University of Waterloo
Engineering 6 room 4022, 200 University Ave, WaterlooMarch 21-22, 2015
9:00 am - 4:30 pm
General Information
Software Carpentry's mission is to help scientists and engineers become more productive by teaching them basic skills for computing like program design, version control, data management, and task automation. This two-day hands-on bootcamp will cover basic concepts and tools with a focus on scientific computing for first-year graduate students. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.
Instructors: Nasser M Abukhdeir, Pawel Pomorski, Albert O'Connor
Helpers: WatPy, SHARCNET
Who: The course is aimed at incoming graduate students who wants to learn basic program skills, Python and scientific computing.
Where: Engineering 6 room 4022, 200 University Ave, Waterloo. Get directions with OpenStreetMap or Google Maps.
Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).
Contact: Please mail nmabukhdeir@uwaterloo.ca for more information.
Schedule
Day 1
| 09:00 | Automating tasks with the Unix shell |
| 10:30 | Coffee break |
| 10:45 | Intro to Source Control |
| 12:00 | Lunch break |
| 13:00 | Intro to Python |
| 14:30 | Coffee break |
| 14:45 | Coding Practice |
| 16:00 | Wrap up |
Day 2
| 09:00 | Numpy |
| 10:30 | Coffee break |
| 10:45 | Numpy |
| 12:00 | Lunch break |
| 13:00 | Plotting with PyLab |
| 14:30 | Coffee break |
| 14:45 | Practice Problem Session |
| 16:00 | Wrap up |
Syllabus
The Unix Shell
Course Materials- Files and directories:
pwd,cd,ls,mkdir, ... - History and tab completion
- Pipes and redirection
- Looping over files
- Creating and running shell scripts
- Finding things:
grep,find, ... - Reference...
Programming in Python
Course Materials- Using libraries
- Working with arrays
- Reading and plotting data
- Creating and using functions
- Loops and conditionals:
for,if,else, ... - Defensive programming
- Using Python from the command line
- Reference...
Version Control with Mercurial
Course Materials- Version control for text based files
- Creating a repository
- Recording changes to files:
add,commit, ... - Viewing changes:
status,diff, ... - Ignoring files
- Working on the web:
clone,pull,push, ... - Resolving conflicts
- Open licenses
- Where to host work, and why
Setup
To participate in a Software Carpentry bootcamp, you will need working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of your bootcamp.
Overview
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. 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.
There are many cross platform options, such as Sublime Text or Atom. If you don't have a preference, we recommend Komodo Edit for Python. Komodo Edit is free, although they do sell an upgraded version called Komodo IDE.
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.
Mercurial
Mercurial 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 bitbucket.org.
Python
Python is becoming very popular in scientific computing, and it's a great language for teaching general programming concepts due to its easy-to-read syntax. We teach with Python the latest version 3.4.x.
If you just want to learn Python and aren't interested in NumPy, you can install Python for your system
directly from python.org or use your system Python if it is 3.4 (try running python3 on your command line). If your goal is scientific computing, individually installing all the scientific packages for Python can be a bit difficult,
so we recommend an all-in-one installer.
Windows
Python
- Download and install Anaconda full installer. Make sure you are downloading the 3.4 version not the 2.7 version.
Bash and Mercurial
Download and install Cygwin. During the installation process, at the "Choose A Download Site" stage specify the UW mirror: http://mirror.csclub.uwaterloo.ca/cygwin/ in the "User URL" box, then click "Add", then select the newly added mirror before clicking "Next". During the "Select Packages" stage search/install the mercurial package located under Python, as well as the nano package located under Editors. In both cases click the "Skip" button to enable installation .
Mac OS X
Bash
The default shell in all versions of Mac OS X is bash, so there is no need to install anything extra. You access bash from
the Terminal (found in /Applications/Utilities). You may want to keep Terminal in your dock for this workshop.
Mercurial
Download a binary installer for Mercurial which matches your Mac OS X version.
Python
- Download and install Anaconda full installer. Make sure you are downloading the 3.4 version not the 2.7 version.
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.
Mercurial
If Mercurial is not already available on your machine (type hg in a shell) then install it using your distro's package manager
(e.g. apt-get install mercurial).
Editor
A useful general purpose editor such as gedit should already be installed as part of your Linux distribution.
Python
Python should be installed on your machine by default, but you will need to install Python packages for the numerical part of the workshop. Download and install Anaconda full installer. Make sure you are downloading the 3.4 version not the 2.7 version.