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%% Cell type:markdown id: tags:
# List of Extensions on Jupyter@JSC
# List of Extensions on Jupyter-JSC
-----------------------------------
%% Cell type:markdown id: tags:
If you want to use any of these extensions, feel free to use our [examples](https://github.com/kreuzert/Jupyter-JSC) as a starting point.
If you want to use any of these extensions, feel free to use our [examples](https://github.com/FZJ-JSC/jupyter-jsc-notebooks) as a starting point.
%% Cell type:markdown id: tags:
## AppMode (Classic Notebook only)
## Dask (only on HPC Systems) <a class="anchor" id="dask"></a>
https://github.com/dask/dask-labextension
%% Cell type:markdown id: tags:
[AppMode](https://github.com/oschuett/appmode) is a Jupyter extension that turns notebooks into web applications.
To use it click on the menu on "Help" -> "Launch Classic Notebook".
<div>
<img src=https://raw.githubusercontent.com/dask/dask-labextension/master/dask.png width="640" style="float:right"/>
</div>
An [extension](https://github.com/dask/dask-labextension) to manage Dask clusters, as well as embed Dask's dashboard plots directly into JupyterLab panes.
Watch [this](https://www.youtube.com/watch?feature=player_embedded&v=EX_voquHdk0) video until the end to unterstand how to use Dask in JupyterLab. At the moment we only offer to use the panels inside of JupyterLab.
We have introduction notebooks for this extensions [here](https://gitlab.version.fz-juelich.de/jupyter4jsc/j4j_notebooks/tree/master/001-Extensions) (or open the gitlab extension on the left sidebar).
%% Cell type:markdown id: tags:
![AppMode](https://raw.githubusercontent.com/oschuett/appmode/master/screenshots.png "AppMode")
## Git
https://github.com/jupyterlab/jupyterlab-git
%% Cell type:markdown id: tags:
## Celltags
<div>
<img src=https://raw.githubusercontent.com/jupyterlab/jupyterlab-git/master/docs/figs/demo-0-10-0.gif width="640" style="float:right"/>
</div>
A JupyterLab [Git](https://github.com/jupyterlab/jupyterlab-git) extension for version control using git.
%% Cell type:markdown id: tags:
The JupyterLab [cell tags](https://github.com/jupyterlab/jupyterlab-celltags) extension enables users to easily add, view, and manipulate descriptive tags for notebook cells.
The extension includes the functionality to select all cells with a given tag, supporting the performance of any operation on those cells.
Click on the wrench Symbol on the left sidebar to use it.
## Table of Contents
https://github.com/jupyterlab/jupyterlab-toc
%% Cell type:markdown id: tags:
![CellTags](https://camo.githubusercontent.com/ef150fb7721d76e00d95225293662a22504d18ed/687474703a2f2f672e7265636f726469742e636f2f4d78774e365561465a6a2e676966 "CellTags")
<div>
<img src=https://raw.githubusercontent.com/jupyterlab/jupyterlab-toc/master/toc.gif width="640" style="float:right"/>
</div>
A [Table of Contents extension](https://github.com/jupyterlab/jupyterlab-toc) for JupyterLab. This auto-generates a table of contents in the left area when you have a notebook or markdown document open.
The entries are clickable, and scroll the document to the heading in question.
%% Cell type:markdown id: tags:
## Codefolding (Classic Notebook only)
## Jupyter ThreeJS
https://github.com/jupyter-widgets/pythreejs
%% Cell type:markdown id: tags:
[CodeFolding](https://github.com/ipython-contrib/jupyter_contrib_nbextensions/tree/master/src/jupyter_contrib_nbextensions/nbextensions/codefolding) adds codefolding functionality from CodeMirror to a codecell.
To use it click on the menu on "Help" -> "Launch Classic Notebook".
<div>
<img src=https://raw.githubusercontent.com/jupyter-widgets/pythreejs/master/screencast.gif width="640" style="float:right"/>
</div>
A Python / [ThreeJS](https://github.com/jupyter-widgets/pythreejs) bridge utilizing the Jupyter widget infrastructure.
