PyCon AU / University of Queensland

Boardroom, St. Leo's College, St. Lucia, Brisbane
Jul 30-31, 2014
9:00 am - 5:00 pm

General Information

Software Carpentry's mission is to help scientists and engineers become more productive by teaching them basic lab skills for computing like program design, version control, data management, and task automation. This two-day hands-on bootcamp will cover basic concepts and tools; participants will be encouraged to help one another and to apply what they have learned to their own research problems.

Instructors: Damien Irving, Philipp Bayer, Tim McNamara

Who: The course is aimed at postgraduate students, post-docs and other researchers who have a basic familiarity with programming concepts like loops, conditionals, and arrays, but need help to translate this knowledge into practical tools to help them work more productively. We particularly encourage researchers attending PyCon Australia to extend their stay in order to participate in the bootcamp.

Where: Boardroom, St. Leo's College, St. Lucia, Brisbane. Get directions with OpenStreetMap or Google Maps. The room is the Boardroom, St. Leo's College, on the campus of the University of Queensland. This map circles the location. Here is an alternative map, this one also shows the location of restaurants and food stores around campus (thanks to Belinda Weaver for the map!).

Requirements: Participants are asked to bring a laptop with some specific software packages installed (see Setup instructions below). If you don't have a laptop, that's completely fine. We'll pair you up with someone who does.

Participants are also asked to fill out a short questionnaire about their previous programming experience. The responses will be used to tailor the teaching material to the knowledge base of the audience. We will send the short questionnaire via email two weeks before the bootcamp.

Contact: Please mail philipp.bayer@uqconnect.edu.au for more information.

Registration: The bootcamp is fully booked out. Feel free to send me a mail (contact above) to ask in case a spot becomes free.

Schedule

An overview of the teaching schedule is given below. Last minute updates to the schedule and links to course notes and materials will be provided at the event Etherpad. Please note that lunch will not be provided, however morning and afternoon tea will.

Wednesday	09:00	Introduction to task automation with the Unix shell
	10:30	Morning tea
	11:00	Introduction to task automation with the Unix shell
	12:30	Lunch
	13:30	Building programs with Python
	15:00	Afternoon tea
	15:30	Building programs with Python
	17:00	Wrap-up
Thursday	09:00	Building programs with Python
	10:30	Morning tea
	11:00	Version control with Git
	12:30	Lunch
	13:30	Managing data
	15:00	Afternoon tea
	15:30	Managing data with SQL
	17:00	Wrap-up

Setup

To participate in a Software Carpentry bootcamp, you will need working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of your bootcamp.

Overview

Editor

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.

The Bash Shell

Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.

Git

Git is a state-of-the-art version control system. It 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.

Python

Python is becoming very popular in scientific computing, and it's a great language for teaching general programming concepts due to its easy-to-read syntax. We teach with Python version 2.7, since it is still the most widely used. Installing all the scientific packages for Python individually can be a bit difficult, so we recommend an all-in-one installer.

SQL

SQL is a specialized programming language used with databases. We use a simple database manager called SQLite, either directly or through a browser plugin.

Windows

Editor

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.

Git Bash

Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.

Python

Download and install Anaconda CE.
Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

SQLite

Download the sqlite3 program and put it in the directory where you are running examples. Alternatively, you may install the Firefox SQLite browser plugin described below.

Mac OS X

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 (found in /Applications/Utilities). You may want to keep Terminal in your dock for this workshop.

Editor

We recommend Text Wrangler or Sublime Text. In a pinch, you can use nano, which should be pre-installed.

Git

Install Git for Mac by downloading and running the installer. For older versions of OS X (10.5-10.7) use the most recent available installer available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.

Python

Download and install Anaconda CE.
Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

SQLite

sqlite3 comes pre-installed on Mac OS X. Alternatively, you may install the Firefox SQLite browser plugin described below.

Linux

Bash

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

If Git is not already available on your machine you can try to install it via your distro's package manager (e.g. apt-get).

Editor

Kate is one option for Linux users. In a pinch, you can use nano, which should be pre-installed.

SQLite

sqlite3 comes pre-installed on Linux. Alternatively, you may install the Firefox SQLite browser plugin described below.

Python

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.)

Download the installer that matches your operating system and save it in your home folder.
Open a terminal window.
Type
```
bash Anaconda-
```
and then press tab. The name of the file you just downloaded should appear.
Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. Type 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).