10-11 Aug 2017
9:00 am - 4:30 pm
Instructors: Liz Cooper-Williams, Belinda Weaver, Amanda Miotto
Helpers: Gareth Moores, Malyon Bimler
Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic programming concepts at an introductory level in a supportive and non-judgemental environment. The course includes data analysis, data visualisation and basic script design for creating reproducible code. We also provide an introduction to using the Unix-style command-line and managing code versions in Git. 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 who need to use Python in their research. You don't need to have any previous knowledge of programming or the tools that will be presented at the workshop.
Cancellations: We have high demand but limited places so if you wish to cancel your registration, please contact us as soon as possible so we can fill your spot from the waitlist.
Where: Room 707, QBI, The University of Queensland (Building 79) St Lucia, Brisbane. Get directions with OpenStreetMap or Google Maps.
When: 10-11 Aug 2017. Add to your Google Calendar.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should install the required software prior to the lessons as listed below. They 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 (using contact details below) and we will attempt to provide them.
Contact: Please email e.cooperwilliams@uq.edu.au for more information.
Surveys
Please be sure to complete these surveys before and after the workshop.
| 09:00 | Introduction to Python basics |
| 10:30 | Coffee |
| 10:45 | Libraries and Pandas |
| 12:00 | Lunch break |
| 13:00 | Loops and Functions |
| 14:30 | Coffee |
| 14:45 | Conditionals |
| 16:00 | Wrap-up |
| 09:00 | Introduction to Unix Shell |
| 10:30 | Coffee |
| 10:45 | Version Control with Git |
| 12:00 | Lunch break |
| 13:00 | Designing Python scripts |
| 14:30 | Coffee |
| 14:45 | Handling Errors |
| 16:00 | Wrap-up |
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
To participate in a Software Carpentry workshop, you will need to bring your own laptop and install the required software described here and 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.
cmd and press [Enter])setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.exit then pressing [Enter]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
(found in
/Applications/Utilities).
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
install anything.
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).
You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.
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
this list.
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 (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
available here.
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 important to have a text editor that does not introduce hidden markup and only stores the text you write. This is known as a "plain text editor". Atom (https://atom.io/) is recommended as a versatile multi-platform plain text editor which has syntax highlighting (ie color coding to highlight different types of functionality). Others specific to each OS are mentioned below. Word processing editors such as Microsoft Word are not suitable as plain text editors.
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.
Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.
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.
Others editors that you can use are Text Wrangler or Sublime Text.
nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.
Others editors that you can use are Gedit, Kate or Sublime Text.
Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research 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 as a follow-me live coding session using the Jupyter notebook, a programming environment that runs in a web browser. It is best to ensure that your browser is up-to-date for this to work properly and also for security on the internet.
Jupyter can be launched from the Anaconda Navigator which has instructions for installation below. To start a session, click on the "New" dropdown (top right corner), then select "Python 3".
bash Anaconda3-and then press tab. The name of the file you just downloaded should appear. If it does not, navigate to the folder where you downloaded the file, for example with:
cd DownloadsThen, try again.
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).