Software Carpentry: University of Helsinki

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 two plus one day hands-on workshop will cover basic concepts and tools; participants will be encouraged to help one another and to apply what they have learned to their own research problems. The goal of the workshop is for participants to acquire skills to:

enable automation of repetitive tasks
version control code for reuse and collaboration
introduce basic programming concpets using Python
improve the reproducibility of your research

This workshop is supported by the DENVI doctoral programme in interdisciplinary environmental sciences. Priority will thus be given to DENVI-affiliated students.

Who: The course is aimed at graduate students, staff, faculty and other researchers at the University of Helsinki. No previous experience with programming is required. If you do have experience in the topics in the syllabus and want to help, send us an email.

Where: Days 1 and 2 in seminar room Aura at the Finnish Meteorological Institute (FMI), Erik Palménin aukio 1. Day 3 in room K232 at the Minerva Plaza Learning Environment, Siltavuorenpenger 9.

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.

No previous programming skills or experience is required, although they will be useful. The lesson contents and exercises are aimed at novices.

Registration: Please sign up using the registration form (maximum number of sudents: 35).

Contact: Please mail joona.lehtomaki@helsinki.fi for more information.

For more information on what Software Carpentry teaches and why, please see this paper "Best Practices for Scientific Computing".

Schedule

The workshop constitutes of three days. On days 2 (Thursday) and 3 (Friday) the morning sessiosn will be on actual lessons while the afternoon sessions are more freeform and you will have a chance to apply what you have learned on your own work. In practice you could for example:

Automate geospatial data converstion using a simple bash script
Put your latest analysis code into a git repository
Upload your code to GitHub
Make your code (e.g. Python or R) more readable by modularizing and commenting it

If you have a particular task in mind that you would like to work on during the afternoons of days 2 and 3 (related to the content of the workshop), let us know in advance so we can give it some thought as well.

It is possible to attend only days 1 and 2 during which we go through the core lessons of Software Carpentry. Note that the venue for days 1+2 and 3 is different.

Day 1 Wednesday 25th Nov, Erik Palménin aukio 1

09:00	Automating tasks with the Unix shell
10:30	Coffee
12:00	Lunch break
13:00	Version control with Git
14:30	Coffee
16:00	Wrap-up

Day 2 Thursday 26th Nov, Erik Palménin aukio 1

09:00	Building programs with Python
10:30	Coffee
12:00	Lunch break
13:00	Work session (optional)
14:30	Coffee
16:00	Wrap-up

Day 3 Friday 27th Nov, Siltavuorenpenger 9

09:00	Best practices in coding
10:30	Break
12:00	Lunch break
13:00	Work session (optional)
14:30	Break
16:00	Wrap-up

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...

Programming in Python

Using libraries
Working with arrays
Reading and plotting data
Creating and using functions
Loops and conditionals
Defensive programming
Using Python from the command line
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...

Best practices in coding

Commenting and documenting code
Designing modular code
Using git effectively with collaborators
Using GitHub
Useful coding tools
Where to find help

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.

Software Carpentry 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

Download the Git for Windows installer.
Run the installer and follow the steps bellow:
1. Click on "Next".
2. Click on "Next".
3. Click on "Next".
4. Click on "Next".
5. Click on "Next".
6. Select "Use Git from the Windows Command Prompt" 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.
7. Click on "Next". Keep "Checkout Windows-style, commit Unix-style line endings" selected.
8. Select "Use Windows' default console window" and click on "Next".
9. Click on "Next".
10. Click on "Finish".

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). 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 10.9 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

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. 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.

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).

Windows

Download and install Anaconda.
Download the default Python 3 installer (do not follow the link 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 default Python 3 installer (do not follow the link 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 workshop.)

Download the installer that matches your operating system and save it in your home folder. Download the default Python 3 installer (do not follow the link to version 2).
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).