honnorat / tutopython

Small tutorial for IPython / Scipy

IPython / Scipy tutorial

Installation

Conda / Anaconda

First we need nuts & bolts.

• Conda [doc] is a package manager application (pip + venv + virtualenvwrapper)
• Anaconda [link] is a Python distribution which include more than 300 of the most popular Python packages for science, math, engineering, and data analysis.

Then we set up an environment for the tutorial:

$ conda create -n tutopython python=3.4
$ source activate tutopython

Python packages

It's now time to install some packages :

$ conda install ipython numpy scipy matplotlib

and you're ready to play with ipython's command line interface.

$ ipython
Python 3.4.3 |Continuum Analytics, Inc.| (default, Mar  6 2015, 12:07:41)
Type "copyright", "credits" or "license" for more information.

IPython 4.0.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]:

But a more powerful environment is available to carry out exploratory computation and data analysis : notebooks.

IPython notebooks

Notebooks are interactive computational environments, in which you can combine code execution, rich text, mathematics, plots and rich media. See http://ipython.org/notebook.html.

Notebooks are stored as JSON files with a .ipynb extension.

$ conda install ipython-notebook
$ ipython notebook
[I 09:30:28.237 NotebookApp] Using MathJax from CDN: https://cdn.mathjax.org/mathjax/latest/MathJax.js
[I 09:30:29.031 NotebookApp] Serving notebooks from local directory: /Users/honnorat/Documents/YeastLab/tutopython
[I 09:30:29.031 NotebookApp] 0 active kernels
[I 09:30:29.032 NotebookApp] The IPython Notebook is running at: http://localhost:8888/
[I 09:30:29.032 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[W 09:30:38.422 NotebookApp] Notebook tuto_filter.ipynb is not trusted
[I 09:30:39.040 NotebookApp] Kernel started: ce530cd1-a559-4e8e-895c-c9543ea61f4f

Now you can open your browser at the given address http://localhost:8888/ and create a new notebook.

Useful reference

• Numpy documentation : http://docs.scipy.org/doc/numpy/user/
• Scipy documentation : http://docs.scipy.org/doc/scipy/reference/