Mar 29-30, 2016
10:00 - 18:00
Instructors: Camille Marini, Jan Antolik, Loïc Estève, Maria Teleńczuk
Helpers: Andrew Davison, Bartosz Teleńczuk, Marcel Stimberg, Samuel Lelièvre
Please note that the workshop is fully booked
and no further registrations are possible. Only registered and accepted
participants will be admitted. Please make sure that you received an
acceptance email (“…we are happy to confirm your application
for the Software Carpentry course…” not just “…Your request registration has been saved…”).
If in doubt, please contact Loïc Estève (firstname.lastname@example.org).
If you want to be notified of future Software Carpentry courses, please leave your contact details in the Contact form.
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".
The teaching language of the course is English (but there will be helpers around that can assist in French).
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.
Access by RER : From Paris, take the RER B direction "Saint Remy lès Chevreuse", to the station Gif-sur-Yvette [Map of the RER network]. When you get off the train cross the train tracks via an underground tunnel, leave the station and walk in the direction of the town centre. Walk for about 500 m and turn left at the roundabout into Rue Henri Amodru. After another 200 m you will reach the post office on your left, turn right into Avenue Emile Thuau. Shortly before the main CNRS gate turn left into a narrow path leading into woods. Follow the path walking along the stream until you reach a bridge, turn left and go straight ahead for about 100 m, then turn right and walk till the entrance of building 32 [Map of the CNRS campus].
Contact: Please mail Loïc Estève ( email@example.com ) for any questions.
|09:30||Registration and help desk for installation problems + coffee and croissants|
|10:15||Automating tasks with the Unix shell (part 1)|
|11:30||Automating tasks with the Unix shell (part 2)|
|13:30||Automating tasks with the Unix shell (part 3)|
|14:45||Building programs with Python (part 1)|
|16:30||Building programs with Python (part 2)|
|09:30||Coffee and croissants|
|10:00||Building programs with Python (part 3)|
|11:30||Building programs with Python (part 4)|
|13:30||Version control with Git (part 1)|
|15:15||Version control with Git (part 2)|
|17:00||Case study: Contributing to an Open Source project|
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
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 and the following two files with example data:
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.
This will provide you with both Git and 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
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. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).
Git should be 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
After installing Git, there will not be anything in your
as Git is a command line program.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
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.
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).
cd DownloadsPress enter.
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).
Once you are done installing the software listed above, please go to this page, which has instructions on how to test that everything was installed correctly.