Software Carpentry: Yale University

Yale University

Oct 11-12, 2014

9:00 am - 4:00 pm

Instructors: Camille Avestruz, Matthew Lightman

Helpers: Jieming Chen, Wendell Smith, Tomomi Sunayama, Manuel Mai, Dan Guest

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 workshop 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.

Who: The course is aimed at graduate students and other researchers.

Where: Sloane Physics Lab, Room 43, 217 Prospect Street, New Haven, CT 06511. Get directions with OpenStreetMap or Google Maps.

Requirements: After registering for the bootcamp, please complete the pre-bootcamp survey. Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Contact: Please mail rbsi.yale@gmail.com for more information.

Link to Etherpad: https://etherpad.mozilla.org/E14yAl1Yau

Notes from the Bootcamp

Thank you to everyone who attended! The instructors and helpers hope you found the bootcamp fun and useful. Here are some links to notes from the bootcamp and other resources to continue learning.

First, if you attended the bootcamp, please take the post-bootcamp survey so that we can get feedback, and find out ways to improve the bootcamp experience.

Notes taken during the bootcamp can be found on the etherpad.

The repository created by the instructors during the bootcamp, including python code from the afternoon of the second day, can be found here.

The ipython notebook created by the instructors on the second day can be found here.

If you want to learn more on the topics we covered, please check out Software Carpentry's web site, especially the lessons section.

Schedule

Saturday, Oct. 11	08:30-9:00	Help with set-up issues if you would like
	09:00-10:00	Introductions / The Unix shell
	10:00 - 10:15	Break
	10:15 - 11:15	Task automation with Bash
	11:15 - 12:15	Introduction to version control and git
	12:15 - 13:30	Lunch break
	13:30 - 15:00	More version control and git
	15:00 - 15:15	Break
	15:15 - 16:00	Adavanced git / Github tools / Wrap-up
Sunday, Oct. 12	09:00 - 10:00	Introduction to Python
	10:00 - 10:15	Break
	10:15 - 12:15	Intermediate Python data types and control flow
	12:15 - 13:30	Lunch break
	13:30 - 15:00	Python functions and file I/O
	15:00 - 15:15	Break
	15:15 - 16:00	Example Python Workflow / Wrap-up

Syllabus

The Unix Shell

Files and directories: pwd, cd, ls, mkdir, ...
History and tab completion
Pipes and redirection
Looping over files
Creating and running shell scripts
Finding things: grep, find, ...
Reference...

Programming in Python

Using libraries
Working with arrays
Reading and plotting data
Creating and using functions
Loops and conditionals: for, if, else, ...
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...

Setup

To participate in a Software Carpentry workshop, 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 workshop.

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.

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.

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.

Windows

Python

Download and install Anaconda.
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.

Software Carpentry Installer

This installer requires an active internet connection

After installing Python and Git Bash:

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

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

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.

Git

For OS X 10.8 and higher, install Git for Mac by downloading and running the installer. 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.

Python

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

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 or yum).

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.)

Download the installer that matches your operating system and save it in your home folder.
Open a terminal window.
Type
```
bash Anaconda-
```
and then press tab. The name of the file you just downloaded should appear.
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).