Feb 4-5, 2016
9:00 am - 5:00 pm
Instructors: Mariela Perignon, Rachel Schwartz
Helpers: Daniel Buscombe, Kristin Berry
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 scientists and engineers affiliated with the USGS. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Contact: Please mail email@example.com for more information.
|09:00||Automating tasks with the Unix shell|
|13:00||Building programs with Python|
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code. Keep the etherpad open in your browser during the workshop so you can quickly access it.
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.
Please install the software below even if you already have a working version of Python in your computer. A common set of software assures that everyone is working in the same environment as the instructors and minimizes time lost to troubleshooting.
Once you are done installing the software listed below, please go to this page, which has instructions on how to test that everything was installed correctly.
Contact the instructors if you run into trouble during installation. We also 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.
These instructions will install both Git and Bash (as the application Git Bash).
All versions of Mac OS X use bash as the default shell, so no installation is necessary. You access bash from the Terminal
/Applications/Utilities). You may want to keep
Terminal in your dock for this workshop.
The default shell in Linux is usually bash. If your
machine is set up differently, you can run bash by opening a
terminal and typing
bash. There is no need to
Git is a version control system that allows you to track changes made to documents, the author of those changes, and when they were made. It is most often used for coding projects, but almost any type of file can be tracked using git. It is also a powerful collaboration tool and can be used to easily share documents with the public through github.com. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above, are supported browsers).
Git should have 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
Git is a command line program, so this installation won't create any new files in the
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 should
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.
The text editors most of us regularly use are not optimized for writing code. An editor with features like automatic color-coding of key words and language-specific commenting make code much easier to read and edit, greatly increasing your productivity as a programmer and reducing frustration. We suggest you install one of several code-friendly text editors, but any simple text editor (that can save as plain text) will work.
There are also many situations where you might need to use a text editor within the command line. These programs don't have a GUI (Graphical User Interface) -- you interact with them exclusively by typing into the terminal. The text editor nano is easy to use and the one that instructors will use in the workshop.
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.
To install nano, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.
The text editor nano should be pre-installed in Mac OS X.
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 use Anaconda, an all-in-one installer. Make sure you install Python version 2.7.
Please install Anaconda even if you already have a working version of Python on your computer. Using a common environment helps workshops run smoothly and facilitate learning. It is easy to uninstall Anaconda after the workshop if you choose to not use it.
We will teach Python using the IPython notebook, a programming environment that runs in a web browser. 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).
SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.
The Software Carpentry Windows Installer installs SQLite for Windows. You don't need to run the installer again if you used it to install nano.
SQLite comes pre-installed on Mac OS X.
SQLite comes pre-installed on Linux.