Media and Arts Technology CDT, Queen Mary University of London

Engineering Building Room G2a, School of Electronic Engineering and Computer Science, Queen Mary University of London, London E1 4NS

20-21 June 2017, 9:30 am - 5:30 pm

Instructors: Raniere Silva, Adam Witney

Helpers:

General Information

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 concepts and tools, including program design, version control, data management, and task automation. Participants will be 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 the paper "Best Practices for Scientific Computing".

Workshop Details

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

When: 20-21 June 2017, 9:30 am - 5:30 pm.

Where: Engineering Building Room G2a, School of Electronic Engineering and Computer Science, Queen Mary University of London, London E1 4NS. Get directions with OpenStreetMap or Google Maps.

Etherpad: http://pad.software-carpentry.org/2017-04-20-qmul.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code during the workshop.

Participants will need to bring their own laptops configured before the workshop according to the setup instructions.

Contact: Please email rebecca.stewart@qmul.ac.uk or a.nenadic@manchester.ac.uk for more information.


Schedule

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Day 1

Time Content References
09:00 Welcome and introduction
09:45 Automating tasks with the Unix Shell (1)
11:00 Coffee
11:15 Automating tasks with the Unix Shell (2)
12:30 Lunch break
13:15 Data organization and cleaning (best practices)
  • Data organisation with spreadsheets
  • Data Cleaning with OpenRefine
  • 15:00 Coffee
    15:15 Version control with Git (1)
  • Why version control
  • Setting up Git
  • Creating a repository
  • Tracking changes
  • Exploring history
  • Ignoring things
  • 17:00 Wrap-up

    Day 2

    Time Content References
    09:00 Recap of Day 1
    09:15 Version control with Git (2)
  • Intro and remote repositories in GitHub
  • Collaborating using Github
  • Managing conflicts
  • 10:30 Coffee
    11:00 Programming in Python (1)
    12:30 Lunch break
    13:15 Programming in Python (2)
  • Creating functions
  • Errors and exceptions
  • Defensive programming
  • 14:45 Coffee
    15:30 Programming in Python (3)
  • Debugging
  • Python programs as command-line tools
  • 16:30 Feedback and wrap-up
  • Post-workshop survey
  • Syllabus

    Below are links to all the lessons taught at the course.


    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. Keep "Use Git from the Windows Command Prompt" selected 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.
      4. Click on "Next".
      5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
      6. Keep "Use Windows' default console window" selected and click on "Next".
      7. Click on "Install".
      8. 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.

    Python

    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 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

    Video Tutorial
    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

    Video Tutorial
    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 Anaconda3-
      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).

    OpenRefine

    OpenRefine (previously Google Refine) is a tool for data cleaning that runs through a web browser, and any browser - Safari, Firefox, Chrome, Explorer - should work fine. You will need to download Google Refine and install it, and when you open it, it will run through the browser, but you don't need an internet connection, and the data will all be stored on your computer.

    Windows

    Go to the OpenRefine download page, and click on Windows kit to download the install file. To use it, unzip, and double-click on openrefine.exe (if you're having issues with openrefine.exe try refine.bat instead). OpenRefine will then open in your web browser. If it doesn't open automatically, open a web broswer after you've started the program and go to the URL http://localhost:3333 and you should see OpenRefine.

    Mac OS X

    Go to the OpenRefine download page, and click on Mac kit to download the install file. Open the downloaded .dmg file and drag the icon in to the Applications folder. Double click on the icon and Google Refine will then open in your web browser. If it doesn't open automatically, open a web broswer after you've started the program and go to the URL http://localhost:3333 and you should see OpenRefine.

    Linux

    Go to the OpenRefine download page. Click on Linux kit to download the install file. Extract the file and type ./refine in your terminal and Google Refine will then open in your web browser. If it doesn't open automatically, open a web broswer after you've started the program and go to the URL http://localhost:3333 and you should see OpenRefine.