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Utah State University

Mar 16-17, 2015

9:00 am - 4:30 pm

Instructors: Greg Wilson, Ethan White

Helpers: Morgan Ernest, Allen Hurlbert, Paul Wolf, Erica Christensen, Sarah Reehl, David Harris, Andrew Kleinhesselink

General Information

Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic skills for scientific computing. 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.

Who: The workshop is designed for graduate students, postdocs, faculty, and other researchers who have a basic understanding of basic programming tasks like how to assign a value to a variable and how to use a for loop. If you have any questions about whether this is a good workshop for you please email Ethan White (ethan.white@usu.edu).

Where: Merrill-Cazier Library - Room 101, 3000 Old Main Hill, Logan, Utah, 84322. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). If you do not have access to a laptop, please email Ethan White (ethan.white@usu.edu) and access to a properly configured laptop can be arranged. Participants are also required to abide by Software Carpentry's Code of Conduct.

Accessibility: The Merrill-Cazier Library meets all Americans with Disabilities Act (ADA) physical facilities requirements. The room is on the ground floor near the entrance and there are accessible restrooms and dining options on the same floor of the building. Materials will be provided in advance of the workshop and large-print handouts are available are available if needed (please let us know in advance by emailing ethan.white@usu.edu). At this time we do not provide remote participation for this workshop, but are working on making this possible in the future. If you have other accessibility needs (e.g. sign-language interpreters, lactation facilities) please get in touch with Ethan White (ethan.white@usu.edu) and we will work hard to provide them.

Contact: Please mail ethan.white@usu.edu for more information.

Schedule

Day 1

09:00 Automating tasks with the Unix shell
10:30 Coffee break
12:00 Lunch break
13:00 Building programs with Python
14:30 Coffee break
16:00 Wrap-up

Day 2

09:00 Version control with Git
10:30 Coffee break
12:00 Lunch break
13:00 Managing data with SQL
14:30 Coffee break
16:00 Wrap-up

Etherpad: https://etherpad.mozilla.org/usu-march-2007.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

Syllabus

The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things
  • Reference...

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
  • Reference...

Version Control with Git

  • Creating a repository
  • Recording changes to files: add, commit, ...
  • Viewing changes: status, diff, ...
  • Ignoring files
  • Working on the web: clone, pull, push, ...
  • Resolving conflicts
  • Open licenses
  • Where to host work, and why
  • Reference...

Managing Data with SQL

  • Reading and sorting data
  • Filtering with where
  • Calculating new values on the fly
  • Handling missing values
  • Combining values using aggregation
  • Combining information from multiple tables using join
  • Creating, modifying, and deleting data
  • Programming with databases
  • Reference...

Setup

This page has instructions on testing that you have the right software installed.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on Mac OS X and Linux is usually set to Vim, which is not famous for being intuitive. if you accidentally find yourself stuck in it, try typing the escape key, followed by ':q!' (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

Windows

nano is the editor installed by the Software Carpentry Installer, it is a basic editor integrated into the lesson material.

Notepad++ is a popular free code editor for Windows. Be aware that you must add its installation directory to your system path in order to launch it from the command line (or have other tools like Git launch it for you). Please ask your instructor to help you do this.

Mac OS X

We'll be using nano, which should be pre-installed.

If you're looking for a more full featured text editor we recommend Text Wrangler or Sublime Text.

Linux

We'll be using nano, which should be pre-installed.

If you're looking for a more full featured editor Kate is one option for Linux users.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

Install Git for Windows by downloading and running the installer. This will provide you with both Git and Bash in the Git Bash program.

Software Carpentry Installer

This installer requires an active internet connection.

After installing Git Bash:

  • Download the installer.
  • Double click on the file to run it.

Information about the SWC Windows Installer, including the source code, can be found at https://github.com/swcarpentry/windows-installer.

Mac OS X

The default shell in all versions of Mac OS X is bash, so no need to install anything. You access bash from the Terminal (found in /Applications/Utilities). You may want to keep Terminal in your dock for this workshop.

Linux

The default shell is usually bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com.

Windows

Git should be installed on your computer as part of your Bash install (described above).

Mac OS X

For OS X 10.8 and higher, install Git for Mac by downloading and running the installer. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.7) use the most recent available installer for your OS available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.

Linux

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo yum install git.

Python

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

Windows

  • Download and install Anaconda.
  • Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

  • Download and install Anaconda.
  • Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Linux

We recommend the all-in-one scientific Python installer Anaconda. (Installation requires using the shell and if you aren't comfortable doing the installation yourself just download the installer and we'll help you at the boot camp.)

  1. Download the installer that matches your operating system and save it in your home folder.
  2. Open a terminal window.
  3. Type 
    bash Anaconda-
    and then press tab. The name of the file you just downloaded should appear.
  4. Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. 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).

SQLite

SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.

  1. If you don't already have Firefox on your computer, download and install it.
  2. Go to the SQLite Manager page, click **Add to Firefox**, and choose to **Allow** Firefox to install the add-on.
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