CCP-CoDiMa SageMath training

Lancaster University

Feb 20-21, 2020

9:00 am - 5:00 pm

Instructors: Alexander Konovalov (University of St Andrews), Samuel Lelièvre (Université Paris-Sud), Fredrik Strömberg (University of Nottingham)

Helpers: TBC

This workshop is brought to you by CCP-CoDiMa - Collaborative Computational Project in the area of Computational Discrete Mathematics (EPSRC grant EP/M022641/1).

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 our paper "Best Practices for Scientific Computing".

Who: The course is aimed at UK-based graduate students and other researchers in the area of discrete computational mathematics. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

For UK-based researchers in the area of discrete computational mathematics located outside Lancaster, certain financial support is available to cover travel, accommodation and subsistence to attend both days of the workshop. To apply, please tick the appropriate box in the registration form, and the organisers will contact you for further details. In case of being oversubscribed, we reserve the right to prioritise applications from PhD students and early career researchers.

External participants are asked to make their own arrangements for travel and accommodation. On campus, there is a standard student-style ensuite B&B accommodation which you can book here, and also a more expensive Lancaster House hotel. Alternatively, there's a Travelodge hotel in the city centre and regular buses to campus from there.

Where: Bowland Hall, Bailrigg, Lancaster LA1 4ZA. Get directions with OpenStreetMap or Google Maps.

When: Feb 20-21, 2020. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Code of Conduct: Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers 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 (using contact details below) and we will attempt to provide them.

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


Surveys

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

Pre-workshop Survey

Post-workshop Survey


Schedule

Day 1

Before Pre-workshop survey
09:00 Automating Tasks with the Unix Shell
10:30 Morning break
11:00 Automating Tasks with the Unix Shell (Continued)
12:30 Lunch break
13:30 Programming with SageMath
15:00 Afternoon break
15:30 Programming with SageMath (Continued)
16:30 Wrap-up
17:00 END

Day 2

09:00 Version Control with Git
10:30 Morning break
11:00 Version Control with Git (Continued)
12:30 Lunch break
13:30 Programming with SageMath (Continued)
15:00 Afternoon break
15:30 Programming with SageMath (Continued)
16:30 Wrap-up
16:45 Post-workshop Survey
17:00 END

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 SageMath

  • First session with SageMath
  • Polynomials and linear algebra
  • Elements of programming and 3D graphics
  • Matrix Groups
  • Orbits and conjugacy classes
  • Defensive Programming
  • 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.

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. From the dropdown menu select "Use the nano editor by default" and click on "Next".
    3. Ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
    4. Ensure that "Use the native Windows Secure Channel library" is selected and click on "Next".
    5. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    6. Ensure that "Use Windows' default console window" is selected and click on "Next".
    7. Ensure that "Enable file system caching" and "Enable Git Credential Manager" are selected and click on "Next".
    8. Click on "Install".
    9. 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.

The default shell in all versions of macOS 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.

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.

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.

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

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. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. 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.

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 dnf 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 macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.

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.

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 BBEdit or Sublime Text.

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.

SageMath

SageMath is a free open-source mathematical software system licensed under the GPL. Its areas of application for education and research include basic algebra, calculus, elementary to very advanced number theory, cryptography, numerical computation, commutative algebra, group theory, combinatorics, graph theory, exact linear algebra and much more. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more, combining and seamlessly integrating their functionality into a common experience. That makes it a popular system for research computing, and the fact that it is written in Python makes it useful to study general-purpose programming as well.

We will teach SageMath using the Jupyter 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).