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