Jul 13-15, Jul 17 2015
1:00 pm - 5:00 pm
Instructors: Isabell Kiral-Kornek, Rob Kerr, Alistair Walsh
Helpers: Soroor Hediyeh Zadeh, Zaki Akhmad, Aliza Wajih, Andrea Bedini, Kerry Halupka, Lachlan Musicman
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.
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 email@example.com for more information.
|15:30||Analysing data with python|
|13:00||Analysing multiple files, conditionals|
|13:00||Errors and Exceptions|
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
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.
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:
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.
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.
nano is the editor installed by the Software
Carpentry Installer, it is a basic editor integrated into the
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.
Kate is one option for
Linux users. In a pinch, you can use
should be pre-installed.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.
This installer requires an active internet connection.
After installing Python and Git 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
/Applications/Utilities). You may want to keep
Terminal in your dock for this workshop.
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
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.
Git should be installed on your computer as part of your Bash install (described above).
For OS X 10.8 and higher, install Git for Mac
by downloading and running
After installing Git, there will not be anything in your
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
here. Use the Leopard installer for 10.5 and the Snow
Leopard installer for 10.6-10.7.
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 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.
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.)
bash Anaconda-and then press tab. The name of the file you just downloaded should appear.
yesand press enter to approve the license. Press enter to approve the default location for the files. Type
yesand press enter to prepend Anaconda to your
PATH(this makes the Anaconda distribution the default Python).