%% Cell type:markdown id: tags:
![CodeFolding](https://raw.githubusercontent.com/ipython-contrib/jupyter_contrib_nbextensions/master/src/jupyter_contrib_nbextensions/nbextensions/codefolding/codefolding_indent_unfolded.png "codefolding")
## Leaflet
https://github.com/jupyter-widgets/ipyleaflet
%% Cell type:markdown id: tags:
## Code Formatter
<div>
<img src=https://raw.githubusercontent.com/jupyter-widgets/ipyleaflet/master/basemap.gif width="640" style="float:right"/>
</div>
The [Jupyterlab Leaflet extension](https://github.com/jupyter-widgets/ipyleaflet) enables interactive maps.
You can find several example notebooks [here](https://github.com/jupyter-widgets/ipyleaflet/tree/master/examples).
%% Cell type:markdown id: tags:
[Code Formatter](https://github.com/ryantam626/jupyterlab_code_formatter) allows you to format a Notebook for.
You can use it as shown below or you click on "Format notebook" at the top of your notebook.
## Sidecar
https://github.com/jupyter-widgets/jupyterlab-sidecar
%% Cell type:markdown id: tags:
![CodeFormatter](https://raw.githubusercontent.com/ryantam626/jupyterlab_code_formatter/master/code-formatter-demo.gif "CodeFormatter")
<div>
<img src=https://raw.githubusercontent.com/jupyter-widgets/jupyterlab-sidecar/master/sidecar.gif width="640" style="float:right"/>
</div>
A [sidecar](https://github.com/jupyter-widgets/jupyterlab-sidecar) output widget for JupyterLab
%% Cell type:markdown id: tags:
## Dask (only on HPC Systems)
## Voilà Preview
https://github.com/voila-dashboards/voila
%% Cell type:markdown id: tags:
An [extension](https://github.com/dask/dask-labextension) to manage Dask clusters, as well as embed Dask's dashboard plots directly into JupyterLab panes.
Watch [this](https://www.youtube.com/watch?feature=player_embedded&v=EX_voquHdk0) video until the end to unterstand how to use Dask in JupyterLab. At the moment we only offer to use the panels inside of JupyterLab.
We have introduction notebooks for this extensions [here](https://gitlab.version.fz-juelich.de/jupyter4jsc/j4j_notebooks/tree/master/001-Extensions) (or open the gitlab extension on the left sidebar).
<div>
<img src=https://jupyter-jsc.fz-juelich.de/hub/static/images/voila_preview.png width="640" style="float:right"/>
</div>
[Voilà](https://github.com/voila-dashboards/voila) turns Jupyter notebooks into standalone web applications.
Unlike the usual HTML-converted notebooks, each user connecting to the Voilà tornado application gets a dedicated Jupyter kernel which can execute the callbacks to changes in Jupyter interactive widgets.
This extension allows you to render a Notebook with Voilà, so you can see how your Notebook will look with it.
You can download a test notebook with the following command:
```
$ wget --no-check-certificate https://jupyter-jsc.fz-juelich.de/static/files/voila_basics.ipynb
```
and get a preview of it with the button at the top of your notebook.
%% Cell type:markdown id: tags:
## Drawio
## Quick Open
https://github.com/parente/jupyterlab-quickopen
%% Cell type:markdown id: tags:
[Drawio](https://github.com/QuantStack/jupyterlab-drawio) is a JupyterLab extension for standalone integration of drawio / mxgraph into jupyterlab.
<div>
<img src=https://raw.githubusercontent.com/parente/jupyterlab-quickopen/master/doc/quickopen.gif width="640" style="float:right"/>
</div>
[Quick Open](https://github.com/parente/jupyterlab-quickopen) allows you to quickly open a file in JupyterLab by typing part of its name. Just click on the lens symbol at the left sidebar.
