University of Alberta

May 15-16, 2017

9:00 am - 4:00 pm

Instructors: John Simpson

Helpers: TBD

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

Where: Business B24. Get directions with OpenStreetMap or Google Maps.

When: May 15-16, 2017. 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). They are also required to abide by Software Carpentry's Code of Conduct.

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 email or john.simpson@computecanada.ca 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

09:00 Automating tasks with the Unix shell
10:30 Coffee
12:00 Lunch break
13:00 Basics of sharing & version control with Git/GitHub Desktop
14:30 Coffee
14:45 Exploring Regular Expressions
15:45 Setting up for Twitter and Python
16:00 End Day 1

Day 2

09:00 Python Part 1 - Programming Language Fundamentals
10:30 Coffee
12:00 Lunch break
13:00 Python Part 2 - Mining Twitter
14:30 Coffee
16:00 End Day 2

Etherpad: http://pad.software-carpentry.org/2017-05-15-ualberta.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.


Syllabus

Note that the content listed here are links to the standard Software Carpentry class, which is an ideal rather than something that actually happens because there simply isn't enough time over two days to cover it all. What will happen is that your instructor will basically follow the high-level goals of each section but with shifts to the content and the emphasis; in particular, this workshop will focus on text manipulation and regular expressions. The end result will be divergence from what is highlighted here but as a result you will have two examples to work from: what you did in class and what is summarized in the sections shared here.

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 Python

  • Using libraries
  • Working with arrays
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Defensive programming
  • Using Python from the command line
  • 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.

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

  1. Download the MobaXterm installer.
  2. Run the installer.
  3. Open the program. If there are no errors then you can assume that it was installed properly and close it.

This will provide you with the free home edition of MobaXterm, a tool that provides a very nice command-line shell within Windows. We will review how to use MobaXterm in class.

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). 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). While we will be installing Git on your system our focus will be on GitHub and the GUI (Graphic User Interface) tools that are provided for working with it.

Windows

We will install Git within MobaXterm during lunch on the first day. This is fairly straightforward to do. If you would like a headstart on this then download the Git plugin for MobaXterm and place it in the same directory as the MobaXterm executable (should be in "C:\Program Files (x86)\Mobatek\MobaXterm Personal Edition\").

You need to create a GitHub account. This can be done by visiting https://github.com/ and using the account creation feature as you would for any website.

You need to install the GitHub Desktop Tool. You can find the download at https://desktop.github.com/. Download the tool and install it.

Mac 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.

You need to create a GitHub account. This can be done by visiting https://github.com/ and using the account creation feature as you would for any website.

You need to install the GitHub Desktop Tool. You can find the download at https://desktop.github.com/. Download the tool and install it.

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.

You need to create a GitHub account. This can be done by visiting https://github.com/ and using the account creation feature as you would for any website.

Unfortunately there is no GitHub Desktop Tool for Linux. Not to worry, we will make sure that you are able to use the git commandline tool to access GitHub.

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

nano is a basic editor and the default that instructors use in the workshop. It does not come pre-packaged in MobaXterm but it is easy to install and we will do so during the workshop. If you would like to try to do this in advance then open MobaXterm, start a local terminal, and when you see a command prompt (an arrow with a block cursor after it) type "apt-get install nano" (without the quotes) and press enter.

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. 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 scientific computing, and great for general-purpose programming as well. Installing all of its scientific 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

  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

  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).