Jupyter.md

Instructions

We first need to open the ports. So go in your MRC Dashboard, then from the left sidebar go to network -> Security groups. I set it my Jupyter notebook to run on port 7000. Add the following rules for that port:

• TCP Ingress
• TCP Egress
• UDP Ingress
• UDP Egress

Jupyter also uses websockets so add another set of those rules (TCP Ingress/Egress and UDP Ingress/Egress) with port range 49152-65535.

After this, go to Compute -> Instances, from your instance click on the little dropdown on the right, under Actions and select "Edit Security Groups". Move all the security groups you need to the right

Generate the config file with:

$ jupyter notebook --generate-config

And then edit it with:

$ sudo nano ~/.jupyter/jupyter_notebook_config.py

Anyways once you get that working, generate a jupyter notebook config file and uncomment and change these lines:

c.NotebookApp.allow_origin = '*'
c.NotebookApp.allow_remote_access = True
c.NotebookApp.ip = '0.0.0.0'
c.NotebookApp.notebook_dir = '/var/www/external/gabry/project/' # or whatever folder you prefer
c.NotebookApp.open_browser = False
c.NotebookApp.port = 7000
#  The string should be of the form type:salt:hashed-password.
c.NotebookApp.password = u'sha1:ae1c52ce1e8a:2f010047f883c5950a76acbe8a977c057a5e49db'

It took me ages to find these lines to add in the config file, without these it does not work.

Last tip, add these lines at the end of your .bashrc. So sudo nano ~/.bashrc and then add these:

$ alias start_jupyter_notebook='sudo nohup jupyter notebook --allow-root &'
$ alias start_jupyter_lab='sudo nohup jupyter lab --allow-root --no-browser &'
$ alias sudo='sudo '

Then run this (do not sudo this one):

source ~/.bashrc

So now you can start either of them in the background by just calling one of these two So you won't need to keep the ssh open

$ start_jupyter_notebook
(or) $ start_jupyter_lab

If by any chance something is wrong and you need to restart the notebook or lab just call:

$ ps -ef | grep jupyter

Look for the PID and then just call:

$ sudo kill [PID]

Extensions

Install jupyterthemes

$ conda install -c conda-forge jupyterthemes

$ jupyter nbextension install https://rawgithub.com/minrk/ipython_extensions/master/nbextensions/gist.js

$ jupyter nbextension enable gist

$ jupyter nbextension install --user https://rawgithub.com/minrk/ipython_extensions/master/nbextensions/toc.js

$ curl -L https://rawgithub.com/minrk/ipython_extensions/master/nbextensions/toc.css > $(jupyter --data-dir)/nbextensions/toc.css

Alternatively just run this and check the folder path:

jupyter --data-dir

Download toc.ss from here and put it in: C:\Users\Gabryxx7\AppData\Roaming\jupyter\nbextensions

$ jupyter nbextension enable toc

Update to latest version

$ conda update jupyterthemes

Custom themes

Theme customised by Gabryxx7

jt -t onedork -fs 10 -altp -tfs 135 -nfs 115 -cellw 80% -T -f firacode

jt_toc.css:

/* extracted from https://gist.github.com/magican/5574556
   slightly modified for the selectors of toc-items */

#toc {
  overflow-y: auto;
  max-height: 300px;
  padding: 0px;
}

#toc ol.toc-item {
    counter-reset: item;
    list-style: none;
    padding: 0.1em;
}

#toc ol.toc-item  li {
    display: block;
}

#toc ol.toc-item li:before {
    counter-increment: item;
    content: counters(item, ".")" ";
}

#toc-wrapper {
  position: fixed;
  top: 120px;
  max-width:230px;
  left: 30px;
  border: thin solid rgba(0, 0, 0, 0.38);
  border-radius: 5px;
  padding:10px;
  background-color: #fff;
  opacity: .8;
  z-index: 100;
}

#toc-wrapper.closed {
  min-width: 100px;
  width: auto;
  transition: width;
}
#toc-wrapper:hover{
  opacity: 1;
}
#toc-wrapper .header {
  font-size: 18px;
  font-weight: bold;
}
#toc-wrapper .hide-btn {
  font-size: 14px;
  font-family: monospace;
}

#toc-wrapper .reload-btn {
  font-size: 14px;
  font-family: monospace;
}


/* don't waste so much screen space... */
#toc-wrapper .toc-item{
  padding-left: 20px;
}

#toc-wrapper .toc-item .toc-item{
  padding-left: 10px;
}