Contents

Software and Installation¶

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 3.8 (or newer — Python 3.9 is fine) in this class. Older versions of Python may work, but I will be testing my example code and instructions with Python 3.8.

Department Computers

If you want to use the department’s computer lab for your work, see the Onyx setup instructions as well as the instructions for remotely using Onyx.

Required Software¶

Our primary software is:

To complete assignments on department computers, you also need:

  • An SSH client (MobaXterm for Windows, ssh on Mac or Linux)

  • The Boise State VPN for convenient access to Onyx nodes

For building more advanced workflows, there are many text editors you can use. I use Visual Studio Code, which has very good remote editing support and also directly supports Jupyter notebooks (although I do not use this feature much).

The rest of this document walks through some details.

About Conda¶

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 pip. 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 Anaconda Python¶

!!! note Platform Support

The full Anaconda distribution works on x86_64 platforms - most Windows and Linux computers, and Macs
with Intel processors.  If you have a Mac with an M1 processor, or an ARM-based Linux computer, go to
the [miniconda instructions](miniconda) and use the Miniforge installer.

To install Anaconda on your computer:

  1. 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).

  2. Run the installer.

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. Miniforge is an equivalent community-maintained distribution that has support for more hardware platforms (including Linux and Mac on ARM-based chips).

  1. Download the installer for your platform and run it. On M1 Macs and ARM-based Linux, get the appropriate installer from miniforge.

  2. Install the base packages we will need:

    conda install pandas scipy scikit-learn notebook ipython \
    seaborn statsmodels

Additional Packages¶

I use seedbank in many of my examples for seeding the random number generator. Seedbank is not currently available through the main Anaconda channel, so you will needt to install it with pip:

pip install seedbank

Do this after installing your other packages with conda, so seedbank doesn’t try to pull in a non-Conda NumPy.

It is fine to use pip to install packages that are not available in Conda. It also works to use it to install packages that are, but I do not recommend this, particularly for core compute packages such as numpy, scipy, and scikit-learn — the versions in Conda are more optimized.

Installing Git and Command-Line Tools¶

We will be using Git later in the semester.

To install Git, the instructions differ based on your platform:

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

Onyx already has Git installed.

Using Anaconda¶

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.

previous

Assignment 7

next

Documentation & Reading