Sep 20-21, 2016
9:00 am - 5:00 pm
Instructors: Doug Latornell, Nancy Soontiens, Karina Ramos Musalem
Helpers: Tereza Jarnikova, Idalia Machuca, Anna Mittelholz, Keelin Scully, Cindy Yu
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.
Specific focuses of the workshop will be:
For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".
Who: The workshop is aimed at graduate students and other researchers who are familiar with basic programming concepts (like loops, conditionals, arrays, and functions) but need help to translate that knowledge into practical tools to help them work more productively. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Where: ESB-5104, 2207 Main Mall, Vancouver. 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.
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
Susan Allen
Surveys
Please be sure to complete these surveys before and after the workshop.
| 09:00 | The Unix shell |
| 10:30 | Break |
| 12:30 | Lunch break |
| 13:30 | Version Control with Mercurial |
| 15:00 | Break |
| 16:50 | Wrap-up |
| 09:00 | Building Programs with Python |
| 10:30 | Break |
| 12:30 | Lunch break |
| 13:30 | Building Programs with Python (cont'd) |
| 15:00 | Break |
| 16:50 | Wrap-up |
Etherpad: http://pad.software-carpentry.org/2016-09-20-ubc.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
Coffee, tea, and snacks will be provided during the mid-morning and mid-afternoon breaks each day of the workshop.
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.
cmd and press [Enter])setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.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 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.
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.
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. 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.
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.
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.
Mercurial is a version control system that lets you track what changes were made when to files. It has options for easily updating a shared or public version of your code on bitbucket.org. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer).
You will need an account at bitbucket.org for parts of the Mercurial lesson. Basic Bitbucket accounts are free. We encourage you to create a Bitbucket account if you don't have one already.
Install Mercurial and KDiff3 by downloading and running the TortoiseHg installer.
Install Mercurial by downloading and running the installer for your version of OS X from the downloads page. Also, please install the KDiff3 diff and merge tool. Be aware that you must add the KDiff3 installation directory to your system path. The workshop etherpad has some tips for doing that. If you need help with this, please ask one of the instructors before the workshop.
If you use the homebrew package manager,
you can install Mercurial with brew install mercurial,
and KDiff3 with brew install kdiff3.
If Mercurial 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 mercurial and for Fedora run
sudo yum install mercurial.
Also,
please install the KDiff3 diff and merge tool.
It should also be available via your package manager.
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).