Add custom launcher

.github/workflows/test.yml

@@ -23,4 +23,9 @@ jobs:
       - name: Build the JupyterLite site
         run: |
           cp README.md content
+          cd tskit-launcher
+          jlpm install
+          jlpm run build
+          pip install .
+          cd ..
           jupyter lite build --contents content --output-dir dist

repl/jupyter-lite.json

@@ -2,9 +2,12 @@
     "jupyter-lite-schema-version": 0,
     "jupyter-config-data": {
       "disabledExtensions": [
-        "@jupyterlab/drawio-extension",
-        "jupyterlab-kernel-spy",
-        "jupyterlab-tour"
+        // "@jupyterlab/drawio-extension",
+        // "jupyterlab-kernel-spy",
+        "@jupyterlab/launcher",
+        "@jupyterlab/launcher-extension",
+        "@jupyterlab/launcher-extension:plugin"
+        "@jupyterlab/application-extension:logo"
       ]
     }
   }

repl/jupyter_lite_config.json

@@ -0,0 +1,9 @@
+{
+  "LiteBuildConfig": {
+    "contents": ["content"],
+    "output_dir": "dist"
+  },
+  "FederatedExtensionAddon": {
+    "enabled_extensions": ["tskit_custom_jupyter_launcher"]
+  }
+}

requirements.txt

@@ -7,23 +7,13 @@ notebook~=7.4.3
 # Python kernel (optional)
 jupyterlite-pyodide-kernel==0.6.1
 
-# JavaScript kernel (optional)
-jupyterlite-javascript-kernel==0.3.0
-
-# Language support (optional)
-jupyterlab-language-pack-fr-FR
-jupyterlab-language-pack-zh-CN
-
-# P5 kernel (optional)
-jupyterlite-p5-kernel==0.1.0
 
 # JupyterLab: Fasta file renderer (optional)
 jupyterlab-fasta>=3.3.0,<4
 # JupyterLab: Geojson file renderer (optional)
 jupyterlab-geojson>=3.4.0,<4
 # JupyterLab: guided tour (optional)
-# TODO: re-enable after https://github.com/jupyterlab-contrib/jupyterlab-tour/issues/82
-# jupyterlab-tour
+jupyterlab-tour
 # JupyterLab: dark theme
 jupyterlab-night
 # JupyterLab: Miami nights theme (optional)
@@ -37,9 +27,3 @@ ipyevents>=2.0.1
 ipympl>=0.8.2
 # Python: ipycanvas library for Jupyter notebooks (optional)
 ipycanvas>=0.9.1
-# Python: ipyleaflet library for Jupyter notebooks (optional)
-ipyleaflet
-
-# Python: plotting libraries (optional)
-plotly>=6,<7
-bqplot

tskit-launcher/.gitignore

@@ -0,0 +1,121 @@
+*.bundle.*
+lib/
+node_modules/
+*.log
+.eslintcache
+.stylelintcache
+*.egg-info/
+.ipynb_checkpoints
+*.tsbuildinfo
+tskit_launcher/labextension
+# Version file is handled by hatchling
+tskit_launcher/_version.py
+
+# Created by https://www.gitignore.io/api/python
+# Edit at https://www.gitignore.io/?templates=python
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage/
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# End of https://www.gitignore.io/api/python
+
+# OSX files
+.DS_Store
+
+# Yarn cache
+.yarn/

tskit-launcher/.prettierignore

@@ -0,0 +1,6 @@
+node_modules
+**/node_modules
+**/lib
+**/package.json
+!/package.json
+tskit_launcher

tskit-launcher/.yarnrc.yml

@@ -0,0 +1 @@
+nodeLinker: node-modules

tskit-launcher/README.md

@@ -0,0 +1,77 @@
+# tskit_launcher
+
+[![Github Actions Status](n/a/workflows/Build/badge.svg)](n/a/actions/workflows/build.yml)
+
+Tskit custom launcher
+
+## Requirements
+
+- JupyterLab >= 4.0.0
+
+## Install
+
+To install the extension, execute:
+
+```bash
+pip install tskit_launcher
+```
+
+## Uninstall
+
+To remove the extension, execute:
+
+```bash
+pip uninstall tskit_launcher
+```
+
+## Contributing
+
+### Development install
+
+Note: You will need NodeJS to build the extension package.
+
+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.
+
+```bash
+# Clone the repo to your local environment
+# Change directory to the tskit_launcher directory
+# Install package in development mode
+pip install -e "."
+# Link your development version of the extension with JupyterLab
+jupyter labextension develop . --overwrite
+# 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.
+
+```bash
+# 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:
+
+```bash
+jupyter lab build --minimize=False
+```
+
+### Development uninstall
+
+```bash
+pip uninstall tskit_launcher
+```
+
+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 `tskit_launcher` within that folder.
+
+### Packaging the extension
+
+See [RELEASE](RELEASE.md)

tskit-launcher/install.json

@@ -0,0 +1,5 @@
+{
+  "packageManager": "python",
+  "packageName": "tskit_launcher",
+  "uninstallInstructions": "Use your Python package manager (pip, conda, etc.) to uninstall the package tskit_launcher"
+}