May 4-5, 2015
9:30 am - 5:00 pm
Instructors: Ewan Barr, Genevieve Shattow
Helpers: Pablo Rosado, Vivek Krishnan, Antonio Bibiano, Fabian Jankowski, Arna Karick
The mission of the Software Carpentry project is to help researchers be more productive by teaching them basic computing skills. Researchers often 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 be encouraged to help one another and to apply what they have learned to their own research problems.
Who: This two-day workshop is aimed at graduate students (Honours students are also welcome) and other researchers who are interested in getting started with Python. Previous experience with Unix will be helpful but it's not required. We will be teaching the basics of Unix on the first day. Register here to attend the workshop or to volunteer as a helper on the day. The workshop will be limited to 35 participants.
A short meeting will be held a few days before the workshop to give instructors and helpers a better understanding of what will be expected on the day. Participants experiencing problems with software installations are welcome to bring their laptops to the helper meeting for troubleshooting.
Start time: 9:30apm. Please arrive 15 minutes earlier so we can start on time.
Requirements: Participants are asked to bring their laptop and it's critical that this laptop be able to connect to the Eduroam wifi network. Python and iPython Notebook will need to be installed before you arrive. See below for the relavent software installation instructions. Also note that participants are required to abide by Software Carpentry's Code of Conduct.
Contact: Please mail email@example.com for more information.
|09:30||Welcome and Introduction|
|09:45||Automating tasks with the Unix shell|
|11:00||Coffee (20 min)|
|11:20||Automating tasks with the Unix shell|
|12:45||Lunch break (45 min)|
|13:30||Building programs with Python|
|15:00||Coffee (20 min)|
|15:20||Building programs with Python|
|16:30||Wrap-up (30 min)|
|18:00||Dinner at Glenferrie Hotel (optional)|
|09:30||Python continued: loops and conditionals, lists|
|11:00||Coffee (20 min)|
|11:20||Python continued: functions, defensive programming (?)|
|13:30||Version control with Git|
|15:00||Coffee (20 min)|
|16:20||Version control with Git|
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. Once you are done installing the software listed below, please go to this page, which has instructions on how to test that everything was installed correctly.
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 OSX and Linux is sometimes 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. Many researchers in the physical sciences use Emacs. There is quite a nice version for Mac OSX.
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 downloading and running the installer. This will provide you with both Git and Bash in the Git Bash program.
It installs and configures
nano (Among other things)
This installer requires an active internet connection.
After installing 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. 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 10.8 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.
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).
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).
SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.
The Software Carpentry
Windows Installer installs
sqlite3 for Windows. If
you used the installer to configure `nano`, you don't need to run it again.
sqlite3 comes pre-installed on Mac OS X.
sqlite3 comes pre-installed on Linux.