Software Carpentry: Swinburne University of Technology

Swinburne University of Technology

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

Two-day Software Carpentry Python/Unix Workshop

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.

Where: AMDC Building (Boardroom 206), Swinburne Hawthorn Campus.. Get directions with OpenStreetMap or Google Maps.

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 akarick@swin.edu.au for more information.

Schedule

Day 1

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)

Day 2

09:30	Python continued: loops and conditionals, lists
11:00	Coffee (20 min)
11:20	Python continued: functions, defensive programming (?)
12:45	Lunch break
13:30	Version control with Git
15:00	Coffee (20 min)
16:20	Version control with Git
16:30	Wrap-up

Syllabus

The Unix Shell

Files and directories
History and tab completion
Pipes and redirection
Looping over files
Creating and running shell scripts
Finding things
Reference...

Programming in Python

Using libraries
Working with arrays
Reading and plotting data
Creating and using functions
Loops and conditionals
Defensive programming
Using Python from the command line
Reference...

Version Control with Git

Creating a repository
Recording changes to files: add, commit, ...
Viewing changes: status, diff, ...
Ignoring files
Working on the web: clone, pull, push, ...
Resolving conflicts
Open licenses
Where to host work, and why
Reference...

Managing Data with SQL

Reading and sorting data
Filtering with where
Calculating new values on the fly
Handling missing values
Combining values using aggregation
Combining information from multiple tables using join
Creating, modifying, and deleting data
Programming with databases
Reference...

Setup

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.

Text 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 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.

Windows

nano is the editor installed by the Software Carpentry Installer, it is a basic editor integrated into the lesson material.

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.

Mac OS X

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

Linux

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

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

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

Software Carpentry Windows Installer

It installs and configures nano (Among other things)

This installer requires an active internet connection.

After installing Git Bash:

Download the Software Carpentry Windows installer.
Double click on the file to run it.

Mac OS X

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.

Linux

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

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).

Windows

Git should be installed on your computer as part of your Bash install (described above).

Mac OS X

For OS X 10.8 and higher, install Git for Mac by downloading and running the installer. 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 (10.5-10.7) use the most recent available installer for your OS available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.

Linux

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

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).

Windows

Download and install Anaconda.
Download the default Python 2 installer (do not follow the link to version 3). Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Download and install Anaconda.
Download the default Python 2 installer (do not follow the link to version 3). Use all of the defaults for installation.

Linux

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. Download the default Python 2 installer (do not follow the link to version 3).
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).

SQLite

SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.

Windows

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.

Mac OS X

sqlite3 comes pre-installed on Mac OS X.

Linux

sqlite3 comes pre-installed on Linux.