Summary and Setup
Python is a general purpose programming language that is useful for writing scripts to work effectively and reproducibly with data.
This is an introduction to Python designed for participants with no programming experience. These lessons can be taught in one and a half days (~ 10 hours). They start with some basic information about Python syntax, the Jupyter notebook interface, and move through how to import CSV files, using the pandas package to work with data frames, how to calculate summary information from a data frame, and a brief introduction to plotting. The last lesson demonstrates how to work with databases directly from Python.
JupyterHub
For this workshop, we will use a web-based Python environment, JupyterHub, that UCSB Letters & Science IT has graciously setup for us:
Use your UCSB NETID to sign into the JupyterHub.
If you prefer to use Python on your own computer, you may use the setup instructions below, but this is not required.
Data
These files should already be downloaded if you are using JupyterHub (see above).
Data for this lesson is from the Portal Project Teaching Database. Specifically, we use the following eight data files:
- surveys.csv
- surveys2001.csv
- surveys2002.csv
- species.csv
- speciesSubset.csv
- plots.csv
- bouldercreek_09_2013.txt
- portal_mammals.sqlite
Please download them (by clicking on the corresponding links) and move them to the same directory, or download all the files as a zip which will give you everything in a single compressed file. You’ll need to unzip this file after downloading it.
Installing Python using Anaconda
Python is a popular language for scientific computing, and great for general-purpose programming as well. Installing all of the scientific packages we use in the lesson individually can be a bit cumbersome, and therefore recommend the all-in-one installer Anaconda.
Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine).
Installing Anaconda
This is not necessary if you are using JupyterHub. If you still want to install Anaconda on your local computer, select your operating system from the options below.
Open https://www.anaconda.com/products/individual in your web browser.
Download the Anaconda Python 3 installer for Windows.
Double-click the executable and install Python 3 using the recommended settings. Make sure that Register Anaconda as my default Python 3.x option is checked – it should be in the latest version of Anaconda.
Verify the installation: click Start, search and select
Anaconda Promptfrom the menu. A window should pop up where you can now type commands such as checking your Conda installation with:
Visit https://www.anaconda.com/products/individual in your web browser.
Download the Anaconda Python 3 installer for macOS. These instructions assume that you use the graphical installer
.pkgfile.Follow the Anaconda Python 3 installation instructions. Make sure that the install location is set to “Install only for me” so Anaconda will install its files locally, relative to your home directory. Installing the software for all users tends to create problems in the long run and should be avoided.
Verify the installation: click the Launchpad icon in the Dock, type Terminal in the search field, then click Terminal. A window should pop up where you can now type commands such as checking your conda installation with:
Note that the following installation steps require you to work from the terminal (shell). If you run into any difficulties, please request help before the workshop begins.
Open https://www.anaconda.com/products/individual in your web browser.
Download the Anaconda Python 3 installer for Linux.
Install Anaconda using all of the defaults for installation.
- Open a terminal window.
- Navigate to the folder where you downloaded the installer.
- Type
bash Anaconda3-and press Tab. The name of the file you just downloaded should appear. - Press Return
- Follow the text-only prompts. When the license agreement appears (a
colon will be present at the bottom of the screen) press
Spacebar until you see the bottom of the text. Type
yesand press Return to approve the license. Press Return again to approve the default location for the files. Typeyesand press Return to prepend Anaconda to yourPATH(this makes the Anaconda distribution your user’s default Python).
- Verify the installation: this depends a bit on your Linux distribution, but often you will have an Applications listing in which you can select a Terminal icon you can click. A window should pop up where you can now type commands such as checking your conda installation with:
Required Python Packages
The following are packages needed for this workshop:
All packages apart from plotnine will have automatically
been installed with Anaconda and we can use Anaconda as a package
manager to install the missing plotnine package: You need
to open up a Terminal, if you are using Mac OSX, or Linux (see
instructions above), or launch an anaconda-promt, if you are
using Windows. In your terminal window type the following:
This will then install the latest version of plotnine into your conda environment.
Required packages: Miniconda
Miniconda is a lightweight version of Anaconda. If you install Miniconda instead of Anaconda, you need to install required packages manually in the following way:
(Alternative) Installing required packages with environment file
Download the environment.yml file by right-clicking the link and selecting save as. In the directory where you downloaded the environment.yml file run:
Activate the new environment with:
You can deactivate the environment with:
Launch a Jupyter notebook
After installing either Anaconda or Miniconda and the workshop packages, launch a Jupyter notebook by typing this command from the terminal:
The notebook should open automatically in your browser. If it does not or you wish to use a different browser, open this link: http://localhost:8888.
For a brief introduction to Jupyter Notebooks, please consult our Introduction to Jupyter Notebooks page.