Working with Python: functions and modules - course materials

Materials for the course run by the Graduate School of Life Sciences, University of Cambridge.

• Course website: http://pycam.github.io/
• Booking website: http://www.training.cam.ac.uk/

If you wish to run the course on your personal computer, here are the steps to follow to get up and running.

Clone this github project

git clone https://github.com/pycam/python-functions-and-modules.git
cd python-functions-and-modules

Dependencies

Install Python 3 by downloading the latest version from https://www.python.org/. For Mac OSX, just run brew install python3.

Python 2.x is legacy, Python 3.x is the present and future of the language.

Create first a virtual environment using the venv library. Update pip if needed, install jupyter and RISE to get a slideshow extension into jupyter.

Note A virtual environment is a Python environment such that the Python interpreter, libraries and scripts installed into it are isolated from those installed in other virtual environments.

python3 -m venv venv
# activate your virtual environment
source venv/bin/activate
# update pip if needed
pip install --upgrade pip
# install jupyter
pip install jupyter

# slideshow extension
pip install rise
jupyter-nbextension install rise --py --sys-prefix
jupyter nbextension enable rise --py --sys-prefix

# matplotlib
pip install matplotlib

# biopython
pip install biopython

# pandas
pip install pandas

On mac OSX you may need to run this command to accept the XCode license, before installing biopython:

sudo xcodebuild -license

Usage

Go to the directory where you've cloned this repository, activate your virtual environment and run jupyter.

Your web browser should automatically open with this url http://localhost:8888/tree where you see the directory tree of the course with all the jupyter notebooks.

cd python-functions-and-modules
source venv/bin/activate
jupyter notebook

To shutdown jupyter, type ctrl-C into the terminal you've ran jupyter notebook, answer y and press enter.

You may wish to deactivate the virtual environment, by entering into the terminal:

deactivate