Most of the software you will need is available through Anaconda, a distribution of scientific software for Python (and R). It is the easiest way to install Python with the packages we need. The one additional piece of software we will need is Git.
We are using Python 3.7 (or newer) in this class. Python 3.8 is fine.
If you are looking for a text editor for editing Python scripts, I recommend Visual Studio Code. It also has support for Jupyter notebooks.
Anaconda (and Miniconda, described at the end of this document) is a scientific software distribution. It is built around the Conda package manager.
Conda installs precompiled binary versions of software, including but not limited to Python packages. The versions of Scientific Python software distributed through Conda are compiled against more optimized versions of the core math libraries than the packages available through standard Python channels (the Python Package Index).
When you are looking online for instructions for Python software, it will usually tell you to install it with
However, since we are using Conda, it works better to install the Conda version of a package (with
conda) if possible.
It will usually, but not always, have the same name as the Python package.
You can search for Conda packages on anaconda.org.
Installing on Your Computer
To install Anaconda on your computer:
Download the appropriate installer for your platform from Anaconda Python.
If your computer has a 64-bit operating system (most do, except for Windows on ARM platforms like the Surface X), download the 64-bit version of Anaconda. Make sure you get the Python 3 verision (it is the default).
Run the installer.
To install Git, the instructions differ based on your platform:
- On Windows, download and run the installer
- On macOS, install Xcode from the App Store
- On Linux, install
gitfrom your package manager
Saving Space with Miniconda
We don't need all of Anaconda. If you want to save disk space, Miniconda is a much smaller distribution that just contains Python and the Conda package manager, so you can install the packages you need yourself.
Download the installer and run it.
Install the base packages we will need:
conda install pandas scipy scikit-learn notebook ipython \ seaborn statsmodels
Installing on Onyx
Unlike a lot of other software, Anaconda is designed to be installed separately by each user.
To setup on Anaconda on Onyx, you need to download the installer and run it on Onyx (or an Onyx node). Once you have set it up on any Onyx node, it will be available across Onyx, no matter which node you log in to. Due to Onyx's network file system performance, I recommend using Miniconda.
You can do this with:
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh /bin/bash Miniconda3-latest-Linux-x86_64.sh rm Miniconda3*.sh
This will install Miniconda (which by default will also configure your shell to activate the Miniconda environment). Log out and log back in to Onyx and Conda will be active. Install the base packages:
conda install pandas scipy scikit-learn notebook ipython \ seaborn statsmodels plotnine
Onyx already has Git installed.
On Linux and Mac, the installer will, by default, modify your Bash startup scripts to activate Anaconda.
On Windows, it will install a separate ‘Anaconda Prompt’ and ‘Anaconda PowerShell’ that you can use from the start menu.