National Socio-Environmental Synthesis Center (SESYNC)
Dec 3-6, 2013
9:00 am - 4:30 pm
Instructors: Will Trimble, Amanda Whitlock, Bernhard Konrad, Aron Ahmadia, R. David Murray
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 boot camp, 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 boot camp.)
Content: The syllabus for this boot camp 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 mshelley@sesync.org for more information.
Setup
To participate, you will need working copies of bash, git, a Text editor, and python.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.
Windows / Git Bash
Install Git Bash following these instructions. This gives you Git as well as Bash.
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.
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.
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.
Windows / Editor
Notepad++ is a popular free code editor for Windows.
Mac OS X / Editor
We recommend Text Wrangler or Sublime Text.
Linux / Editor
Kate is one option for Linux users.
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.
Load the VM into VirtualBox by doing Import Appliance and loading the .ova file.
The ova file is 2Gbytes, and isn't anything special--it is just a linux
environment in which git and python work that we have as a backup.
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.
Windows / Git Bash
Install Git Bash following the instructions here. This gives you Bash as well as Git.
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.
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.
Windows / Python
For Windows we recommend the Enthought Canopy distribution since it seems to work well with Git Bash and usually "works" out of the box.
For other options check the Python4Astronomers page on installing scientific Python.
Mac OS X / Python
We recommend the all-in-one scientific Python installer Anaconda.
Lessons
Schedule
Subject to Change
| 8:30 - 8:45 | Breakfast, Setup Help | Breakfast, Setup Help |
| 8:45 - 9:00 | Overview | Overview |
| 9:00 - 10:30 | Navigating in the Shell; Python data types | Shell automation; Python data structures |
| 10:50 - 12:30 | Python data types | Python flow control; python debugging tools |
| 12:30 - 1:30 | Lunch | Lunch |
| 1:30 - 3:30 | Python Data structures | Python Data Structures |
| 3:50 - 4:30 | Python Flow Control | Python Functions and Modules |
| 9:00 - 10:30 | Version Control Local | Version Control Local |
| 10:50 - 12:30 | Version Control Remote | Version Control Remote |
| 12:30 - 1:30 | Lunch | Lunch |
| 1:30 - 3:30 | Python functions and modules; python testing | Python testing ; numpy |
| 3:50 - 4:30 | Shell automation; regular expressions | pandas; python regular expressions |
| 9:00 - 10:30 | Introduction to R(Ian Munoz) | 1:30 - 2:30 | Introduction to SQL (Mary Shelley) |
| Projects |
Chatrooms
- https://etherpad.mozilla.org/2013-12-03-sesync-intermediate
- https://etherpad.mozilla.org/2013-12-03-sesync-beginner