Software Carpentry: University of Adelaide

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, 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 is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Room 422, Horace Lamb Building, North Terrace Campus, University of Adelaide. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a wifi-capable laptop, from which they will logon to the Data Intensive Tools for the Cloud (DIT4C) environment on the NeCTAR Research Cloud. This environment has all the required software pre-installed, so there's nothing participants need to bring or do in preparation for the workshop.

Having said that, there are software installation instructions below for participants who'd like to install the software on their own computer before or after the workshop. Also note that participants are required to abide by Software Carpentry's Code of Conduct.

Wifi: Laptops must have a working WiFi adapter, and connection will be through your usual University of Adelaide login. Attendees from other academic institutions will have a login provided on the day.

Contact: Please mail stephen.pederson@adelaide.edu.au for more information.

Schedule

Day 1

09:00	Automating tasks with the Unix shell
10:30	Coffee
12:00	Lunch break
13:00	Version control with Git
14:30	Coffee
16:00	Wrap-up

Day 2

09:00	Building programs with Python
10:30	Coffee
12:00	Lunch break
14:30	Coffee
16:00	Wrap-up

Etherpad: http://pad.software-carpentry.org/2015-11-26-adelaide-python.
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...

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...

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...

Workshop Setup

Create a GitHub account

GitHub is an online hosting service for all your code. We'll be using it in the lesson on version control, and GitHub credentials are used for login authentication on DIT4C. GitHub accounts are free, so sign up for one if you don't already have an account.

Login to DIT4C

During the first session of the workshop, the instructors will give you the compute node name and access code you'll need for the Data Intensive Tools for the Cloud (DIT4C) environment that is hosted on the NeCTAR Research Cloud. Once you've got that name and code, navigate to the DIT4C homepage (it works best in the Chrome browser) and follow these instructions:

Click the "login" button and proceed to login using your GitHub credentials.
Go to the "compute nodes" tab and click "claim compute node access".
From the drop down menu, select the name of the compute node that the instructor gave you and enter the corresponding access code.
Go to the "containers" tab and add a new container named after yourself (e.g. johnsmith). The reason for this is that container names are unique (i.e. you can't have the same container name as anyone else in the room). Select the "IPython" image from the drop down menu, set the initial state to on and then hit the create button.
When the container is "on", its name should turn blue and you can click on it to launch your environment in a new tab of your browser.
Once you're finished for the day, simply close all the extra tabs that have opened up and turn your container "off". When you come back tomorrow, simply switch back to the 'on' position to continue using that container.

(Optional) software installation instructions

The DIT4C environment comes with all the required software pre-installed, however if you would like to install the software on your own computer (either before or after the workshop), here are the instructions to do so.

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

Download the Git for Windows installer. Run the installer. Important: on the 6th page of the installation wizard (the page titled `Configuring the terminal emulator...`) select `Use Windows' default console window`. If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option. 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

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 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., 3.4 is fine).

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

Open http://continuum.io/downloads with your web browser.
Click on "I want Python 3.X" link.
Download this Python 3 installer.
Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Open http://continuum.io/downloads with your web browser.
Click on "I want Python 3.X" link.
Download this Python 3 installer.
Install Python 3 using all of the defaults for installation.

Linux

Open http://continuum.io/downloads with your web browser.
Click on "I want Python 3.X" link.
Download this Python 3 installer, save it in your home folder.
Install Python 3 using all of the defaults for installation. (Installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
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.