Software Carpentry: CoDiMa - University of Manchester

This workshop is brought to you by CoDiMa - Collaborative Computational Project (CCP) in the area of Computational Discrete Mathematics (EPSRC grant EP/M022641/1). It constitutes the initial part of the First CoDiMa Training School in Computational Discrete Mathematics (November 16th-20th, 2015). By registering for this workshop you will automatically register for the whole School.

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, 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 our paper "Best Practices for Scientific Computing".

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

Where: University Place, Oxford Road, Manchester. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

This workshop constitutes the initial part of the First CoDiMa Training School in Computational Discrete Mathematics which runs until Friday November 20th. By registering for this workshop you will automatically register for the whole School. Please see the School's page for further details.

Contact: Please mail alexander.konovalov@st-andrews.ac.uk for more information.

Schedule

Day 1: University Place, room 2.219

09:30	Automating tasks with the Unix shell
11:00	Coffee
12:30	Lunch break
13:30	Automation with Make
15:00	Coffee
16:30	Wrap-up

Day 2: University Place, rooms 5.211 (until 1pm), 2.220 (after 1pm)

09:00	Coffee - at Alan Turing Building, Atrium Bridge Level 1
09:30	Version control with Git
11:00	Break
11:20	Version control with Git - continued
13:00	Lunch break (room 2.220)
14:00	Programming with GAP
15:00	Coffee
15:30	School activities (see schedule here)

Day 3: Alan Turing Building, Room Frank Adams 1

09:30	Programming in GAP
11:00	Coffee
12:00	Wrap-up
12:30	Lunch break
13:30	School activities (see schedule here)

The full programme for each day of the Training School is available here

Etherpad: http://pad.software-carpentry.org/2015-11-16-manchester-codima.
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...

Automation with Make

Basic Tasks
Automatic Variables and Wildcards
Patterns
Variables
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...

Programming in GAP

First session with GAP
Functions in GAP
Using regression tests
Small groups search
Attributes and methods
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.

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

Download the Git for Windows installer. Run the installer. Important: on the 6th page of the installation wizard (the page titled `Configuring the terminal emulator...`) select `Use Windows' default console window`. 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. This will provide you with both Git and Bash in the Git Bash program.

OS X

The default shell in all versions of 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).

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.

GAP

GAP is a system for discrete computational algebra. It provides a programming language, a library of thousands of functions implementing algebraic algorithms written in the GAP language as well as large data libraries of algebraic objects. Its latest version may be found on the GAP Downloads page.

Windows

From the GAP Downloads page, download the .exe installer and double click on the file to run it. When you will be asked for the installation path, note that it should not contain spaces. For example, you may install GAP in C:\gap4r7 (default), D:\gap4r7p8 or C:\Math\GAP\gap4r7, but you must not install it in a directory named like C:\Program files\gap4r7 or C:\Users\alice\My Documents\gap4r7 etc.

OS X

On OS X, we suggest to install GAP using Homebrew. After installing Homebrew, open the Terminal and call brew install homebrew/science/gap --with-InstPackages. Please be patient - this may take a while. If Homebrew is already installed on your Mac, you may have to call brew update first.

Alternatively, you may also install GAP from source as explained at the GAP Downloads page. The BOB installer, suggested in the next column for Linux, is also available for OS X.

Linux

We suggest to use an alternative GAP source installer BOB which will first check whether everything it needs from your system is installed and if not it will warn you and tell you what is needed. Please see BOB page for further instructions. To be able to compile GAP you may need to install some tools as described here. Alternatively, you may also install GAP from source as explained at the GAP Downloads page.

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 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.

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.

OS X

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 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.