Chicago FED

Nov 1-2, 2016

9:00am - 5:00pm

Instructors: Dirk Eddelbuettel, Kyler Brown

Helpers:

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 aimed at research assisantants and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: 230 South LaSalle St, Chicago, IL 60604. Get directions with OpenStreetMap or Google Maps.

Requirements: Typically, participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.
However, for this workshop, computers will be provided.

Contact: Please email edd@debian,org for more information.


Schedule

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Day 1

08:30 Breakfast
09:00 Automating tasks with the Unix shell: Shell
10:30 Coffee
10:45 Automating tasks with the Unix shell: Make
12:00 Lunch break
13:00 Basic Programming with Matlab
14:30 Coffee
14:45 Basic Programming with Matlab (continued)
16:00 Wrap-up

Day 2

08:30 Breakfast
09:00 Version control with Git
10:30 Coffee
09:00 Version control with Git (continued)
12:00 Lunch break
13:00 Advanced Matlab
14:30 Coffee
14:45 Advanced Matlab (continued)
16:00 Wrap-up

Etherpad

Etherpad: http://pad.software-carpentry.org/2016-11-01-chifed.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

Files

Use e.g. curl -s -k -L -O URL on these URLs:


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...

Automation and Make

  • Making results easier to reproduce
  • Writing simple Makefiles
  • Abbreviating rules in Makefiles
  • Dependencies on Data and Code
  • Using Pattern in Rules
  • Eliminate Redundancy in Makefiles
  • Self-Documenting Makefiles
  • Advantages and disadvantages of using tools like Make
  • Reference...

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...

Programming in MATLAB

  • Working with arrays
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Defensive programming
  • Reference...

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. For this workshop, participants will be given suitable machines so the following section does not strictly apply. It is left as a reference in case a personal computer or laptop is need of a similar setup.

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.

The Bash Shell

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

Windows

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on "Next".
    2. Click on "Next".
    3. Keep "Use Git from the Windows Command Prompt" selected and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Keep "Use Windows' default console window" selected and click on "Next".
    7. Click on "Install".
    8. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

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). See the Git installation video tutorial for an example on how to open the Terminal. 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).

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Windows

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

Mac OS X

Video Tutorial

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. 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 (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

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.

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

Video Tutorial

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.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

Mac OS X

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Others editors that you can use are Text Wrangler or Sublime Text.

Linux

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.