G-β - Python & Jupyter

How to install packages from the Jupyter Notebook safely

  • pip installs in any environment
  • conda installs conda environments
  • the shell environment and the Python executables are disconnected
  • Anaconda pre-install assumed below.
 
import sys
!conda install --yes --prefix {sys.prefix} <package>

See further discussion here.

How to enable Python debugger capabilities in Jupyter

  • Install the kernel xeus-python (new conda env or base env)
  • (It works fine with new fresh conda-env create/activate workflow)
  • Install debugger extension
 
conda install xeus-python notebook -c conda-forge
jupyter labextension install @jupyterlab/debugger

See further discussion here and here.

Learning resources

Journals

  • Journal of Open Source Software
    • Journal that is bursting on open source, counting with renowned people involved with machine learning, data science, and torrents of projects using Jupyter NBs.

Autograding

  • Autograding tools for testing Jupyter or making assignments easier to handle
    • nbgrader by Jupyter team.
    • autograde
    • Otter-Grader @Berkeley
    • Interesting report talking about graders and the alternative Web Cat.
    • Security failure in nbgrader is alleged and a solution is proposed by the Finnish SciComp group Aalto here.
    • This video shows nicely how to use grader with Github Classroom and accompanies this handout.

Lecturing with RISE

  • Notes on RISE Slideshow troubleshooting:
    • RISE stopped working correctly on Safari with Big Sur 11.2.3 suddenly.
    • Go to fix…
    • With version 5.7.1, I had an issue with
 
	pkg_resources.ContextualVersionConflict: 
	(jedi 0.15.2 ... Requirement.parse('jedi>=0.16'), {'ipython'})
  • With conda update jedi; conda list jedi, the version was not being upgraded to 0.18 (available on PyPi);
  • Worked only with conda update -c conda-forge jedi=0.17.2 after a long wait on “frozen/flexible solve… solving environment…”;
  • Then, launching Jupyter on Safari, the Cell Toolbar > Slideshow could be visible, but the button to launch RISE Slideshow was not showing up.
    • Current solution: use Chrome (see info in this page on how to set browser on Jupyter config file).
    • Persisting, try jupyter-nbextension install rise --py --sys-prefix and button should (luckly) appear!
  • How to customize RISE’s chalkboard and themes
    • List of available themes here.
    • From version 5.7.1, colors are customizable for chalkboard.
    • Options can be found in the reveal.js-plugins/chalkboard README
    • Here is an example on how to change chalkboard options:
 
"rise": {
  "chalkboard": {
      "boardmarkerWidth": 3,      
      "grid": {
        "color": "rgb(50,50,10,0.5)",
        "distance": 80,
        "width": 2
      }
    },
 }

How to edit the font color of a postscripted PDF

  • I will report a pathway although I have not gotten to a final solution yet:
  • Stefano Chizzolini, PDFClown’s developer proposed a code in this post. At the current version, however, PDFClown possibly has embedded all those isolated Java elements.
  • The idea would be try to follow SC’s approach.
  • Secondly, PyPDF2 might be a Python alternative. There is a tutorial here, but font color changes seems to be a hard stuff.
    • Why I wanted that? Modify color of latexized PDF text from black to CMY-balanced (after K=0) color to fill out CMY printer cartridges.
    • Let us leave that for future…

Python ‘gotchas’

Encoding/decoding characters

  • To print symbols for musical notes it is necessary to have a font in the computer capable to represent the Unicode. See here.
  • The Unicode table for music is here.
  • So, to print the G clef, we’d use print('\U0001D120'), with Unicode \U escape. Seemingly, there are few font types that handle music symbols. One available is Bravura.

Set browser for Jupyter Notebook or Jupyter-Lab

  • To choose a different browser from the computer’s default where to run Jupyter-Lab, run jupyter server --generate-config (or jupyter-notebook --generate-config) and edit the option c.ServerApp.browser in $HOME/.jupyter/jupyter_server_config.py
 
 #  Default: ''
import webbrowser
c.ServerApp.browser = u'/Applications/Google\ Chrome.app/Contents/MacOS/Google\ Chrome %s'
  • The module webbrowser allows us to choose among many known browsers. See table here.
  • For further detail, see this discussion.

PDF parsing end editing

  • pdfminer.six. Install with pip install pdfminer.six and run with pdf2txt.py file.pdf (install adds to PATH).
  • PyPDF2: good option.
  • WeasyPrint: conversion from HTML/CSS to PDF.
  • ReportLab
  • pyFPDF: ported from PHP.
  • Pyppeteer: JavaScript chrome/chromium browser automation library.
  • PDFKit: Javascript for Node and browser.

DataViz Tools

CSV to MD conversion

 
from mdtable import MDTable 
MDTable('input.csv').save_table('output.csv')