Software Carpentry: School of Earth and Space Exploration, ASU

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 lab skills for scientific computing. This hands-on workshop will cover basic concepts and tools, including program design, version control, 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 is aimed at graduate students and other researchers.

Where: ISTB4, Arizona State University, Tempe, AZ 85281, Rm 296 (TEAL Room). Get directions with OpenStreetMap or Google Maps. Inexpensive parking is available at several parking garages scattered across campus.

Requirements: 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 abhijithrajan@asu.edu for more information.

Schedule

Participants can attend either the Python or the Matlab session, which will happen in parallel in separate rooms. The lessons on the Unix shell and Git will take place in one room.

Day 1

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

Day 2

09:00	Python continued	Matlab continued
10:30	Coffee
12:00	Lunch break
13:00	Version control with Git
14:30	Coffee
16:00	Wrap-up

Etherpad: https://etherpad.mozilla.org/LqL3VHHWxy.
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...

Programming in Matlab

Working with arrays
Reading and plotting data
Creating and using functions
Loops and conditionals
Defensive programming
Writing Matlab scripts

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 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.

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.

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. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

Windows

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

Mac OS X

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. 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 (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

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.

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 a basic editor and the default that instructors use in the workshop. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

Mac OS X

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Text Wrangler or Sublime Text.

Linux

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.

Python (only install if you are attending the Python lesson)

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.

Regardless of how you choose to install it, please make sure you install Python version 2.x and not version 3.x (e.g., 2.7 is fine but not 3.4). Python 3 introduced changes that will break some of the code we teach during the workshop.

We will teach Python using the IPython 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

Download and install Anaconda.
Download the default Python 2 installer (do not follow the link to version 3). Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Download and install Anaconda.
Download the default Python 2 installer (do not follow the link to version 3). Use all of the defaults for installation.

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 workshop.)

Download the installer that matches your operating system and save it in your home folder. Download the default Python 2 installer (do not follow the link to version 3).
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).

Once you are done installing the software listed above, please go to this page, which has instructions on how to test that everything was installed correctly.

Matlab/Octave (only install if you are attending the Matlab lesson)

Installing/Accessing Matlab

Matlab is a widely used software package for scientific and engineering computing. Installing it on a personal/work machine requires purchasing a license. For ASU students, Matlab is available online via MyApps. Please ensure that you have access to Matlab before arriving at the workshop.

Login to MyApps here
Search for Matlab (use the 2014 version if possible) and click "Run App now"
Follow the instructions to "Install Client"
Once the client is installed, launch Matlab from the MyApps website

Note: when running Matlab through MyApps, all scripts/data are stored on your M drive, which is accessible from MyASU by clicking on My Files in the left sidebar. We will download the required datasets and learn how to upload them to your M drive at the beginning of the first Matlab lesson.

Octave (Free Matlab Alternative)

GNU Octave is a free alternative to Matlab with nearly identical syntax. While it does not have quite as many pre-built function libraries as Matlab, it is under active development and the most commonly used functions are available. If you choose to use Octave instead of Matlab for the workshop, it is your responsibility to install it on your machine.

Instructions for downloading and installing Octave are available here. Octave 4.0 has a graphical user interface similar to that in Matlab by default, while version 3.x operates in a command line environment (e.g., Command Prompt on Windows, Terminal on Linux/Mac OSX). To enable the GUI in Octave 3.x, you can launch it using the command octave --force-gui.