Caltech Library

March 9-10, 16-17

9:00 am - 12:00 pm

Instructors: Tom Morrell, Yuping Huang, Charles Guan, Stephen Davison

Helpers: Mike Hucka

This workshop is customized for the Caltech Postdoc association to focus only on Python. While it uses content from the Software and Data Carpentry curriculum, it is not an official workshop because it does not include instruction on the command line and version control. Please fill out the post-workshop survey before you leave. Want to hear about future workshops? Sign up for our mailing list to be the first to know.

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course for Caltech Postdocs. The library will offer additional general Software and Data Carpentry courses soon. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Millikan 9th Floor. Get directions with OpenStreetMap or Google Maps.

When: March 9-10, 16-17. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email library@caltech.edu for more information.


Schedule

Day 1

09:00 Jupyter Notebooks, Basic Data Plotting, Loops
10:30 Break
10:45 Lists and Files
12:00 END

Day 2

09:00 Conditionals and Functions
10:30 Break
10:45 Errors and Defensive Programming
12:00 END

Day 3

09:00 Working with the command line and using Pandas
10:30 Break
10:45 Managing DataFrames to work with tabular data
12:00 END

Day 4

09:00 Data types and combining data
10:30 Break
10:45 Advanced plotting (ggplot) and Open Science
12:00 END

Syllabus

Jupyter Notebooks

Programming in Python

  • Using libraries
  • Working with arrays
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Defensive programming
  • Using Python from the command line
  • Full lesson content...

Pandas and DataFrames

Advanced Plotting


Notebooks

We used Jupyter notebooks during the workshop to collect our code. Here are the instructor notebooks from the end of each day:

Day 1 and 2

Day 3: Python Script Notebook

Day 3: Python Script

Day 4

Setup

To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

Data Files

Download the data files and extract and save them somewhere where you can find them easily (like your Desktop).

Python

Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine).

We will teach Python using the Jupyter notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

Windows

Video Tutorial
  1. Open https://www.anaconda.com/download/#windows with your web browser.
  2. Download the Python 3 installer for Windows.
  3. Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.
  4. Open Anaconda Prompt (Start/Anaconda/Anaconda Prompt)
  5. Type 'conda install -c conda-forge plotnine'. Hit enter

macOS

Video Tutorial
  1. Open https://www.anaconda.com/download/#macos with your web browser.
  2. Download the Python 3 installer for OS X.
  3. Install Python 3 using all of the defaults for installation.
  4. Open Terminal (Applications/Utilities/Terminal)
  5. Type 'conda install -c conda-forge plotnine'. Hit enter

Linux

  1. Open https://www.anaconda.com/download/#linux with your web browser.
  2. Download the Python 3 installer for Linux.
    (The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  3. Open a terminal window.
  4. Type
    bash Anaconda3-
    and then press tab. The name of the file you just downloaded should appear. If it does not, navigate to the folder where you downloaded the file, for example with:
    cd Downloads
    Then, try again.
  5. Press enter. You will follow the text-only prompts. To move through the text, press the space key. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
  6. Type 'conda install -c conda-forge plotnine'. Hit enter
  7. Close the terminal window.