Software Carpentry: University of Melbourne

General Information

Researchers spend much of their time wrestling with software, but most are self-taught programmers. As a result, they spend hours doing things that should take minutes, reinvent a lot of wheels, and still don't know if their results are reliable. To tackle this problem, Software Carpentry runs two-day workshops at hundreds of sites around the world. These hands-on workshops cover basic concepts and tools, including program design, version control, data management, and task automation. Participants are 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: Collaborative learning space 3, Old Arts, University of Melbourne. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants are asked to bring their laptop. They will be given access to the resbaz.cloud.edu.au environment on the NeCTAR Research Cloud (see login instructions below). The resbaz.cloud.edu.au environment has all the required software installed, however there are software installation instructions below for participants who would like to install the software on their own laptop after the workshop is over. Also note that participants are required to abide by Software Carpentry's Code of Conduct.

Wifi: Access to the wifi network is required to access resbaz.cloud.edu.au. University of Melbourne staff/students can connect to the UniWireless network; instructions on how to do this and where to get assistance can be found here. Attendees from other Australian universities should find out (from the IT website of their home institution) how to connect to the Eduroam wireless network. If you don't have access to UniWireless or Eduroam, please contact the workshop coordinator in advance of the workshop.

Contact: Please mail isa.kiral@gmail.com for more information.

Schedule

Day 1

13:00	Shell
15:00	Coffee break
15:30	Analysing data with python
17:00	Wrap-up

Day 2

13:00	GitHub
15:00	Coffee break
15:30	Loops, lists
17:00	Wrap-up

Day 3

13:00	Analysing multiple files, conditionals
15:00	Coffee break
15:30	Functions
17:00	Wrap-up

Day 4

13:00	Errors and Exceptions
15:00	Coffee break
15:30	Command-line programs
17:00	Wrap-up

Etherpad: https://etherpad.mozilla.org/2015-07-13-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...

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...

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 resbaz.cloud.edu.au. GitHub accounts are free, so sign up for one if you don't already have an account.

Login to resbaz.cloud.edu.au

During the first session of the workshop, the instructors will give you the compute node name and access code you'll need for resbaz.cloud.edu.au. Once you've got that name and code, navigate to resbaz.cloud.edu.au (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 "INSERT IMAGE NAME" 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.

Software Installation (not required)

resbaz.cloud.edu.au 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.

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

Linux

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

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 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.

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.)

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).