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QUT - Research Bazaar (Python)

February 1-2, 2016

9:00 am - 5:00 pm

Instructors: Amanda Miotto, Belinda Weaver, Heidi Perrett, Anup Shah, Selene Fernandez-Valverde

Helpers: TBC

General Information

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, version control and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. We are running two Software Carpentry workshops in parallel as part of the "Research Bazaar" in Brisbane. This workshop will cover task automation with the Unix shell Bash, programming with Python and version control with Git. (The other workshop is the same, except it will cover R instead of Python.)

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: All Research Bazaar attendees are welcome to attend this course. We particularly encourage early career researchers to attend and kickstart their digital skills. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Room P413a, P Block, Queensland University of Technology, Gardens Point Campus. Get directions with OpenStreetMap or Google Maps.

Requirements: You will need to bring a laptop with the specific software packages installed as detailed below. You are also required to abide by Software Carpentry's Code of Conduct.

Contact: Please mail s.hames@uq.edu.au for more information.

Schedule

Day 1

08:30 Setting up and software installation help
09:00 Automating tasks with the Unix shell
10:30 Morning tea
11:00 Automating tasks with the Unix shell
12:30 Lunch break
13:30 Introduction to Python with the Jupyter notebook
15:00 Afternoon tea
15:30 Analysing data with Python
16:45 Wrap-up

Day 2

08:30 Setting up and software installation help
09:00 Python conditionals and functions
10:30 Morning tea
11:00 When things go wrong: errors, exceptions and debugging in Python
12:30 Lunch break
13:30 Version control with Git - Intro
15:00 Afternoon tea
15:30 Version control with Git - Collaboration
16:45 Wrap-up

Etherpad: http://pad.software-carpentry.org/ResBaz-BNE-Python.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

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

  • Working with Python in the Jupyter notebook
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Debugging and testing your programs
  • 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...

Wireless Internet Access

You will be able to access wireless internet through eduroam - check your institutions IT support pages for how to connect. If you aren't affiliated with an eduroam institution we will have temporary usernames and passwords for you on the day.

Setup Option 1: Local Installation On Your Laptop

As an alternative to the DIT4C cloud option, you can install the software locally on your machine, using the instructions below. Please arrive before 9:00am to get your install checked by a helper. We can also help you setup your own machine during the ResBaz Hacky Hour on the day after the workshop.

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.

The Bash Shell

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

Windows

  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on "Next".
    2. Click on "Next".
    3. Click on "Next".
    4. Click on "Next".
    5. Click on "Next".
    6. Select "Use Git from the Windows Command Prompt" and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    7. Click on "Next". Keep "Checkout Windows-style, commit Unix-style line endings" selected.
    8. Select "Use Windows' default console window" and click on "Next".
    9. Click on "Next".
    10. Click on "Finish".

This will provide you with both Git and Bash in the Git Bash program.

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 10.9 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.

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.

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 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.

Windows

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.

Mac OS X

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Linux

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

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 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., 3.5 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).

Windows

  1. Open http://continuum.io/downloads with your web browser.
  2. Download the Python 3 installer for Windows.
  3. Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

  1. Open http://continuum.io/downloads with your web browser.
  2. Download the Python 3 installer for OS X.
  3. Install Python 3 using all of the defaults for installation.

Linux

  1. Open http://continuum.io/downloads with your web browser.
  2. Download the Python 3 installer for Linux.
  3. Install Python 3 using all of the defaults for installation. (Installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  4. Open a terminal window.
  5. Type 
    bash Anaconda-
    and then press tab. The name of the file you just downloaded should appear.
  6. 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).

Once you are done installing the software listed above, please go to this page, which has instructions on how to test that everything was installed correctly.

Setup Option 2: The DIT4C cloud

We have a cloud based environment available with all the software needed for the workshop pre installed. For this option to work you will need to setup Eduroam (differs for each institution) so you have a working wireless internet connection.

We'll give instructions on how to connect to this on the day of the workshop.

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