<span style="color:darkorange">Takes a long time on HPC systems.</span>
%% Cell type:markdown id: tags:
<p style="color:red">There is a known save-bug in this extension. Please use the menu of JupyterLab to save files from this extension.</p>
## JupyterLab LaTeX Extension
https://github.com/jupyterlab/jupyterlab-latex
%% Cell type:markdown id: tags:
![Drawio](https://raw.githubusercontent.com/QuantStack/jupyterlab-drawio/master/drawio.gif "drawio")
The [LaTeX Extension](https://github.com/jupyterlab/jupyterlab-latex) is an extension for JupyterLab which allows for live-editing of LaTeX documents.
[Here](https://annefou.github.io/jupyter_publish/03-latex/index.html) you can find a short example.
%% Cell type:markdown id: tags:
## Git
## Code Formatter
https://github.com/ryantam626/jupyterlab_code_formatter
%% Cell type:markdown id: tags:
A JupyterLab [Git](https://github.com/jupyterlab/jupyterlab-git) extension for version control using git.
<div>
<img src=https://jupyterlab-code-formatter.readthedocs.io/en/latest/_images/demo.gif width="640" style="float:right"/>
</div>
.....
%% Cell type:markdown id: tags:
<div>
<img src=https://raw.githubusercontent.com/parente/jupyterlab-quickopen/master/doc/quickopen.gif width="640" style="float:right"/>
</div>
%% Cell type:code id: tags:
``` python
```
%% Cell type:code id: tags:
``` python
```
%% Cell type:markdown id: tags:
This is a small Jupyterlab plugin to support using various code formatter on the server side and format code cells/files in Jupyterlab.
%% Cell type:code id: tags:
``` python
```
%% Cell type:code id: tags:
``` python
```
%% Cell type:markdown id: tags:
![Git](https://camo.githubusercontent.com/8e2f2b6abdaff6b180bf6aee95b288a7af0fde4d/687474703a2f2f672e7265636f726469742e636f2f4e39496b7a62796b38502e676966 "Git")
<div>
<img src=https://jupyterlab-code-formatter.readthedocs.io/en/latest/_images/demo.gif width="640" style="float:right"/>
</div>
%% Cell type:code id: tags:
``` python
<div>
<img src=https://jupyterlab-code-formatter.readthedocs.io/en/latest/_images/demo.gif width="640" style="float:right"/>
</div>
```
%% Cell type:markdown id: tags:
## Ipydatawidgets
%% Cell type:markdown id: tags:
[Ipydatawidgets](https://github.com/vidartf/ipydatawidgets) is a set of widgets to help facilitate reuse of large datasets across different widgets, and different packages.
%% Cell type:code id: tags:
``` python
import numpy as np
from ipydatawidgets import DataImage
np.random.seed(0)
data = np.array(255 * np.random.rand(200, 200, 4), dtype='uint8')
DataImage(data=data)
```
%% Cell type:code id: tags:
``` python
SIDELEN = 300
grad = np.linspace(0, 255, SIDELEN, dtype='uint8')
# red and green components:
rg = np.dstack(np.meshgrid(grad, grad))
# add blue and alpha components (zero and 255):
rgba = np.dstack([
rg,
np.zeros((SIDELEN, SIDELEN), dtype='uint8'),
255 * np.ones((SIDELEN, SIDELEN), dtype='uint8')
])
DataImage(data=rgba)
```
%% Cell type:markdown id: tags:
## IPyVolume
%% Cell type:markdown id: tags:
[IPyvolume](https://buildmedia.readthedocs.org/media/pdf/ipyvolume/latest/ipyvolume.pdf) is a Python library to visualize 3d volumes and glyphs.
%% Cell type:code id: tags:
``` python
import numpy as np
import ipyvolume as ipv
V = np.zeros((128,128,128))# our 3d array
# outer box
V[30:-30,30:-30,30:-30] = 0.75
V[35:-35,35:-35,35:-35] = 0.0
# inner box
V[50:-50,50:-50,50:-50] = 0.25
V[55:-55,55:-55,55:-55] = 0.0
ipv.quickvolshow(V, level=[0.25, 0.75], opacity=0.03, level_width=0.1, data_min=0, data_max=1)
```
%% Cell type:markdown id: tags:
## JupyterLab LaTeX Extension
%% Cell type:markdown id: tags:
The [LaTeX Extension](https://github.com/jupyterlab/jupyterlab-latex) is an extension for JupyterLab which allows for live-editing of LaTeX documents.
