University of New Brunswick
Jan 6-7, 2014
9:00 am - 4:30 pm
Instructors: Julia Gustavsen, Ross Dickson
What: Our goal is to help scientists and engineers become more productive by teaching them basic computing skills like program design, version control, testing, and task automation. In this two-day bootcamp, short tutorials will alternate with hands-on practical exercises. Participants will be encouraged both to help one another, and to apply what they have learned to their own research problems during and between sessions. Attendants are offered online office hours: regular events to get one-on-one help from Software Carpentry instructors, online.
Who: The course is aimed at postgraduate students and other scientists who are familiar with basic programming concepts (like loops, conditionals, arrays, and functions) but need help to translate this knowledge into practical tools to help them work more productively.
Requirements: Participants must bring a laptop with a few specific software packages installed. (The list will be sent to participants a week before the bootcamp.)
Content: The syllabus for this bootcamp will include:
- using the shell to do more in less time
- using version control to manage and share information
- basic Python programming
- how (and how much) to test programs
- documentation and debugging
Contact: Please mail jgustavsen@eos.ubc.ca for more information.
Etherpad: etherpad.mozilla.org/2014-01-06-unb
Registration: Register here at EventbriteSTRIKE CONTINGENCY:
There is the possibility of a faculty strike at UNB any time after January 2 (UNB Bargaining updates). If a work stoppage should occur, the bootcamp will not take place on Jan 6-7. If that should happen we will attempt to reschedule for a later date.
Setup
The Bash Shell
Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.
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.
Git
Git is a state-of-the-art version control system. It 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.
Python
Python is becoming more and more popular in scientific computing, and it's a great language for teaching general programming concepts due to its easy-to-read syntax. We will be using Python version 2.7. Installing all the scientific packages for Python individually can be a bit difficult, so we recommend using an all-in-one installer.
Please follow the setup instructions below (pick the appropriate operating system) to install those tools on the laptop that you will be bringing to the bootcamp. (If you are having problems you can install the VM-virtual machine, but otherwise it is not needed.)
Windows
Windows / Editor
Notepad++ is a popular free code editor for Windows.
Windows / Git Bash
Install Git Bash following the instructions here. This gives you Bash as well as Git.
Windows / Git Bash
Install Git Bash following these instructions. This gives you Git as well as Bash.
Windows / Editor
Notepad++ is a popular free code editor for Windows.
Windows / Anaconda Python
- Download and install Anaconda CE.
- Use all of the defaults for installation except before pressing Finish make sure to check Make Anaconda the default Python.
Windows / Add Nano text editor
-
Download the swc-nano-installer.py script and save it in your user directory
C:\Users\YourNameHerefolder. - Go to the Start menu, select 'Run' and type 'cmd' (without the quotes) to run the 'cmd.exe' Windows Command Prompt. The Windows Command Prompt has the default configuration to launch in your home User folder. Type `dir` to make sure that the downloaded python file is in this directory.
python swc-nano-installer.pyand press enter. The script installs a sensible text editor you can use during the bootcamp.
Mac OS/X
Mac OS X / Bash
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.
Mac OS X / Git
Installing Git may require you to first install XCode. This is a very large download (several gigabytes), so please do it before arriving at the bootcamp.
For Mac OS X 10.7 and 10.8:
Go to the Xcode website. Get XCode from the App Store making certain to install the command line tools (from the Download preferences pane). Git is included in the command line tools.
For Mac OS X 10.6
If you have Mac OS X 10.6,
first get XCode by going to
the Apple developer site.
You have to sign in with an Apple ID linked to a Developer account.
If you don't have one,
you can register and create one.
Once you log in,
go to page 8 and find "XCode 3.2.6 and iOS SDK 4.3 for Snow Leopard".
Click to open that section,
and then download the .dmg file.
Finally,
install just git.
Mac OS X / Editor
We recommend Text Wrangler or Sublime Text.
Mac OS X / Python
We recommend the all-in-one scientific Python installer Anaconda.
- Download the non-GUI installer (MacOSX (10.5 or higher - bash installer) 64-bit) and save it in your home folder.
- Open a terminal window.
-
Type
bash Anaconda-
and then press tab. The name of the file you just downloaded should appear. -
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
yesand press enter to approve the license. Press enter to approve the default location for the files. Typeyesand press enter to prepend Anaconda to yourPATH(this makes the Anaconda distribution the default Python).
Linux
Linux / Bash
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.
Linux / Git
If Git is not already available on your machine you can try
to install it via your distro's package manager
(e.g. apt-get).
Linux / Editor
Kate is one option for Linux users.
Linux / Anaconda Python
We recommend the all-in-one scientific Python installer Anaconda.
- Download the installer that matches your operating system and save it in your home folder.
- Open a terminal window.
-
Type
bash Anaconda-
and then press tab. The name of the file you just downloaded should appear. -
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
yesand press enter to approve the license. Press enter to approve the default location for the files. Typeyesand press enter to prepend Anaconda to yourPATH(this makes the Anaconda distribution the default Python).
Virtual machine
Virtual Machine
Installation issues can and do happen. To ensure that you
can continue to participate in a lesson even if one of your
software programs fails, we provide a Linux virtual machine
that contains all the necessary software
pre-installed. Please install
VirtualBox
and download
this virtual machine image that is google drive hosted(~2.3gigs, if the download is slow and long, don't worry we will have it on USB sticks at the bootcamp)
Load the VM into VirtualBox by doing Import Appliance and loading the .ova file.
Coffee and Food
Coffee, tea, and snacks will be provided at morning and afternoon breaks during the bootcamp. Lunch will not be provided, but your are welcome to bring your lunch to eat nearby.