vnellore/pybay_2019-pandas_tutorial

PyBay 2019 Pandas Tutorial

The course website: https://chendaniely.github.io/pybay_2019-pandas_tutorial/

Pre-readings

1. A Quick Guide to Organizing Computational Biology Projects
2. Tidy Data
3. Best Practices for Scientific Computing
4. Good enough practices in scientific computing

Setup

Python

Anaconda, an all-in-one installer, is recommended.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.7 is fine).

When using the IPython notebook, a programming environment that runs in a web browser, you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

Windows

Video Tutorial

1. Open http://continuum.io/downloads with your web browser.
2. Download the Python 3 installer for Windows.
3. Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Video Tutorial

1. Open http://continuum.io/downloads with your web browser.
2. Download the Python 3 installer for OS X.
3. Install Python 3 using all of the defaults for installation.

Linux

1. Open http://continuum.io/downloads with your web browser.
2. Download the Python 3 installer for Linux.
   (Installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
3. Open a terminal window.
4. Type

   bash Anaconda3-

   and then press tab. The name of the file you just downloaded should appear. If it does not, navigate to the folder where you downloaded the file, for example with:

   cd Downloads

   Then, try again.
5. Press enter. You will follow the text-only prompts. To move through the text, press the space key. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
6. Close the terminal window.

Testing If Anaconda was installed

1. Open up the Anaconda Command Prompt
2. Type "ipython" into the prompt
3. You should see Python open up with Python 3.7.x and using the Anaconda distribution
4. Type "quit()" to exit
5. Type "jupyer notebook" to launch the notebook (this may take a while if it is the first time you are launching it)
6. Note the URL (with the token), paste it into your browser
7. Close the anaconda prompt when you're done