[Here](https://annefou.github.io/jupyter_publish/03-latex/index.html) you can find a short example.
%% Cell type:markdown id: tags:
## JupyterLab LMod
%% Cell type:markdown id: tags:
[An extension](https://github.com/cmd-ntrf/jupyter-lmod) that allows user to interact with environment modules before launching kernels.
To check the Pythonpath/PATH of your current kernel just run the following command. Remember to restart the kernel after loading other modules.
%% Cell type:code id: tags:
``` python
!echo $PATH # or !echo $PYTHONPATH
```
%% Cell type:markdown id: tags:
!["Lmod"](https://camo.githubusercontent.com/2a1fa198b6b7f35c7b9751664dfe5102fa5aa595/68747470733a2f2f692e696d6775722e636f6d2f3148444837694e2e676966 "lmod")
%% Cell type:markdown id: tags:
## JupyterLab Table of Contents
%% Cell type:markdown id: tags:
A [Table of Contents extension](https://github.com/jupyterlab/jupyterlab-toc) for JupyterLab. This auto-generates a table of contents in the left area when you have a notebook or markdown document open.
The entries are clickable, and scroll the document to the heading in question.
%% Cell type:markdown id: tags:
![ToC](https://raw.githubusercontent.com/jupyterlab/jupyterlab-toc/master/toc.gif "ToC")
%% Cell type:markdown id: tags:
## Jupyter ThreeJS
%% Cell type:markdown id: tags:
A Python / [ThreeJS](https://github.com/jupyter-widgets/pythreejs) bridge utilizing the Jupyter widget infrastructure.
%% Cell type:markdown id: tags:
![ThreeJS](https://raw.githubusercontent.com/jupyter-widgets/pythreejs/master/screencast.gif "ThreeJS")
%% Cell type:markdown id: tags:
## Leaflet
%% Cell type:markdown id: tags:
The [Jupyterlab Leaflet extension](https://github.com/jupyter-widgets/ipyleaflet) enables interactive maps.
You can find several example notebooks [here](https://github.com/jupyter-widgets/ipyleaflet/tree/master/examples).
%% Cell type:markdown id: tags:
![Leaflet](https://raw.githubusercontent.com/jupyter-widgets/ipyleaflet/master/basemap.gif "leaflet")
%% Cell type:markdown id: tags:
## MatplotLib
%% Cell type:markdown id: tags:
[MatplotLib](https://www.github.com/matplotlib/jupyter-matplotlib) enables the interactive features of matplotlib in Jupyterlab.
Besides, the figure canvas element is a proper Jupyter interactive widget which can be positioned in interactive widget layouts.
%% Cell type:code id: tags:
``` python
# Enable the matplotlib widget
%matplotlib widget
```
%% Cell type:code id: tags:
``` python
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import axes3d
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# Grab some test data.
X, Y, Z = axes3d.get_test_data(0.05)
# Plot a basic wireframe.
ax.plot_wireframe(X, Y, Z, rstride=10, cstride=10)
fig.canvas.layout.max_width = '800px'
plt.show()
```
%% Cell type:code id: tags:
``` python
# When using the `widget` backend from ipympl,
# fig.canvas is a proper Jupyter interactive widget, which can be embedded in
# Layout classes like HBox and Vbox.
# One can bound figure attributes to other widget values.
import numpy as np
from ipywidgets import HBox, FloatSlider
plt.ioff()
plt.clf()
slider = FloatSlider(
orientation='vertical',
value=1.0,
min=0.02,
max=2.0
)
fig = plt.figure(3)
x = np.linspace(0, 20, 500)
lines = plt.plot(x, np.sin(slider.value * x))
def update_lines(change):
lines[0].set_data(x, np.sin(change.new * x))
fig.canvas.draw()
fig.canvas.flush_events()
slider.observe(update_lines, names='value')
HBox([slider, fig.canvas])
```
%% Cell type:markdown id: tags:
## NBDime
%% Cell type:markdown id: tags:
[NBDime](https://github.com/jupyter/nbdime) provides tools for diffing and merging of Jupyter Notebooks.
