Aug 29 - Sept 1, 2016
8:30 am - 13:00 pm
Instructors: Cameron Macdonell, Juan Steyn
Helpers: Adewale W. Adeogun, Caroline F. Ajilogba, Martin Dreyer, Anelda van der Walt
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".
This event forms part of a series of Software and Data Carpentry workshops which are run by newly qualified African-based instructors in collaboration with international mentors. The workshops form part of a twelve month program developed by the North-West University, University of Cape Town, Talarify, the Software Carpentry Foundation, Data Carpentry, and Mozilla Science Labs. For more information about the programme, please see A Programme for the Development of Computational and Digital Research Capacity in South Africa and Africa.
Who: The course is aimed at graduate students and other researchers from all disciplines, including but not limited to humanities and social sciences, biological and life sciences, economics, engineering, physical sciences. Limited space is available. Preference will be given to those affiliated with the North-West University. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Cost: A R500 non-refundable registration is payable. The fee covers workshop expenses.
Meals: Tea/Coffee and light snacks will be served at 10:30 daily. No lunch is provided.
Registration: Please register at https://goo.gl/forms/9cN0osLIpYvTNlAp1
Where: Mafikeng Campus, Albert Luthuli & University Drive, Mmabatho, Mahikeng, 2790, South Africa. Get directions with OpenStreetMap or Google Maps.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers have checked that:
Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch and we will attempt to provide them.
Contact: Please mail eresearch@nwu.ac.za for more information.
Surveys
Please be sure to complete these surveys before and after the workshop.
| 08:30 | Introducing Software & Data Carpentry and Reproducible Research |
| 09:30 | Better Use of Spreadsheets |
| 10:30 | Coffee |
| 11:00 | OpenRefine for Cleaning Data |
| 13:00 | Break |
| 14:00 | Open Discussion About Own Projects |
| 15:00 | Wrap-up |
| 08:30 | Automation of Repetitive Tasks Using the Shell |
| 10:30 | Coffee |
| 11:00 | Automation With the Shell (continues) |
| 13:00 | Break |
| 14:00 | Open Discussion About Own Projects |
| 15:00 | Wrap-up |
| 08:30 | Python for Reproducible Research |
| 10:30 | Coffee |
| 11:00 | Python for Reproducible Research (continues) |
| 13:00 | Break |
| 14:00 | Open Discussion About Own Projects |
| 15:00 | Wrap-up |
| 08:30 | Python for Reproducible Research (continues) |
| 10:30 | Coffee |
| 11:00 | Python for Reproducible Research (continues) |
| 12:45 | Wrap-up |
| 13:00 | Workshop ends |
Etherpad: http://pad.software-carpentry.org/2016-08-29-nwu-mafikeng.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
add, commit, ...status, diff, ...clone, pull, push, ...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.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
cmd and press [Enter])setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.exit then pressing [Enter]This will provide you with both Git and Bash in the Git Bash program.
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).
See the Git installation video tutorial
for an example on how to open the Terminal.
You may want to keep
Terminal in your dock for this workshop.
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 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. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).
You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.
Git should be installed on your computer as part of your Bash install (described above).
For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
this list.
After installing Git, there will not be anything in your /Applications folder,
as Git is a command line program.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
available here.
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.
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.
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.
nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.
Others editors that you can use are Text Wrangler or Sublime Text.
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 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).
bash Anaconda3-and then press tab. The name of the file you just downloaded should appear.
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).
For this workshop you will need a spreadsheet program. Many people already have Microsoft Excel installed, and if you do, you're set!
If you need a spreadsheet program, there are a few other options, like OpenOffice and LibreOffice. Install instructions for LibreOffice, which is free and open source, are here.
OpenRefine (previously Google Refine) is a tool for data cleaning that runs through a web browser, and any browser - Safari, Firefox, Chrome, Explorer - should work fine. You will need to download OpenRefine and install it, and when you open it, it will run through the browser, but you don't need an internet connection, and the data will all be stored on your computer.
http://localhost:3333 and you should see OpenRefine.
http://localhost:3333 and you should see OpenRefine.
http://localhost:3333 and you should see OpenRefine.
OpenRefine may require you to install Java, please follow the instructions it provides to do so.