Software Carpentry: University of British Columbia

General Information

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.

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: Earth, Ocean and Atmospheric Sciences, ESB-5104. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Contact: Please mail Susan Allen for more information.

Schedule

Tue 22-Sep

09:00	Automating tasks with the Unix shell
10:30	Break
11:50	Wrap-up

Wed 23-Sep

09:00	Version control with Mercurial
10:30	Break
11:50	Wrap-up

Thu 24-Sep

09:00	Building Programs with Python
10:30	Break
11:50	Wrap-up

Fri 25-Sep

09:00	More Python
10:30	Break
11:50	Wrap-up

Etherpad: https://etherpad.mozilla.org/RCWyhBJImc.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

Coffee, Tea and Snacks

Coffee, tea, and snacks will be provided during the mid-morning break each day of the workshop.

Syllabus

The Unix Shell

Introducing the Shell
Files and directories
Creating Things
Pipes and Filters
Loops
Shell Scripts
Finding things
Shell Command Reminders

Version Control with Mercurial

Automated Version Control
Configuring Mercurial
Creating a Repository
Tracking Files
Recording Changes
Exploring History
Recovering Old Versions
Ignoring Files
Remote Repositories
Working with Clone Repositories
Collaboration
Merging Changes from Different Clones
Merge Conflicts
Mercurial Command Reminders

Programming in Python

Analyzing Patient Data
Repeating Actions with Loops
Storing Multiple Values in Lists
Analyzing Data from Multiple Files
Making Choices
Python Command Reminders

Programming in Python (cont'd)

Creating Functions
Errors and Exceptions
Command-Line Programs
Python Command Reminders

Workshop Introduction Slides

Setup

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.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

Download the Git for Windows installer. Run the installer. Important: on the 6th page of the installation wizard (the page titled `Configuring the terminal emulator...`) select `Use Windows' default console window`. If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option. This will provide you with Bash in the Git Bash program.

Mac OS X

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

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

Mercurial 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 bitbucket.org. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 10 or above).

If you don't already have one, please create an account for yourself on bitbucket.org.

Windows

Install Mercurial and KDiff3 by downloading and running the TortoiseHg installer.

Mac OS X

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 Mac section of the KDiff3 page in the Mercurial wiki 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.

Linux

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.

Text 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.

Windows

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.

Mac OS X

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 or Sublime Text.

Linux

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.

Python

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).

Windows

Open http://continuum.io/downloads with your web browser.
Click on "I want Python 3.X" link.
Download this Python 3 installer.
Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Open http://continuum.io/downloads with your web browser.
Click on "I want Python 3.X" link.
Download this Python 3 installer.
Install Python 3 using all of the defaults for installation.

Linux

Open http://continuum.io/downloads with your web browser.
Click on "I want Python 3.X" link.
Download this Python 3 installer, save it in your home folder.
Install Python 3 using all of the defaults for installation. (Installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help from one of the instructors before the workshop.)
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 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).

If you are comfortable running Python scripts from the command-line, there are isntructions on this page about how to test that everything was installed correctly. If not, just install the software as described above.