%% Cell type:markdown id: tags:
## NBExtensions Configurator (Classic Notebook only)
%% Cell type:markdown id: tags:
A server extension for jupyter notebook which provides configuration interfaces for notebook extensions (nbextensions).
Works only with the classic notebook, not with JupyterLab.
To use it click on the menu on "Help" -> "Launch Classic Notebook".
%% Cell type:markdown id: tags:
!["NBExtensions"](https://raw.githubusercontent.com/Jupyter-contrib/jupyter_nbextensions_configurator/master/src/jupyter_nbextensions_configurator/static/nbextensions_configurator/icon.png "nbextensions")
%% Cell type:markdown id: tags:
## Plotly
%% Cell type:markdown id: tags:
A JupyterLab [extension](https://github.com/plotly/plotly.py) for [plotly](https://plot.ly/)
%% Cell type:code id: tags:
``` python
import plotly
from plotly.offline import init_notebook_mode, iplot
init_notebook_mode(connected=True)
trace0 = plotly.graph_objs.Scatter(
x=[1, 2, 3, 4],
y=[10, 15, 13, 17]
)
trace1 = plotly.graph_objs.Scatter(
x=[1, 2, 3, 4],
y=[16, 5, 11, 9]
)
iplot([trace0, trace1])
```
%% Cell type:markdown id: tags:
## Quick Open
----------------
%% Cell type:markdown id: tags:
[Quick Open](https://github.com/parente/jupyterlab-quickopen) allows you to quickly open a file in JupyterLab by typing part of its name. Just click on the lens symbol at the left sidebar.
<span style="color:darkorange">Takes a long time on HPC systems.</span>
--------------
%% Cell type:markdown id: tags:
![QuickOpen](https://raw.githubusercontent.com/parente/jupyterlab-quickopen/master/doc/quickopen.gif "quickopen")
## AppMode (Classic Notebook only)
%% Cell type:markdown id: tags:
## RISE (Classic Notebook only)
<div>
<img src=https://raw.githubusercontent.com/oschuett/appmode/master/screenshots.png width="640" style="float:right"/>
</div>
[AppMode](https://github.com/oschuett/appmode) is a Jupyter extension that turns notebooks into web applications.
To use it click on the menu on "Help" -> "Launch Classic Notebook".
%% Cell type:markdown id: tags:
With [RISE](https://rise.readthedocs.io/en/latest), a Jupyter notebook extension, you can instantly turn your jupyter notebook into a live reveal.js-based presentation.
## Celltags
%% Cell type:markdown id: tags:
<div>
<img src=https://camo.githubusercontent.com/ef150fb7721d76e00d95225293662a22504d18ed/687474703a2f2f672e7265636f726469742e636f2f4d78774e365561465a6a2e676966 width="640" style="float:right"/>
</div>
The JupyterLab [cell tags](https://github.com/jupyterlab/jupyterlab-celltags) extension enables users to easily add, view, and manipulate descriptive tags for notebook cells.
The extension includes the functionality to select all cells with a given tag, supporting the performance of any operation on those cells.
Click on the wrench Symbol on the left sidebar to use it.
%% Cell type:markdown id: tags:
## Codefolding (Classic Notebook only)
%% Cell type:markdown id: tags:
<div>
<img src=https://raw.githubusercontent.com/ipython-contrib/jupyter_contrib_nbextensions/master/src/jupyter_contrib_nbextensions/nbextensions/codefolding/codefolding_indent_unfolded.png width="640" style="float:right"/>
</div>
[CodeFolding](https://github.com/ipython-contrib/jupyter_contrib_nbextensions/tree/master/src/jupyter_contrib_nbextensions/nbextensions/codefolding) adds codefolding functionality from CodeMirror to a codecell.
