Software Carpentry: Christian Albrechts University, Kiel

Christian Albrechts University, Kiel

Am Botanischen Garten 7, R.E49 - PC-room, Kiel
Aug 21-22, 2014
9:00 am - 4:00 pm

General Information

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. 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 research problems during and between sessions. At the end of the bootcamp you should be able to conduct the following tasks with two python scripts: 1.) read in data from a file and load the data into a sql-database 2.) read out data from a sql-database and generate different outputs (summarized data, figures) Furthermore, you should be able to better organize your file system and to keep your work under version control

Instructors: Rainer Kiko, Bernhard Konrad

Helpers: Pieter Vandromme, Pina Springer

Who: The course is aimed at postgraduate students and other scientists who are not or only slightly familiar with scripting or writing programs. Registration is now open for members of the Kiel scientific community.

Where: Am Botanischen Garten 7, R.E49 - PC-room, Kiel. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).

Contact: Please mail rkiko@geomar.de for more information.

Etherpad: Click here.

Schedule

Day 1

09:00	Welcome, Set up and installation check
10:00	Automating tasks with the Unix shell
11:00	Version control with Git
12:00	Lunch break
13:00	Version control with Git
14:30	Managing data with SQL
15:30	Wrap-up

Day 2

09:00	Introduction to Python
11:00	Managing SQL with Python
12:00	Lunch break
13:00	Data analysis with Python
14:00	Extracting Data from SQL and plotting with Python
15:30	Wrap-up

Setup

To participate in a Software Carpentry bootcamp, 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 bootcamp.

Windows

Editor

Please install Notepad++, which 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.

Git Bash

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

Python

Download and install Anaconda CE.
Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

PostgreSQL

Install PostgreSQL9.3.5.1.. You will find the PostgreSQL documentation here: http://www.postgresql.org/ To enable Python to work with PostgreSQL you need to install Psycopg2. For this download the appropriate release file from this site win-psycopg and execute it. The proper Python version is 2.7. If you have a 64-bit architecture, you will probably need the 64 bit version.

Mac OS X

Editor

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

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.

Git

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.

Python

Download and install Anaconda CE.
Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

PostgreSQL

Install PostgreSQL9.3.5.1.. You will find the PostgreSQL documentation here: http://www.postgresql.org/. To enable Python to work with PostgreSQL you need to install Psycopg2. For this install MacPorts. Then install psycopg2 using "sudo port install py27-psycopg2" in the terminal. We will help you to get this running during the bootcamp if you are not able to install it on your own.

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.

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 or yum).

Editor

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

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.)

Download the installer that matches your operating system and save it in your home folder.
Open a terminal window.
Type
```
bash Anaconda-
```
and then press tab. The name of the file you just downloaded should appear.
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).

PostgreSQL

Install PostgreSQL9.3.5.1. using "sudo apt-get install postgresql-9.3". You will find the PostgreSQL documentation here: http://www.postgresql.org/ To enable Python to interact with PostgreSQL you then need to "apt-get install python-dev", "apt-get install libpq-dev" and "pip install psycopg2" in the Terminal. Pip install only works if you have Python - Pip installed.