Pathogen evolution, selection and immunity

Installing Python

For the course, you’ll need a the ability to run python from the command line and have a couple standard libraries installed (numpy, scipy and matplotlib). You should be running Python 3. To check if you have Python installed and which version, run

python --version

from the command line. It should print something like:

Python 3.9.2

if it’s properly installed.

Easy install through Anaconda

The easiest way to install Python and standard scientific libraries on Mac or Windows is through Anaconda. Go here www.anaconda.com/products/individual and follow instructions to download and install.

More future-proof install on Mac

Anaconda is convenient, but I prefer having more control over dependencies that are installed. For a quick install on an Intel Mac, the following should hopefully work for you:

Install Homebrew

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Install Python with Homebrew

brew install gcc
brew install python
brew install zmq

Install pip package manager

sudo easy_install pip

Install Python packages

pip install numpy
pip install scipy
pip install matplotlib

On M1 Macs, you’ll need to do the following instead:

Install Python with Homebrew

brew install gcc
brew install python
brew install zmq
brew install cython
brew install numpy
brew install scipy

brew link python@3.9
ln -s -f /opt/homebrew/opt/python/bin/python3 /opt/homebrew/opt/python/bin/python

Install pip package manager

ln -s -f /opt/homebrew/opt/python/bin/pip3 /opt/homebrew/opt/python/bin/pip

Install Python packages

pip install matplotlib

MyBinder

It’s probably best to have a local install of Python on your computer, but if it’s being difficult, you can always use MyBinder for the course exercises.

To do so, click on:

Binder

It will take a little while to launch, but you’ll get a working Jupyter Notebook interface and you’ll be able to navigate through the repo contents to find .ipynb files to run within your browser.