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James Cook University, Townsville

14-15 July, 2016

9:00 am to 4:00 pm

Instructors: Jay van Schyndel, Daniel Baird

Helpers: Collin Storlie, Clair Meade

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, **Library Carpentry** workshop will cover basic concepts and tools, including regular expressions, recommended data structures, version control, task automation, and data clean up. The datasets used for analysis during the workshop will be relevant to librarians. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. This workshop is based on the original Library Carpentry curriculum intitally developed by Dr James Baker, Owen Stephens, and Daniel van Strien, which was further adapted by a global team during the recent Mozilla Science Lab Global Sprint.

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

Who: The course is aimed at librarians and humanities researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: 14-July (Room 002C, Building 18 - Library) 15-July (Room 011C, Building 34 - Earth and Environmental Sciences), James Cook University, Townsville, QLD, Austalia.. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must 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). 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:

  • The room is wheelchair / scooter accessible.
  • Accessible restrooms are available.
  • check these details??

Contact: Please mail jay.vanschyndel@jcu.edu.au for more information.


Schedule

Day 1

09:00 Introduction, jargon busting
10:00 Break
10:30 Data structures, regular expressions
12:00 Lunch break
13:00 Introduction to the command line
14:30 Break
15:00 Using grep and sed
16:00 Close

Day 2

09:00 Introduction to version control
10:00 Break
10:30 Using Git
12:00 Lunch break
13:00 Introduction to OpenRefine
14:30 Break
15:00 OpenRefine 2 and workshop wrap-up
16:00 Close

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


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.

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

Video Tutorial
  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".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

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). 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.

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).

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.

Windows

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

Mac OS X

Video Tutorial

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

Video Tutorial

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.

Mac OS X

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.

Linux

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.

OpenRefine

OpenRefine (formerly Google Refine) is a powerful tool for working with messy data: cleaning it; transforming it from one format into another; and extending it with web services and external data.

Windows

Please download OpenRefine 2.6 from the OpenRefine website: Download OpenRefine To install it, unzip and double-click on refine.exe.

Mac OS X

Please download OpenRefine 2.6 from the OpenRefine website: Download OpenRefine To install it, open, drag icon into the Applications folder and double click on it. Using your web browser go to http://localhost:3333

Linux

Please download OpenRefine 2.6 from the OpenRefine website: Download OpenRefine To install it, extract then type ./refine to start.
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