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 three-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: Aron Ahmadia, Chris Kees
Who: This is an internal training for FRF members.
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.
|09:00||Introduction and Overview|
|09:30||Automating Your Actions|
|10:45||Functions and Pipelines|
|13:00||Fundamentals of Python|
|14:45||Fundamentals of Python|
|09:00||Introduction to Version Control with Git|
|10:45||The Git Developer's Workflow|
|13:00||Introduction to the IPython Notebook (Jupyter)|
|13:30||Scientific Computing with NumPy and SciPy|
|14:45||Visualization with Matplotlib|
|15:15||Advanced Jupyter: Widgets|
|16:00||Advanced Jupyter: The SPOD Tools|
|09:00||Testing in Python|
|10:45||The Scientific Software Engineer's Toolbox: Consoles, IDEs, Notebooks, and when to use them|
|13:00||Distributed, Continuous Development: Git, GitHub, Slack, and Travis|
To participate in this workshop 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 workshop.
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.
Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.
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.
Windows users will need to complete one last step. After installing both Python and Git Bash, download this file, making sure that it has a
.py extension on the end when you save it. Next, open Git Bash and type each of these three commands, hitting Return after each one:
python swc-windows-installer.py. You'll see a blinking underscore for a bit, and then eventually you'll once again see a
$ symbol with the blinking underscore after it. You can close Git Bash at this point.
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.
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 available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.
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.
We recommend the all-in-one scientific Python installer Anaconda.
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).
To test that your system is configured properly, complete the following four steps. If any of these do not succeed, or if you run into any other trouble, please email Aron Ahmadia immediately.
ipythonand hit Return. After a few seconds, you should see some text printed on your screen that starts with a line like "Python 2.7.6 | Anaconda 1.9.0". Hit
Ctrl-dtwice to return to the command line.
nano --versionand hit Return. You should see some text printed on your screen that starts with something like "GNU nano version 2.0.6".
git --versionand hit Return. You should be see something like "git version 22.214.171.124" printed on your screen.