Jun 7-8, 2016
9:00am - 5:00pm
Instructors: Moritz Neeb, Vasileios Panagiotis Lenis, Marek Cmero
Helpers: Martin Page, Matthew Hartley
Registration for this event is now closed. If you have any queries about upcoming training events, please contact the organisers.
Software Carpentry and TGAC are committed to ensuring a safe and accessible learning environment for all attendees of all backgrounds. Participants are therefore required to abide by Software Carpentry's Code of Conduct.
You will need to bring a laptop with some required software already installed in order to attend the bootcamp. Please let us know as soon as possible if you are not able to bring your own laptop.
The easiest way to get set up with the prerequisites for the bootcamp is to install the preconfigured virtual machine (VM). This VM contains the Linux operating system and all the software needed. As such, we suggest that participants bring their laptop with NoMachine installed.
If you are confident to install the requirements on your own laptop, please follow the setup directions below.
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.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
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.
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. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).
Git should be installed on your computer as part of your Bash install (described above).
For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
After installing Git, there will not be anything in your
as Git is a command line program.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
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.
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 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.
nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.
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).
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).
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.
During the workshop we will be usign Etherpad to chat, take notes, share URLs, and trace some feedback. You can get to the Etherpad at this page.
Please be sure to complete these surveys before and after the workshop.
|09:00||Welcome and Software set up|
|09:30||Part 1: Using the shell to do more in less time|
|11:00||Part 2: Using the shell to do more in less time|
|13:30||Part 1: Using version control to manage and share information|
|15:30||Part 2: Using version control to manage and share information|
|16:00||Part 1: Python and good programming practice|
|17:00||End of day|
|09:00||Recap and questions|
|09:30||Part 2: Python and good programming practice|
|11:00||Using Python for scientific programming|
|13:30||Debugging and testing|