June 1st and 2nd, 2016
09:30 am - 4:00 pm
Instructors: Dan MacLean
Helpers: Martin Page
TSL uses Software Carpentry Training Courses. 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, 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. Please note that this is not a full SWC workshop, we will be leaving out the Git version control section (in response to previous feedback and time constraints) in favour of concentrating more on the Python section.
For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".
Who: The course is aimed at TSL researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Requirements: Participants are encouraged to bring a laptop with a Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). If you do not have access to one, then you can use the JIC machines in the training theatre. Participants are also required to abide by Software Carpentry's Code of Conduct.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers have checked that:
Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch and we will attempt to provide them.
Contact: Please mail firstname.lastname@example.org for more information.
|09:30||Automating tasks with the Unix shell|
|13:30||Building programs with Python|
|09:30||Building programs with Python|
|13:00||Building programs with Python|
Materials for this day can be found here:Python
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.
The instructions below will install everything you need, one-by-one and the software will be available on your machine after the workshop - but it is a lot of installing. If you'd rather use a virtual machine that can be disposed of after the workshop please see the instructions here: Virtual Machine Install Instructions
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.
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
See the Git installation video tutorial
for an example on how to open the Terminal.
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
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. See the Git installation video tutorial for an example on how to open nano. 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 Anaconda3-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).
You may prefer to use a virtual machine (VM) rather than install lots of software on your own computers. Use these instructions for this option.