Find us on GitHub

Berkeley Institute for Data Science (BIDS)

Jun 4-5, 2015

9:00 am - 4:30 pm

Instructors: Katy Huff, Fatma Imamoglu, Thomas Kluyver, Daniel Turek

Helpers: Chris Holdgraf, Kunal Marwaha, Allison Ngo, Thomas Tu, Donny Winston, Qingpeng Zhang

General Information

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".

Who: The course is geared towards members of the broad UC Berkeley community, including faculty, staff, students, alumni, visitors, and affiliates of UC Berkeley and the Lawrence Berkeley National Laboratory. This workshop will target researchers with an intermediate level of programming experience, and possibly with some exposure to version control software or shell scripting.

To participate, please be able to:

  • Open a terminal.
  • Edit a plain text file.
  • Explain, to a friend, what a "for loop" is.
  • Be familiar enough with any computational tool (MATLAB, Java, C++, Python, etc.) to write a program which imports some data and calculates mean and standard deviation of that data.

If you do not have this skill level yet, please wait to sign up for the Novice workshop which will take place at the end of this summer.

Where: 190 Doe Library, University of California, Berkeley. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Contact: Please mail katyhuff@gmail.com for more information.

Schedule

Day 1: Thursday, 4 June

09:00 The Unix Shell (Fatma Imamoglu)
10:30 Coffee
12:00 Lunch break
13:00 Python Programming (Thomas Kluyver)
14:30 Coffee
16:00 Wrap-up

Day 2: Friday, 5 June

09:00 Version Control With Git (Daniel Turek)
10:30 Coffee
12:00 Lunch break
13:00 Testing (Katy Huff)
14:30 Coffee
16:00 Wrap-up

Etherpad: https://etherpad.mozilla.org/2015-06-04-berkeley.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

Syllabus

The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things
  • Reference...
  • Lesson index...

Programming in Python

  • Using libraries
  • Working with arrays
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Bonus material:
    • Machine learning with scikit learn
    • Parallel computing with multiprocessing
  • Reference...
  • Lesson index...

Version Control with Git

  • Creating a repository
  • Recording changes to files: add, commit, ...
  • Viewing changes: status, diff, ...
  • Ignoring files
  • Working on the web: clone, pull, push, ...
  • Resolving conflicts
  • Open licenses
  • Where to host work, and why
  • Reference...
  • Lesson index...

Testing

  • Assertions
  • Exceptions
  • Unit Testing
  • Continuous Integration
  • Integration Testing
  • Regression Testing
  • Test-Driven Development
  • Reference...
  • Lesson index...

Setup

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. Once you are done installing the software listed below, please go to this page, which has instructions on how to test that everything was installed correctly.

Text Editor

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.

Windows

nano is the editor installed by the Software Carpentry Installer, it is a basic editor integrated into the lesson material.

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.

Mac OS X

We recommend Text Wrangler or Sublime Text. In a pinch, you can use nano, which should be pre-installed.

Linux

Kate is one option for Linux users. In a pinch, you can use nano, which should be pre-installed.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

Install Git for Windows by downloading and running the installer. This will provide you with both Git and Bash in the Git Bash program.

Software Carpentry Windows Installer

It installs and configures nano (Among other things)

This installer requires an active internet connection.

After installing Git Bash:

Mac OS X

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 in /Applications/Utilities). You may want to keep Terminal in your dock for this workshop.

Linux

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 install anything.

Git

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).

Windows

Git should be installed on your computer as part of your Bash install (described above).

Mac OS X

For OS X 10.8 and higher, install Git for Mac by downloading and running the installer. After installing Git, there will not be anything in your /Applications folder, 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 OS available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.

Linux

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

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.

Regardless of how you choose to install it, please make sure you install Python version 3.x and not version 2.x (e.g., 3.4 is fine but not 2.7). We will teach this workshop using Python 3.

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).

Windows

  • Download and install Anaconda.
  • Download the Python 3 installer from that link (do not switch to version 2). Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

  • Download and install Anaconda.
  • Download the Python 3 installer from that link (do not switch to version 2). Use all of the defaults for installation.

Linux

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.)

  1. Download the installer that matches your operating system and save it in your home folder. Download the Python 3 installer (do not switch to version 2).
  2. Open a terminal window.
  3. Type 
    bash Anaconda-
    and then press tab. The name of the file you just downloaded should appear.
  4. Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
License Blog GitHub Twitter Issues