Mar 16-17, 2015
9:00 am - 4:30 pm
Instructors: Greg Wilson, Ethan White
Helpers: Morgan Ernest, Allen Hurlbert, Paul Wolf, Erica Christensen, Sarah Reehl, David Harris, Andrew Kleinhesselink
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 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 workshop is designed for graduate students, postdocs, faculty, and other researchers who have a basic understanding of basic programming tasks like how to assign a value to a variable and how to use a for loop. If you have any questions about whether this is a good workshop for you please email Ethan White (firstname.lastname@example.org).
Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). If you do not have access to a laptop, please email Ethan White (email@example.com) and access to a properly configured laptop can be arranged. Participants are also required to abide by Software Carpentry's Code of Conduct.
Accessibility: The Merrill-Cazier Library meets all Americans with Disabilities Act (ADA) physical facilities requirements. The room is on the ground floor near the entrance and there are accessible restrooms and dining options on the same floor of the building. Materials will be provided in advance of the workshop and large-print handouts are available are available if needed (please let us know in advance by emailing firstname.lastname@example.org). At this time we do not provide remote participation for this workshop, but are working on making this possible in the future. If you have other accessibility needs (e.g. sign-language interpreters, lactation facilities) please get in touch with Ethan White (email@example.com) and we will work hard to provide them.
Contact: Please mail firstname.lastname@example.org 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.
This page has instructions on testing that you have the right software installed.
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 the editor installed by the Software
Carpentry Installer, it is a basic editor integrated into the
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.
We'll be using
nano, which should be
We'll be using
nano, which should be
If you're looking for a more full featured editor Kate is one option for Linux users.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
Install Git for Windows by downloading and running the installer. This will provide you with both Git and Bash in the Git Bash program.
This installer requires an active internet connection.
After installing Git Bash:
Information about the SWC Windows Installer, including the source code, can be found at https://github.com/swcarpentry/windows-installer.
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
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.
Git should be installed on your computer as part of your Bash install (described above).
For OS X 10.8 and higher, install Git for Mac
by downloading and running
After installing Git, there will not be anything in your
as Git is a command line program.
For older versions of OS X (10.5-10.7) use the
most recent available installer for your
here. Use the Leopard installer for 10.5 and the Snow
Leopard installer for 10.6-10.7.
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 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.
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.)
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.