Dec 11-12, 2014
9:00 am - 5:00 pm
Instructors: Alistair Grant, Norman Gray
Helpers: Paul Mullen, Sean Leavey, Gavin Kirby
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.
Who: The course is aimed at graduate students and other researchers.
If for some reason you won't be able to bring a laptop to the workshop, we should be able to lend you one. Get in touch with firstname.lastname@example.org promptly.
Contact: Please mail email@example.com for more information.
|09:00||Introduction and software set-up|
|10:00||Version control with Git|
|11:00||Version control with Git|
|14:00||Building programs with Python|
|15:30||Building programs with Python|
|09:00||Automating tasks with Make|
|11:00||Automating tasks with Make|
|13:00||How (and how much) to test programs|
|15:00||How (and how much) to test programs|
|16:00||Best practices for scientific computing|
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.
Kate is one option for
Linux users. In a pinch, you can use
should be pre-installed.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
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:
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 the installer. For older versions of OS X (10.5-10.7) use the most recent available installer for your OS available 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).
Originally invented to manage compilation of programs written in languages like C, Make can be used to automatically update any set of files that depend on another set of files. This makes it a good solution for many data analysis and data management problems. While there are many build tools now in existence (e.g. ANT and CMake) they share the same fundamental concepts as Make.
Once you have installed Git Bash you can install Make by:
bindirectory where you installed Git Bash e.g.
C:\Program Files (x86)\Git\bin.
make, and press Enter.
make: *** No targets specified and no makefile found. Stop.This means that Make was successfully installed. Otherwise, you'll see this error message:
bash: make: command not found
For OS X, version 10.9 (Mavericks) or above, download the Command Line Tools by doing:
For more information, see the OSX Daily blog.If you have an over OS X version and you do not already have access to
makefrom within your shell, you will need to install XCode (which is free, but over a gigabyte to download).
Once XCode has installed:
You will now be able to run
make within your shell.
Make is a standard tool on Linux systems and should already be available.
Running the below scripts can help highlight any issues with your setup from the above instructions.
To check you have the necessary software and tools: