Python/Jupyter

Magic Functions

Timing

• %timeit (time line)
• %%timeit (time block in lines below, same line = not timed setup)

importing other jupyter notebook

• run.ipynb:

% run 'lib_testprog.ipynb'
testfunct()

• lib_testprog.ipynb:

def testfunct()
    return 1

if __name__ == '__main__' and '__file__' not in globals():
    print(testfunct())

sharing variables between notebooks

• test1.ipynb:

variable = 'testdata'
%store variable

• test2.ipynb:

%store -r variable
print(variable)

• hints:
  • use "global" in functions

Autorun notebooks on startup

simple, but no start/stop control later

• /home/user/.ipython/profile_default/startup/startup.ipy

#!/usr/bin/ipython

%run /srv/python/script_a.ipynb

complex, with full control

• /home/user/.ipython/profile_default/startup/startup.ipy

#!/usr/bin/ipython

%run /srv/python/startup.ipynb

• /srv/python/startup.ipynb

from selenium import webdriver  
from selenium.webdriver.common.by import By

urls = ["http://192.168.111.11:8888/notebooks/projects/test.ipynb"]

def start_notebook(url):
    browser = webdriver.PhantomJS(service_args=['--ssl-protocol=any'])  
    browser.set_window_size(1280, 1400)
    browser.implicitly_wait(10)  
    browser.get(url) 
    
    browser.find_element(By.LINK_TEXT, 'Cell').click()
    browser.find_element(By.LINK_TEXT, 'Run All').click()
    browser.quit()

for url in urls:
    print ("starting: " + url)
    start_notebook(url)

Initial Setup

Installation

apt install python3-pip python3-setuptools
pip3 install --upgrade pip
pip3 install jupyter

Config

• full width:
  • ~/.jupyter/custom/custom.css

.container { width:100% !important; }

• autostart from rc.local

sudo -u pi /usr/local/bin/jupyter-notebook --config=/home/pi/.jupyter/jupyter_notebook_config.py

• create config file

jupyter notebook --generate-config

• insecure access without token/password (/home/pi/.jupyter/jupyter_notebook_config.py)

c.NotebookApp.ip = '*'
c.NotebookApp.notebook_dir = '/srv/Python'
c.NotebookApp.open_browser = False
c.NotebookApp.password = ''
c.NotebookApp.token = ''

nbextensions

pip3 install jupyter_contrib_nbextensions
jupyter contrib nbextension install --user

• codefolding
• Codefolding in editor
• Collapsible Headings
• Table of contents
• Variable inspector
• Toggle all line numbers

Other Kernels

• scijava-jupyter-kernel
  • https://github.com/scijava/scijava-jupyter-kernel

Links

• https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/
• https://github.com/jupyter/jupyter/wiki/a-gallery-of-interesting-jupyter-notebooks
• https://stackoverflow.com/questions/26126853/verifying-pep8-in-ipython-notebook-code
• https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/