University of Cape Town
TS 3B and TS 3C, Snape Building, Upper CampusNov 27-28, 2014
9:00 am - 5:00 pm
General Information
Software Carpentry's mission is to help scientists and engineers 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 bootcamp 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.
Instructors: Jonah Duckles (University of Oklahoma, USA), James Hetherington (University College London, UK), , David Merand (University of the Witwatersrand, South Africa)
Helpers: Dane Kennedy (CSIR), Hein de Jager (UCT), Ashley Rustin (UCT), David Matten (SU), Armin Deffur (UCT), Anelda van der Walt (UCT), Warren Jacobus (UWC), Chris Mitsengu (UCT), Gustavo Salazar (UCT), Jon Ambler (UCT), Benjamin Hugo (UCT), Jon Zwart (UCT), Adrianna Pinska (UCT), Timothy Povall (UCT)
Who: The course is aimed at postgraduate students, post-docs and other researchers affiliated with South African or African academic or research institutes with a specific focus on Bioinformatics and Astronomy although a number of seats will be reserved for students in other research areas. Two parallel workshops will be run – introductory level python, shell, etc and advanced research software development.
Where: TS 3B and TS 3C, Snape Building, Upper Campus. 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 admin@software-carpentry.org for more information.
Registration
Cost: ZAR 500.00 (Course fees will contribute to international trainers’ travel cost as well as catering including tea breaks and lunch for all participants) To register, or to get more information, please, visit http://www.eresearch.ac.zaMore Information
The eResearch Africa Conference organizers in collaboration with the UCT eResearch Centre, the Council for Scientific and Industrial Research (CSIR) the South African National Bioinformatics Institute (SANBI), and Witwatersrand University (WITS) will be hosting the first South African Software Carpentry bootcamp back-to-back with the eResearch Africa Conference. The workshop is supported through a Knowledge, Interchange, and Collaboration grant awarded by the South African National Research Foundation and donations from SANBI and UCT ICTS.
The organisers’ vision is to build software development capacity in South Africa and Africa through partnering with Software Carpentry, to support ongoing training initiatives in research communities where limited computational proficiency is hampering analysis in data-intensive research projects. To this effect we are hoping to train both novices and participants who themselves may proceed to become Software Carpentry instructors and participate in future local Software Carpentry bootcamps and other research software development workshops
The workshop will be open to any postgraduate students and researchers affiliated with academic or research institutes in South Africa and the rest of Africa with preferene given to those involved in Bioinformatics and Astronomy.
Schedule
Day 1
| 09:00 | Automating tasks with the Unix shell |
| 10:30 | Tea (New Engineering food court) |
| 11:00 | Unix shell (cont) |
| 12:30 | Lunch break (New Engineering food court) |
| 13:30 | Git local |
| 15:00 | Tea (New Engineering food court) |
| 15:30-17:00 | Git remote |
Day 2
| 09:00 | Python block 1 |
| 10:30 | Tea (New Engineering food court) |
| 12:30 | Lunch break |
| 13:00 | Python Block 2 |
| 15:00 | Tea (New Engineering food court) |
| 16:00-17:00 | Wrap-up |
Syllabus
The Unix Shell
- 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
- 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 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...
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.
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.
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.
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.
Windows
Python
- Download and install Anaconda.
- Use all of the defaults for installation except make sure to check Make Anaconda the default Python.
Git Bash
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.
Editor
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
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.
Editor
We recommend
Text Wrangler or
Sublime Text.
In a pinch, you can use nano,
which should be pre-installed.
Git
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.
Python
- Download and install Anaconda.
- Use all of the defaults for installation except make sure to check Make Anaconda the default Python.
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.
Git
If Git is not already available on your machine you can try
to install it via your distro's package manager
(e.g. apt-get or yum).
Editor
Kate is one option for Linux users.
In a pinch, you can use nano,
which should be pre-installed.
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
yesand press enter to approve the license. Press enter to approve the default location for the files. Typeyesand press enter to prepend Anaconda to yourPATH(this makes the Anaconda distribution the default Python).