Harvard University

Phillips Auditorium at the Center for Astrophysics, 60 Garden Street
August 23-24, 2013
9:00 am - 4:30 pm

Instructors: Erik Bray, Jessica McKellar, R. David Murray, Mike Selik

What: Our goal is to help librarians and graduate students become more productive by teaching them basic computing skills like program design, version control, testing, and task automation. In this two-day boot camp, short tutorials will alternate with hands-on practical exercises. Participants will be encouraged both to help one another, and to apply what they have learned to their own library-related problems during and between sessions.

Who: The course is aimed at librarians and graduate students who are new to programming and need help familiarizing themselves with different aspects of the research data lifecycle. The topics covered will help attendees build better library data services and work more productively.

Requirements: Participants must bring a laptop with a few specific software packages installed. (The list will be sent to participants a week before the boot camp.)

Content: The syllabus for this boot camp will include:

Contact: Please mail harvard@lists.software-carpentry.org for more information.


Etherpad for Day 1: https://swcarpentry.etherpad.mozilla.org/2013-08-23-harvard

Etherpad for Day 2: https://swcarpentry.etherpad.mozilla.org/2013-08-24-harvard

Schedule

Day 1
9:00 - 9:30 Setup Help
9:30 - 10:00 Introduction
10:00 - 11:00 Shell I
11:00 - 11:10 Break
11:10 - 12:00 Shell II
12:00 - 1:00 Lunch
1:00 - 2:00 Python I
2:00 - 2:10 Break
2:10 - 3:10 Python II
3:10 - 3:30 Wrap-up
Day 2
9:30 - 10:00 Review / Questions
10:00 - 11:00 Python III
11:00 - 11:10 Break
11:10 - 12:00 Python IV
12:00 - 1:00 Lunch
1:00 - 2:00 Version Control I
2:00 - 2:10 Break
2:10 - 3:10 Version Control II
3:10 - 4:10 Regular Expressions
4:10 - 4:30 Wrap-up

Setup

The following is an overview of the software you will need for this bootcamp. Below the overview are recommendations for specific operating systems. We strongly recommend installing this software ahead of time so that the workshop can get off to a smooth start for everyone. If you have trouble installing any of the recommended software please do not hesistate to contact the mailing list for this workshop and one of the instructors should be able to help you. There may also be some time the morning of to help with any installation issues that may arise.

The Bash Shell

Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.

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.

Git

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

Python is becoming more and more popular in scientific computing, and it's a great language for teaching general programming concepts due to its easy-to-read syntax. We will be using Python version 2.7. Installing all the scientific packages for Python individually can be a bit difficult, so we recommend using an all-in-one installer.

Windows Setup

The Git installer for Windows includes a simple UNIX-like environment for Windows. This includes a Bash shell prompt which you can launch from the icon labeled "Git Bash. As Git was originally developed for use on Linux it works best in that environment. It's worth having this environment in Windows in part to provide a consistent command-line interface across all learners at the bootcamp. It may also come in handy in the future so that you only have to learn one command-line environment (rather than learning a UNIX command line and the native Windows command line).

Windows / Editor

Notepad++ is a popular free code editor for Windows.

Windows / Git Bash

Install Git Bash following the instructions here. This gives you Bash as well as Git.

Windows / Python

For Windows we recommend the Enthought Canopy distribution since it seems to work well with Git Bash.

For other options check the Python4Astronomers page on installing scientific Python.

Mac OSX Setup

Mac OS X / 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 (found in /Applications/Utilities). You may want to keep Terminal in your dock for this workshop.

Mac OS X / Git

Installing Git may require you to first install XCode. This is a very large download (several gigabytes), so please do it before arriving at the bootcamp.

For Mac OS X 10.7 and 10.8:

Go to the Xcode website. Get XCode from the App Store making certain to install the command line tools (from the Download preferences pane). Git is included in the command line tools.

For Mac OS X 10.6

If you have Mac OS X 10.6, first get XCode by going to the Apple developer site. You have to sign in with an Apple ID linked to a Developer account. If you don't have one, you can register and create one. Once you log in, go to page 8 and find "XCode 3.2.6 and iOS SDK 4.3 for Snow Leopard". Click to open that section, and then download the .dmg file. Finally, install just git.

Mac OS X / Editor

We recommend Text Wrangler or Sublime Text.

Mac OS X / Python

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.
  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).

Linux Setup

Linux / Bash

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.

Linux / Editor

Kate is one option for Linux users.

Linux / Git

If Git is not already available on your machine you can try to install it via your distro's package manager (e.g. apt-get).

Linux / Python

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.
  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).

Lesson Notes


Reference Guides