Lecture NotesIPython Notebook

Topics

• IPython notebook
• NBviewer
• Markdown
• LateX
• nbconvert (notebook to slides, html,pdf)
• Handy Linux/Unix Stuff
• Assignment

IPython notebook

• Absolute basics

Example notebook

Material

• Learning IPython Chapters 1 and 2
  • Download all code/notebooks used in Learning Ipython here
• Notebook documentation
• Introduction video by Jake vanderPlas Jake Vanderplas - Python in the Browser Age: Data Exploration in the IPython Notebook, OpenVis Conference 2014.
• Display all kind of things in IPython notebooks
  • images, html, youtube video, latex math, HTML, frames, you name it

NBviewer

• You can nicely view those notebooks at http://nbviewer.jupyter.org/
• Use the icons in the right upper corner:
  • present/book: switch to slides and back (if notebook is a slideshow)
  • download the raw notebook
• You cannot run the notebook!
  • If you want that, download it, and open it from IPython notebook

Markdown

• MarkDown is the language in which readme's, comments, issues and the wiki in the version control systems git and bitbucket are written.
• MarkDown is also the language for comments inside notebooks.
• Markdown web viewer
  • Easy place to learn the syntax and try things out.
• Markdown
  • Great link for intro, philosophy, background, but most of all: syntax guide
• Mou
  • Great MarkDown editor. Ideal to learn markdown. You never use Word anymore.
• Markdown cheatsheet
• How to use markdown for writing articles/theses

LateX

• LateX is used in notebooks to create good looking math and other high level typesetting.
• LateX is the choice for writing a thesis or scientific paper, _well, if MarkDown is not sufficient for you.....
• LateX is ideal for
  • bibliography
    • Using Latex bibs in Markdown
  • changing look and feel of your thesis (two column, like a book, like a paper, etc)
• There are many editors available
  • TexMaker works on all platforms and seems to work well.
  • But note that unless you want to write your thesis or your reports in LateX there is no need to install this editor
• Latex on Dutch Wikipedia
• Math symbols cheat sheet
• In order to generate PDF's from your notebooks (maybe to print them....), you use LateX, and then you need to have pdflatex installed.

nbconvert

• Basic usage of nbconvert is explained here: http://ipython.org/ipython-doc/1/interactive/nbconvert.html

Conversion to slides

• Slides based on notebooks are easy to make and there are really cool options and possibilities.
• There is a 'Cell Toolbar' option 'Slideshow'. This allows you to edit each cell as either a new slide, or something that is revealed after a click, and other options.
• This is added to the metadata for the notebook, and doesn't change the way the notebooks look in anyway.
• After annotating the cells, there is two ways to create the slideshow. See Making slides
• Tutorial and example: http://www.damian.oquanta.info/posts/make-your-slides-with-ipython.html

Making slides

Method 1

• Save SetTheory.ipynb somewhere on the web: http://maartenmarx.nl/pub/SetTheory.ipynb
• Old school: Run it at http://slideviewer.herokuapp.com/url/maartenmarx.nl/pub/SetTheory.ipynb
• Run it at http://nbviewer.ipython.org/url/maartenmarx.nl/pub/SetTheory.ipynb and press the icon which looks like a present. You will be brought to http://nbviewer.ipython.org/format/slides/url/maartenmarx.nl/pub/SetTheory.ipynb#/

Method 2

• Run the command ipython nbconvert SetTheory.ipynb --to slides --reveal-prefix "http://maartenmarx.nl/reveal.js" from the terminal
• Make sure Pandoc is installed
• Make sure the https://github.com/hakimel/reveal.js/downloads reveal.js directory is installed at the right place (here thus "http://maartenmarx.nl/reveal.js" )
• if you add --post serve as an option the result is shown in the browser, as a slideshow!
  • You can't run the code though!

Note

• Latex only works well from Ipython 2.3

Handy Linux/Unix Stuff

These things are handy when you have a mac and use the command line. Or of course when you use a linux terminal.

• Remote Login on another machine without typing your password
• Syncing files to a remote machine Handy for making backups, or for working locally on files stored on a fileserver.
  • Eg, all these teaching files are stored on a webserver, but I edit them locally on my laptop. The only thing is not to forget to rsync them....

Assignment

Make this assignment to get really comfortable with all aspects of the notebook. Really, you will become so happy when you get fluent in it.

Note book Assignment

Abstract

You will create a complete lesson about a theoretical Information Science topic. You will create a notebook, use LateX for formulas, use bibliographic references, use inline pictures, use inline iframes, have small pieces of code, etc.

You will also create slides and a HTML version from your notebook.

Finally you make a set of exercises in a notebook, together with model answers.

Goals

• Learn how to use and integrate all techniques we learned this week.
• Having a template/workflow for more complex tasks.

The topic

The topic of the lesson is Sets), in Dutch Verzamelingen) Note: in some markdown editors, this link is broken, as the last parenthesis is not parsed as being part of the URL

The lesson follows the order and the topics in http://en.wikipedia.org/wiki/Set_(mathematics). For each topic (a section in the wikipedia article), you create a section in your notebook too. In the accompanying sideshow, you go down in the slides when you enter a topic. You do all sections up to (and including) http://en.wikipedia.org/wiki/Set_(mathematics)#Basic_operations. You end with a section on Boolean Logic, described below.

Form

Each topic consists of the following items:

1. Definition
2. Illustration of the definition
   • often with an image
3. Implementation of the topic in Python
4. Construction
   • often involving Python code
5. Application and examples
   • also often involving code
6. Exercises

Boolean Logic

End with a section on Boolean Logic in which you explain the meaning of the connectives and,or,xor and not using sets. http://en.wikipedia.org/wiki/Boolean_algebra#Venn_diagrams is a good place to start.

Notebook to get you started.

Use this notebook as the basis for your assignment. In particular make the programming exercises in them.