CoDiMa - International Centre for Mathematical Sciences, Edinburgh

Oct 17-18, 2016

9:30 am - 5:00 pm

Instructors: Alexander Konovalov (University of St Andrews), Leighton Pritchard (James Hutton Institute), Alexey Tarutin (University of Edinburgh)

Helpers: Awss Al-Ogaidi (University of Sussex), Christopher Jefferson (University of St Andrews), Markus Pfeiffer (University of St Andrews), Michael Torpey (University of St Andrews)


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 Second CoDiMa Training School in Computational Discrete Mathematics (October 17th-21st, 2016). By registering for this workshop you will automatically register for the whole School.
CoDiMa

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: 15 South College Street, Edinburgh, EH8 9AA. 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.

Etherpad: Etherpad will be used throughout this course to take notes and share information. The course etherpad can be found at http://pad.software-carpentry.org/2016-10-17-edinburgh.

CoDiMa: This workshop constitutes the initial part of the Second CoDiMa Training School in Computational Discrete Mathematics which runs until Friday October 21st. By registering for this workshop you will automatically register for the whole School. Please see the School's page for further details.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch and we will attempt to provide them.

Contact: Please mail alexander.konovalov@st-andrews.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

October 17th, 2016

09:30 Automating tasks with the Unix shell
11:00 Coffee
13:00 Lunch break
14:00 Version control with Git
15:30 Coffee
16:00 Version control with Git

October 18th, 2016

09:30 Programming with GAP
11:00 Coffee
13:00 Lunch break
14:00 Programming with GAP
15:30 Coffee

Etherpad: http://pad.software-carpentry.org/2016-10-17-edinburgh.
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 GAP

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

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.

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:\gap4r8 (default), D:\gap4r8p4 or C:\Math\GAP\gap4r8, but you must not install it in a directory named like C:\Program files\gap4r8 or C:\Users\alice\My Documents\gap4r8 etc.

OS X

On OS X, you need to install GAP from source as explained at the GAP Downloads page. Download one of the archives provided there, unpack it and run ./configure; make in the unpacked directory. Then change to the pkg subdirectory and call ../bin/BuildPackages.sh to run the script which will build most of the packages that require compilation (provided sufficiently many libraries, headers and tools are available).

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

Linux

On Linux, you need to install GAP from source as explained at the GAP Downloads page. Download one of the archives provided there, unpack it and run ./configure; make in the unpacked directory. Then change to the pkg subdirectory and call ../bin/BuildPackages.sh to run the script which will build most of the packages that require compilation (provided sufficiently many libraries, headers and tools are available).

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.