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: Cliburn Chan, Karen Cranston, Joshua Granek
Who: The course is aimed at graduate students and other researchers.
Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).
Contact: Please mail firstname.lastname@example.org for more information.
We willl be using Etherpad to receive real-time comments.
|Monday||08:30||Software installation help|
|09:00||Using a text editor|
|10:30||Working with the Unix Shell|
|13:00||Version control with Git|
|15:00||Introduction to Python|
|Tuesday||09:00||Writing Python functions|
|10:30||I/O and Python modules|
|13:00||Managing data with SQL|
|15:00||Putting it all together|
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.
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.
Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.
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 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.
SQL is a specialized programming language used with databases. We use a simple database manager called SQLite, either directly or through a browser plugin.
Install Git for Windows by download 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 Python and Git Bash:
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.
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
/Applications/Utilities). You may want
to keep Terminal in your dock for this workshop.
The default shell is usually
but if your machine is set up differently
you can run it by opening a terminal and typing
There is no need to install anything.
If Git is not already available on your machine you can try
to install it via your distro's package manager
Kate is one option for Linux users.
In a pinch, you can use
which should be pre-installed.
sqlite3 comes pre-installed on Linux.
Please also install the Firefox SQLite browser plugin described below.
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).
Instead of using
sqlite3 from the command line,
you may use this plugin
for Firefox instead.
To install it: