May 14-15, 2018
9:00 am - 4:30 pm
Instructors: John Simpson, Wendy Lam, Denny Yang
Helpers: TBD
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: ECHA L1-350. Get directions with OpenStreetMap or Google Maps.
When: May 14-15, 2018. 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@ualberta.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 | 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/2018-05-14-ualberta-sc.
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.
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).
We will install Git for Windows during the morning of the first day. This is fairly straightforward to do. If you would like a headstart on this then download Git for Windows and install it in advance. If you install this on your own then make sure that if you are offered a choice of Text Editor that you choose Nano.
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.
There is a GitHub Desktop Tool for Windows. We will not be using it but you can find the download at https://desktop.github.com/. Download the tool and install it for your future use if you would like.
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.
There is a GitHub Desktop Tool for OSX. We will not be using it but you can find the download at https://desktop.github.com/. Download the tool and install it for your future use if you would like.
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 now comes bundled with Git for Windows so make sure to choose this if it is presented as an option during the Git install.
Others editors that you can use are Notepad++ 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 Text Wrangler (Now depricated. Use the free verison of BBEdit instead.) or Sublime Text.
nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed. If this is not the case then the workshop instructors will help you install it.
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 Microsoft Visual Studio Code (it is bundled with Anaconda). If you install Anaconda on your own make sure that VS Code is part of the install options you choose.
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).