Columbia Applied Data Science

Software Carpentry Workshop Computer Setup

Follow these instructions to prepare your computer for the software carpentry bootcamp

Note: People in the Course "Applied Data Science" should instead follow these instructions

Stuff to Download

  • A version of Anaconda appropriate for you machine
  • If you have Windows, download and unzip either this VM image.
  • If you have a mac, download Xcode
    • First try getting it from the app store
    • If this doesn't work (due to an older OSX), you have to register as a developer

Software Installation

Overview

  • Python distribution
  • Editor
    • vim-gnome, macvim, gedit, or sublime text
  • Version control
  • Additional libraries
    • pdbpp
    • pep8
    • line_profiler

Installing Python Configurations

If you have Linux

If you have a Mac

  • You need to first install xcode,
    • xcode can be installed by going to the App Store. You need to install xcode, then goto the top left of your screen and click XCode -> Preferences -> Downloads, find "command line tools" and click install.
    • xcode is a 1GB+ download so you will not have time to download it in class on Wednesday
    • Note that the current version of xcode is only supported by OSX 10.7.4+ so we highly recommend you upgrade your operating system. If for whatever reason you absolutely cannot upgrade your os, you need to register for a free Apple developer account and download the appropriate version of xcode
  • For 64 bit OSX, install Anaconda CE
    • By default this is installed in your home directory. Unless you know what you're doing, don't change it.
  • For 32 bit OSX, install EPD academic
  • Remember to read the documentation
  • Remember to configure your environment
  • Install Git version control, and additional packages including VIM and other Python packages

If you have Windows

We will set you up with a Linux virtual machine. You can then follow the Linux instructions

  • Download and unzip the VM image.
  • Download VirtualBox
  • Run the installer
  • Open VirtualBox Manager
  • Click "New" to create new virtual machine
  • Select "Linux" for Type and "Ubuntu" or "Ubuntu (64-bit)" for Version
  • Next, allocate half of your memory for your VM.
  • Next, select "Use an existing virtual hard drive file" and select the VDI file you downloaded
  • Once the VM has been created, select it and click "Start"
  • If the VM image you downloaded already has guest-additions installed then you can skip this step. Otherwise once the setup is complete you need to install guest additions.

Now change the window manager IMPORTANT!!

  1. Turn on your VM and open a terminal
  2. In the terminal, type sudo apt-get install gnome-session-fallback
    • This will install a new graphics manager for your desktop
    • Click Y when asked
  3. Log out (or restart)
  4. When you log in, there will be a "gear shaped" icon near your login name. Click it and select GNOME Classic (No Effects) gnome-classic

Extra Help: Configuring environment variables

  • Modify your shell configuration file, henceforth referred to as your bashrc file.
    • Mac OSX: From your home directory (i.e., ~/) open either .bashprofile or .bashaliases (create one if neither exists), add "export PATH=/path/to/python:$PATH"
    • Linux: From your home directory (i.e., ~/) open .bashrc (create one if neither exists), add "export PATH=/path/to/python:$PATH"
  • Refresh your terminal by typing source ~/.bashrc or just opening a new terminal.

Verify Things

  • Open a terminal and start IPython with: ipython --pylab

    • Verify numpy with import numpy
    • To check pandas and matplotlib, from IPython, type
    from pandas import Series;
Series(randn(10)).plot()

  • Verify the notebook:

    • ipython notebook --pylab=inline should pop up a browser window and show the notebook dashboard

  • Verify your PATH setting:

    • which python should show the directory in which you installed Anaconda/EPD as the first entry

Install additional software

  • Ubuntu users should use "apt-get" command to install software packages. The syntax is "sudo apt-get install ..."
  • VIM (powerful but hard to learn in one day editor)
    • Linux: "sudo apt-get install vim vim-gnome"
    • Mac: download Macvim and follow installation instructions
  • Other (easier) editors
    • Linux: "sudo apt-get install gedit-plugins"
    • Mac: Download and install sublime text

  • Python libraries

    pip install pdbpp line_profiler pep8
    • If you don't have pip, install it first using easy_install pip.

Set up version control

  • Sign-up for free Github account
  • Install git
    • Mac: download from mac.github.com
    • Linux: type sudo apt-get install git
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