Software Carpentry: Edmonton Public Library

Edmonton Public Library

Dec 15 & 16 2014

9:00 am - 4:00 pm

Instructors: Cam MacDonell, Vicky Varga

Helpers: Cody Moorhouse, Katie Thompson

General Information

Software Carpentry's mission is to help scientists, engineers and librarians become more productive by teaching them basic lab skills for computing like program design, version control, data management, and task automation. This two-day hands-on workshop will cover basic concepts and tools; participants will be encouraged to help one another and to apply what they have learned to their own research problems.

Who: The course is aimed at librarians with an interest in using programming to improve their workflow.

Where: 3rd floor Training Room, 7 Sir Winston Churchill Square. 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 vvarga@epl.ca for more information.

Schedule

Day 1

09:00	Bash and python review
10:30	Coffee break
12:00	Lunch break
13:00	Getting started with SQL
14:30	Coffee break
16:00	Wrap-up, poll for next day's content

Day 2

09:00	Regular expressions and cleaning data with Open Refine OR further work with SQL
10:30	Coffee break
12:00	Lunch break
13:00	Programming with python and SQL
14:30	Coffee break
16:00	Wrap-up

Syllabus

The Unix Shell

Files and directories: pwd, cd, ls, mkdir, ...
History and tab completion
Pipes and redirection
Looping over files
Finding things: grep, find, ...
Reference...

Programming in Python

Using libraries
Working with arrays
Reading data
Creating and using functions
Loops and conditionals: for, if, else, ...
Using Python from the command line
Reference...

Managing Data with SQL

Reading and sorting data
Filtering with where
Calculating new values on the fly
Handling missing values
Combining values using aggregation
Combining information from multiple tables using join
Creating, modifying, and deleting data
Programming with databases
Reference...

Setup

To participate in a Software Carpentry workshop, 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 workshop.

Overview

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.

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 version 2.7, since it is still the most widely used. Installing all the scientific packages for Python individually can be a bit difficult, so we recommend an all-in-one installer.

SQL

SQL is a specialized programming language used with databases. We use a simple database manager called SQLite, either directly or through a browser plugin.

Windows

Python

Download and install Anaconda.
Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Editor

Download and install Wing 101.

SQLite

Download the sqlite3 program and put it in the directory where you are running examples. Alternatively, you may install the Firefox SQLite browser plugin described below.

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.

Python

Download and install Anaconda.
Use all of the defaults for installation except make sure to check Make Anaconda the default Python.
Troubleshooting: If you get the following error message "ValueError unknown locale: UTF-8", see instructions on how to fix it here.

Editor

Download and install Wing 101.

SQLite

sqlite3 comes pre-installed on Mac OS X. Alternatively, you may install the Firefox SQLite browser plugin described below.

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.

SQLite

sqlite3 comes pre-installed on Linux. Alternatively, you may install the Firefox SQLite browser plugin described below.

Editor

Download Wing 101

Python

We recommend the all-in-one scientific Python installer Anaconda. (Installation requires using the shell and if you aren't comfortable doing the installation yourself just download the installer and we'll help you at the boot camp.)

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 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).

All operating systems

Firefox SQLite Plugin

Instead of using sqlite3 from the command line, you may use this plugin for Firefox instead. To install it:

Start Firefox.
Go to the plugin homepage.
Click the "Add Now" button.
Click "Install Now" on the dialog that appears after the download completes.
Restart Firefox when prompted.
To check that the plugin installed correctly, select "SQLite Manager" from the "Tools" menu.

In newer versions of Firefox, the menu bar isn't always displayed. To make it appear, use the Alt key next to the space bar on your keyboard, or consult the support page from Firefox for additional help.