xcube
Clone xcube JupyterLab extension repository next to the xcube
source
folder:
cd ${projects}
git clone https://github.com/dcs4cop/xcube-jl-ext.git
cd xcube-jl-ext
Install the initial project dependencies and install the extension into the JupyterLab environment. Copy the frontend part of the extension into JupyterLab. We can run this pip install command again every time we make a change to copy the change into JupyterLab.
pip install -ve .
Create a symbolic link from JupyterLab to our source directory. This means our changes are automatically available in JupyterLab:
jupyter labextension develop --overwrite .
If successful, we can run JupyterLab and check if the extension works as expected:
jupyter lab
Build after changes
Run the following to rebuild the extension. This will be required
after any changes of package.json
or changes of frontend TypeScript
files and other resources.
jlpm run build
If you wish to avoid building after each change, you can run the
jlpm run watch
from your extension directory in another terminal. This will automatically compile the TypeScript files as they are changed and saved.
Contributing
Development install
Note: You will need NodeJS to build the extension package.
The jlpm
command is JupyterLab's pinned version of
yarn that is installed with JupyterLab. You may use
yarn
or npm
in lieu of jlpm
below.
# Clone the repo to your local environment
# Change directory to the xcube_jl_ext directory
# Install package in development mode
pip install -e ".[test]"
# Link your development version of the extension with JupyterLab
jupyter labextension develop . --overwrite
# Server extension must be manually installed in develop mode
jupyter server extension enable xcube_jl_ext
# Rebuild extension Typescript source after making changes
jlpm build
You can watch the source directory and run JupyterLab at the same time in different terminals to watch for changes in the extension's source and automatically rebuild the extension.
# Watch the source directory in one terminal, automatically rebuilding when needed
jlpm watch
# Run JupyterLab in another terminal
jupyter lab
With the watch command running, every saved change will immediately be built locally and available in your running JupyterLab. Refresh JupyterLab to load the change in your browser (you may need to wait several seconds for the extension to be rebuilt).
By default, the jlpm build
command generates the source maps for this extension to make it easier to debug using the browser dev tools. To also generate source maps for the JupyterLab core extensions, you can run the following command:
jupyter lab build --minimize=False
Development uninstall
# Server extension must be manually disabled in develop mode
jupyter server extension disable xcube_jl_ext
pip uninstall xcube_jl_ext
In development mode, you will also need to remove the symlink created by jupyter labextension develop
command. To find its location, you can run jupyter labextension list
to figure out where the labextensions
folder is located. Then you can remove the symlink named xcube-jl-ext
within that folder.
Testing the extension
Server tests
This extension is using Pytest for Python code testing.
Install test dependencies (needed only once):
pip install -e ".[test]"
# Each time you install the Python package, you need to restore the front-end extension link
jupyter labextension develop . --overwrite
To execute them, run:
pytest -vv -r ap --cov xcube_jl_ext
Frontend tests
This extension is using Jest for JavaScript code testing.
To execute them, execute:
jlpm
jlpm test
Integration tests
This extension uses Playwright for the integration tests (aka user level tests). More precisely, the JupyterLab helper Galata is used to handle testing the extension in JupyterLab.
More information are provided within the ui-tests README.
Packaging the extension
See RELEASE
Project details
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