Sep 22-25, 2015
09:00 - 12:00
Instructors: Doug Latornell, Karina Ramos Musalem, Nancy Soontiens
Helpers: Jordan Aaron, Julia Gustavsen, Tereza Jarnikova, Katerena Kuksenok, Jie Liu, Idalia Machuca, Elise Olson, Kathi Unglert, Cindy Yu
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.
|09:00||Automating tasks with the Unix shell|
|09:00||Version control with Mercurial|
|09:00||Building Programs with Python|
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
Coffee, tea, and snacks will be provided during the mid-morning break each day of the workshop.
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.
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.
The default shell in all versions of Mac OS X is bash, so no
need to install anything. You access bash from the Terminal
/Applications/Utilities). 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
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.
Install Mercurial and KDiff3 by downloading and running the TortoiseHg installer.
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.
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.
please install the KDiff3 diff and merge tool.
It should also be available via your package manager.
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.
nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.
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 Anaconda-and then press tab. The name of the file you just downloaded should appear.
yesand press enter to approve the license. Press enter to approve the default location for the files. Type
yesand 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.