Software Carpentry: University of Glasgow

University of Glasgow

Dec 11-12, 2014

9:00 am - 5:00 pm

Instructors: Alistair Grant, Norman Gray

Helpers: Paul Mullen, Sean Leavey, Gavin Kirby

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.

Who: The course is aimed at graduate students and other researchers.

Where: Lab 323, Kelvin Building, G12 8SU. 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.

If for some reason you won't be able to bring a laptop to the workshop, we should be able to lend you one. Get in touch with norman@astro.gla.ac.uk promptly.

Contact: Please mail alistair.grant@ed.ac.uk for more information.

Schedule

Day 1

09:00	Introduction and software set-up
10:00	Version control with Git
10:30	Coffee break
11:00	Version control with Git
13:00	Lunch break
14:00	Building programs with Python
15:00	Coffee break
15:30	Building programs with Python
17:00	Close

Day 2

09:00	Automating tasks with Make
10:30	Coffee break
11:00	Automating tasks with Make
12:00	Lunch break
13:00	How (and how much) to test programs
14:30	Coffee break
15:00	How (and how much) to test programs
16:00	Best practices for scientific computing
17:00	Close

Syllabus

Version Control with Git

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
Reference...

Building programs with Python

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...

Automating tasks with Make

Make is not just for compiling code
Basic Tasks
Automatic Variables and Wildcards
Patterns
Variables
Reference...

How (and how much) to test programs

Can I do testing?
Big Tests and Little Tests
End to End
Unit Testing
Putting Tests Together
Reference...

Setup

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 the editor installed by the Software Carpentry Installer, it is a basic editor integrated into the lesson material.

Notepad++ is a popular free code editor for Windows. Be aware that you must add its installation directory to your system path in order to launch it from the command line (or have other tools like Git launch it for you). Please ask your instructor to help you do this.

Mac OS X

We recommend Text Wrangler or Sublime Text. In a pinch, you can use nano, which should be pre-installed.

Linux

Kate is one option for Linux users. In a pinch, you can use nano, which should be pre-installed.

The Bash Shell

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

Windows

Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.

Software Carpentry Installer

This installer requires an active internet connection.

After installing Python and Git Bash:

Download the installer.
If the file opens directly in the browser select File→Save Page As to download it to your computer.
Double click on the file to run it.

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.

Git

Git 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 github.com.

Windows

Git should be installed on your computer as part of your Bash install (described above).

Mac OS X

For OS X 10.8 and higher, install Git for Mac by downloading and running the installer. For older versions of OS X (10.5-10.7) use the most recent available installer for your OS available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.

Linux

If Git 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 git and for Fedora run sudo yum install git.

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 an all-in-one installer.

Windows

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

Mac OS X

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

Linux

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).

Make

Originally invented to manage compilation of programs written in languages like C, Make can be used to automatically update any set of files that depend on another set of files. This makes it a good solution for many data analysis and data management problems. While there are many build tools now in existence (e.g. ANT and CMake) they share the same fundamental concepts as Make.

Windows

Once you have installed Git Bash you can install Make by:

Download make.exe from here
Place it in the bin directory where you installed Git Bash e.g. C:\Program Files (x86)\Git\bin.
To test: open a Git Bash window, type make, and press Enter.
You should see the following message
```
make: *** No targets specified and no makefile found. Stop.
```
This means that Make was successfully installed. Otherwise, you'll see this error message:
```
bash: make: command not found
```

Mac OS X

For OS X, version 10.9 (Mavericks) or above, download the Command Line Tools by doing:

xcode-select  --install

For more information, see the OSX Daily blog.

If you have an over OS X version and you do not already have access to make from within your shell, you will need to install XCode (which is free, but over a gigabyte to download).

Go to the Apple app store
Search for XCode
Click Free
Click Install App

Once XCode has installed:

Click Applications
Click XCode
Select XCode→Preferences...
Click Downloads
Select Command Line Tools
Click Install

You will now be able to run make within your shell.

Linux

Make is a standard tool on Linux systems and should already be available.

Quick Setup Test

Running the below scripts can help highlight any issues with your setup from the above instructions.

Download swc-installation-test-1.py
Open up a bash shell
Change into the directory where you put the script
Run the script:
```
python swc-installation-test-1.py
```

To check you have the necessary software and tools:

Download swc-installation-test-2.py
Open up a bash shell
Change into the directory where you put the script
Run the script:
```
python swc-installation-test-2.py
```