May 15-16, 2017
9:00 am - 4:00 pm
Instructors: John Simpson
Helpers: Anna Koop, Alicia Cappello, Chelsea Miya, Brian Rusk, Hassaan Ali
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.
Surveys
Please be sure to complete these surveys before and after the workshop.
| 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 |
| 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.
Note that the content listed here are links to the standard Software Carpentry class, which is an
add, commit, ...status, diff, ...clone, pull, push, ...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.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
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.
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.
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 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.
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.
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.
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.
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.
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.
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.
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 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).
bash Anaconda3-and then press tab. The name of the file you just downloaded should appear.
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).