Instructors: Bernhard Konrad, Jenny Bryan, Tommy Guy, Christina Koch, Lynne Williams, Trevor King
What: Our goal is to help scientists and engineers become more productive by teaching them basic computing skills like program design, version control, testing, and task automation. In this two-day bootcamp, 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 research problems during and between sessions. Attendants are offered online office hours: regular events to get one-on-one help from Software Carpentry instructors, online.
Who: The course is aimed at postgraduate students and other scientists who are familiar with basic programming concepts (like loops, conditionals, arrays, and functions) but need help to translate this knowledge into practical tools to help them 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 bootcamp.)
Content: The syllabus for this bootcamp will include:
Contact: Please mail admin@software-carpentry.org for more information.
Time | Python | R |
---|---|---|
8:30 - 9:00 | Setup help | Setup help |
9:00 - 9:15 | Overview and introduction | Overview and introduction |
9:15 - 10:45 | Navigating in the shell | R basics |
10:45 - 11:00 | Break | Break |
11:00 - 12:15 | Shell scripts and automation | Care and feeding of R objects |
12:15 - 1:15 | Lunch | Lunch |
1:15 - 2:45 | Version Control | Version Control |
2:45 - 3:00 | Break | Break |
3:00 - 4:30 | Version Control (remote) | Data Visualization |
Time | Python | R |
---|---|---|
8:30 - 9:00 | Setup help | Setup help |
9:00 - 10:30 | Numpy, variables, slicing | File organization and debugging |
10:30 - 10:45 | Break | Break |
10:45 - 12:15 | Python flow control; Python functions | The shell and remote version control |
12:15 - 1:15 | Lunch | Lunch |
1:15 - 2:30 | Testing and command line arguments | Data aggregation with R |
2:30 - 2:45 | Break | Break |
2:45 - 4:25 | Intro to Databases | Automation and pipelines |
4:25 - 4:30 | Wrap-up | Wrap-up |
For the Python class, please install the Bash shell, a text editor, Git, Python, and SQLite.
For the R class, please install the Bash shell, Git, R, and RStudio.
Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.
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.
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.
Install Git for Windows by downloading and running the installer. This will provide you with both Git as well as Bash in the Git Bash program.
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.
Kate is one option for Linux users.
We recommend Text Wrangler or Sublime Text.
Notepad++ is a popular free code editor for Windows.
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.
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
).
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.
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.
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.
Install Git for Windows by downloading and running the installer. This will provide you with both Git as well as Bash in the Git Bash program.
Please follow these install instructions for R and RStudio.
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.
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.)
bash Anaconda-and then press tab. The name of the file you just downloaded should appear.
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).
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.)
bash Anaconda-and then press tab. The name of the file you just downloaded should appear.
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).
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.
SQLite is a software library that implements a self-contained, serverless, zero-configuration, transactional SQL database engine.
sqlite-shell-linux-x86-SOMENUMBERS.zip
from the SQLite download page.
sqlite-shell-osx-x86-SOMENUMBERS.zip
from the SQLite download page.
SQLite3
to your Applications
folder.
sqlite-shell-win32-x86-SOMENUMBERS.zip
from the SQLite download page.
sqlite.exe
into C:\Windows
.