Glasgow University

Room 320, Kelvin Building
Dec 12-13, 2013
9:00 am - 4:30 pm

Instructors: Ben Morris, James Morrison

What: Our goal is to help scientists and engineers become more productive by teaching them basic computing skills like program design, version control, testing, and task automation. In this two-day bootcamp, short tutorials will alternate with hands-on practical exercises. Participants will be encouraged both to help one another, and to apply what they have learned to their own research problems during and between sessions. Attendants are offered online office hours: regular events to get one-on-one help from Software Carpentry instructors, online.

Who: The course is aimed at postgraduate students and other scientists who are familiar with basic programming concepts (like loops, conditionals, arrays, and functions) but need help to translate this knowledge into practical tools to help them work more productively.

Requirements: The bootcamp will take place in a computer lab with 40 Windows workstations, there will be remote access to a Linux machines provided by the University. Participants may being along their own laptop, it is recommended to install the packages below ahead of the boot camp. (The list will be sent to participants a week before the bootcamp.)

Content: The syllabus for this bootcamp will include:

Contact: Please mail admin-uk@software-carpentry.org for more information.

Timetable:

Day 1:

8:30-9:00 setup, help with installation
9:00-9:30 introduction, etc. (Ben)
9:30-10:30 Shell I (James)
10:30-10:45 coffee break
10:45-12:00 Shell II (James)
12:00-1:00 lunch
1:00-2:00 Regular Expressions (Ben)
2:00-3:00 Python I (James)
3:00-3:15 coffee break
3:15-4:00 Python II (James)
4:00-5:00 Classes & Objects (Ben)


Day 2:

8:30-9:00 questions/problems from day 1
9:00-10:30 Version Control I (Ben)
10:30-10:45 coffee break
10:45-12:00 Version Control II (Ben)
12:00-1:00 lunch
1:00-3:00 Testing (James)
3:00-3:15 coffee break
3:15-4:30 Make (Ben)
4:30-5:00 wrapup (James)

Setup

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.

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.

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 more and more popular in scientific computing, and it's a great language for teaching general programming concepts due to its easy-to-read syntax. We will be using Python version 2.7. Installing all the scientific packages for Python individually can be a bit difficult, so we recommend using an all-in-one installer.

Required Software

In order to take part in the bootcamp, please set up this software before you arrive.

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.

Windows / Editor

Notepad++ is a popular free code editor for Windows.

Mac OS X / Editor

We recommend Text Wrangler or Sublime Text.

Linux / Editor

Kate is one option for Linux users.

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.

Windows / Git Bash

Install Git Bash following these instructions. This gives you Git as well as Bash.

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.

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.

Python

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

Linux / 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.)

  1. Download the installer that matches your operating system and save it in your home folder.
  2. Open a terminal window..
  3. Type 
    bash Anaconda-
    and then press tab. The name of the file you just downloaded should appear.
  4. 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).

Mac OS X / 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.)

  1. Download the installer that matches your operating system and save it in your home folder.
  2. Open a terminal window.
  3. Type 
    bash Anaconda-
    and then press tab. The name of the file you just downloaded should appear.
  4. 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).

Windows / Python

For Windows we recommend Anaconda from Continuum Analytics.

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.

Linux / 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).

Mac OS X / Git

Installing Git may require you to first install XCode. This is a very large download (several gigabytes), so please do it before arriving at the bootcamp.

For Mac OS X 10.7 and 10.8:

Go to the Xcode website. Get XCode from the App Store making certain to install the command line tools (from the Download preferences pane). Git is included in the command line tools.

For Mac OS X 10.6

If you have Mac OS X 10.6, first get XCode by going to the Apple developer site. You have to sign in with an Apple ID linked to a Developer account. If you don't have one, you can register and create one. Once you log in, go to page 8 and find "XCode 3.2.6 and iOS SDK 4.3 for Snow Leopard". Click to open that section, and then download the .dmg file. Finally, install just git.

Windows / Git Bash

Install Git Bash following the instructions here. This gives you Bash as well as Git.

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