Stony Brook University

Hilton Garden Inn conference room, 1 Circle Rd, Stony Brook, NY 11794
Jul 08-09, 2014
9:00 am - 4:30 pm

General Information

Software Carpentry's mission is to help scientists and engineers become more productive by teaching them basic lab skills for computing like program design, version control, data management, and task automation. This two-day hands-on bootcamp will cover basic concepts and tools; participants will be encouraged to help one another and to apply what they have learned to their own research problems.

Instructors: Tommy Guy, Randy Olson

Who: The course is restricted to fellows of the Software Development Summer School for Computational Chemistry and Materials Modeling at Stony Brook University.

Where: Hilton Garden Inn conference room, 1 Circle Rd, Stony Brook, NY 11794. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).

Contact: Please mail olsonran@msu.edu for more information.


Workshop Materials

The workshop materials can be downloaded here: https://github.com/guyrt/2014-07-08-stonybrook/archive/gh-pages.zip

Etherpad

We use Etherpad as a backchannel chat to take and share notes during the workshop. Please also use Etherpad to ask and answer any questions that come up while an instructor is teaching. The workshop Etherpad can be found at: https://etherpad.mozilla.org/2014-07-stonybrook

Schedule

This schedule may be subject to change.

Tuesday 08:00 - 09:00 Pre-workshop office hour
09:00 - 09:30 Introduction to Software Carpentry
09:30 - 10:45 Task automation with the Unix shell
10:45 - 11:00 Coffee break
11:00 - 12:00 Numerical analysis with NumPy
12:00 - 13:00 Lunch break
13:00 - 14:30 Python programming and analysis
14:30 - 14:45 Coffee break
14:45 - 16:00 Modularization and Documentation in Python
16:00 - 16:30 Wrap-up
Wednesday 08:00 - 09:00 Pre-workshop office hour
09:00 - 10:30 Accessing and Creating Software History (Git Part 1)
10:30 - 10:45 Coffee break
10:45 - 12:00 Sharing and Collaborating with GitHub (Git Part 2)
12:00 - 13:00 Lunch break
13:00 - 14:00 Plotting with matplotlib
14:00 - 15:00 Testing
15:00 - 15:15 Coffee break
15:15 - 16:00 Debugging
16:00 - 16:30 Wrap-up

Setup

To participate in a Software Carpentry bootcamp, you will need working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of your bootcamp.

Overview

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.

The Bash Shell

Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.

Python

Python is becoming very popular in scientific computing, and it's a great language for teaching general programming concepts due to its easy-to-read syntax. We teach with Python version 2.7, since it is still the most widely used. Installing all the scientific packages for Python individually can be a bit difficult, so we recommend an all-in-one installer.

Git

Git is a state-of-the-art version control system. It 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

Software Carpentry Installer

For an all-in-one installer:

  • Download the installer.
  • If the file opens directly in the browser select File→Save Page As to download it to your computer.
  • Double click on the file to run it.

Editor

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.

Python

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

Git Bash

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

Mac OS X

Bash

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.

Editor

We recommend Text Wrangler or Sublime Text. In a pinch, you can use nano, which should be pre-installed.

Python

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

Git

Install Git for Mac by download and running the installer.

Linux

Bash

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

If Git is not already available on your machine you can try to install it via your distro's package manager (e.g. apt-get).

Editor

Kate is one option for Linux users. In a pinch, you can use nano, which should be pre-installed.

Python

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).

Miscellaneous