Find us on GitHub

Lund University

May 25-27, 2016

9:00 am - 4:30 pm

Instructors: Alexandre Manhães Savio, Jean-Christophe Leyder, Oier Echaniz

Helpers: Johan Mårtensson, Olof Strandberg, Peter Mannfolk

Organizers: Johan Mårtensson, Titti Owman

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".

Registration Form

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: National 7T Facility. Klinikgatan 13b, Lund. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating sytem (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.

Contact: Please mail johan.martensson@psy.lu.se for more information.

Sponsors

This workshop is possible thanks to the contributions of

Schedule

Surveys

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

Pre-workshop Survey

Post-workshop Survey

Day 1

09:00 Software setup and account signup(Oier)
09:30 Welcome
09:45 Introduction to the Unix shell (Oier)
11:00 Coffee break
11:30 Introduction to the Unix shell (continued) (Oier)
12:45 Lunch break
14:15 Version control with Git (JC)
15:45 Coffee break
16:00 Version control with Git (continued) (JC)
17:15 Wrap Up

Day 2

09:00 Set up and review of day 1 (JC?)
09:30 Programming in Python (Alex)
11:00 Coffee break
11:30 Programming in Python (continued) (Alex)
12:45 Lunch break
14:15 Scientific Python (JC)
15:45 Coffee break
16:00 Scientific Python (continued) (JC)
17:15 Wrap Up

Day 3

09:00 Set up and review of day 2(Alex)
09:30 Introduction to Nipy (Alex)
09:45 Introduction to Nipype (Alex)
11:00 Coffee break
11:30 Introduction to Nipype (continued) (Alex)
12:30 Wrap Up

Etherpad: http://pad.software-carpentry.org/2016-05-25-lunduni.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

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...

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.

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. 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".
  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.

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 Anaconda, an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.4 is fine). We recommend Python 3 for your projects, however Python 2.7 will also work for this workshop.

We will teach Python using the IPython notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

Windows

Video Tutorial
  1. Open http://continuum.io/downloads with your web browser.
  2. Download the Python 3 installer for Windows.
  3. Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Video Tutorial
  1. Open http://continuum.io/downloads with your web browser.
  2. Download the Python 3 installer for OS X.
  3. Install Python 3 using all of the defaults for installation.

Linux

  1. Open http://continuum.io/downloads with your web browser.
  2. Download the Python 3 installer for Linux.
  3. Install Python 3 using all of the defaults for installation. (Installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  4. Open a terminal window.
  5. Type 
    bash Anaconda3-
    and then press tab. The name of the file you just downloaded should appear.
  6. 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).

NiPype

Nipype an open-source, community-developed Python initiative under the umbrella of NiPy. It provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow.

To run the tutorial you will probably need FSL and SPM correctly installed. You must follow each tools' installation procedure. To check if FSL is correctly installed you can run 

fsl
in a terminal and a window must appear. In order to nipype find SPM you must be able to launch Matlab running 
matlab
from a terminal (tip: include its bin folder in your $PATH) and SPM must be in the Path of Matlab. There is a comprehensive set of instructions to install neuroimaging tools here.

In order to install nipype: If you use Python 2.7 you can install it using 

pip install nipype
. If you prefer Python 3.4 or 3.5 you will have to install a newer version from the repository, running: 
pip install git+https://github.com/nipy/nipype

There are other nipy tools that you may find interesting and you can install using the same scheme as in the previous paragraph.

Please send us an email if you have any question or issue with the setup.

To accelerate the beginning of the course, please have the NiPype repository cloned in your computer. To do this, go to the folder where you want to have the source code folder and run: 

git clone https://github.com/nipy/nipype.git
I also need you to download this dataset. And we will start with the notebooks in this repository: 
git clone https://github.com/Neurita/nipype-lessons

Windows

  1. The neuroimaging tools we will use have bad support for Windows.
  2. You could install nipype and other nipy tools in Windows using pip.
  3. The main concern is that some of the exercises where we call FSL, for instance, you won't be able to run it.

Mac OS X

  1. Follow the instructions detailed above to install nipype and other tools.
  2. Install FSL.

Linux

  1. Follow the instructions detailed above to install nipype and other tools.
  2. Install FSL.
  3. If you are using Ubuntu or Debian I recommend using NeuroDebian.
License Blog GitHub Twitter Issues