To use it click on the menu on "Help" -> "Launch Classic Notebook".
%% Cell type:markdown id: tags:
![RISE](https://rise.readthedocs.io/en/latest/_images/basic_usage.gif "rise")
[Code Formatter](https://github.com/ryantam626/jupyterlab_code_formatter) allows you to format a Notebook for.
You can use it as shown below or you click on "Format notebook" at the top of your notebook.
%% Cell type:markdown id: tags:
## Sidecar
![CodeFormatter](https://raw.githubusercontent.com/ryantam626/jupyterlab_code_formatter/master/code-formatter-demo.gif "CodeFormatter")
%% Cell type:markdown id: tags:
A [sidecar](https://github.com/jupyter-widgets/jupyterlab-sidecar) output widget for JupyterLab
## Drawio
%% Cell type:markdown id: tags:
![Sidecar](https://raw.githubusercontent.com/jupyter-widgets/jupyterlab-sidecar/master/sidecar.gif "Sidecar")
<div>
<img src=https://raw.githubusercontent.com/QuantStack/jupyterlab-drawio/master/drawio.gif width="640" style="float:right"/>
</div>
[Drawio](https://github.com/QuantStack/jupyterlab-drawio) is a JupyterLab extension for standalone integration of drawio / mxgraph into jupyterlab.
%% Cell type:markdown id: tags:
## Voilà Preview
<p style="color:red">There is a known save-bug in this extension. Please use the menu of JupyterLab to save files from this extension.</p>
%% Cell type:markdown id: tags:
[Voilà](https://github.com/voila-dashboards/voila) turns Jupyter notebooks into standalone web applications.
## NBExtensions Configurator (Classic Notebook only)
Unlike the usual HTML-converted notebooks, each user connecting to the Voilà tornado application gets a dedicated Jupyter kernel which can execute the callbacks to changes in Jupyter interactive widgets.
%% Cell type:markdown id: tags:
This extension allows you to render a Notebook with Voilà, so you can see how your Notebook will look with it.
<div>
<img src=https://raw.githubusercontent.com/Jupyter-contrib/jupyter_nbextensions_configurator/master/src/jupyter_nbextensions_configurator/static/nbextensions_configurator/icon.png width="640" style="float:right"/>
</div>
You can download a test notebook with the following command:
```
$ wget --no-check-certificate https://jupyter-jsc.fz-juelich.de/static/files/voila_basics.ipynb
```
and get a preview of it with the button at the top of your notebook.
A server extension for jupyter notebook which provides configuration interfaces for notebook extensions (nbextensions).
Works only with the classic notebook, not with JupyterLab.
To use it click on the menu on "Help" -> "Launch Classic Notebook".
%% Cell type:markdown id: tags:
!["VoilaPreview"](https://jupyter-jsc.fz-juelich.de/hub/static/images/voila_preview.png "Voila Preview")
## RISE (Classic Notebook only)
%% Cell type:markdown id: tags:
## WebRTC
<div>
<img src=https://rise.readthedocs.io/en/latest/_images/basic_usage.gif width="640" style="float:right"/>
</div>
With [RISE](https://rise.readthedocs.io/en/latest), a Jupyter notebook extension, you can instantly turn your jupyter notebook into a live reveal.js-based presentation.
To use it click on the menu on "Help" -> "Launch Classic Notebook".
%% Cell type:markdown id: tags:
[WebRTC](https://github.com/maartenbreddels/ipywebrtc) allows you to stream video files into Jupyter Notebooks.
## WebRTC
%% Cell type:markdown id: tags:
![WebRTC](https://user-images.githubusercontent.com/1765949/43977008-03dbfac0-9ce3-11e8-9bb9-4a5f8f2cc79a.gif "WebRTC")
<div>
<img src=https://user-images.githubusercontent.com/1765949/43977008-03dbfac0-9ce3-11e8-9bb9-4a5f8f2cc79a.gif width="640" style="float:right"/>
</div>
[WebRTC](https://github.com/maartenbreddels/ipywebrtc) allows you to stream video files into Jupyter Notebooks.
......
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