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NERC / University of Leeds

Jan 18-20, 2016

9:00 am - 5:30 pm

Instructors: Martin Callaghan, Grace Cox, Andrew Walker

Helpers: George Taylor, Jon Mound, Andrew Evans, Jo Leng

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 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".

The workshop is funded by NERC as part of the Advanced Training Short Courses programme. Priority will thus be given to NERC-funded PhD students and early career researchers from the environmental sciences who should register below or contact Jon Mound for further information. Some funding to cover travel and accommodation costs of these participants is avalable. Any unallocated spaces will be made generally avalable in early December.

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.

This is the second of two workshops in January aimed at the NERC community and funded by the ATSC scheme. This one is aimed at participants with very little (or no) prior knowledge of programming but who want to develop some knowledge of python, and an understanding of good practice in scientific computing and the tools that make this possible. The workshop to be held in Bristol earlier in January will be more appropriate for those with more background knowledge. If you are not sure which workshop is best for you please get in touch with us.

Where: School of Earth and Environment, University of Leeds, Leeds, LS2 9J. Get directions with OpenStreetMap or Google Maps.

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.

Contact: Please mail for more information.

Provisional Schedule

Day 1

09:00 Arrival and Welcome
09:30 Using the shell to do more in less time (1)
10:30 Break
10:45 An introduction to python (1)
12:00 Lunch (provided)
13:30 An introduction to python (2)
15:00 Break
15:15 An introduction to python (3)
17:30 Close

Day 2

09:00 Recap
09:30 Using the shell to do more in less time (2)
10:30 Break
10:45 Using version control to manage information
12:00 Lunch
13:00 Using version control to share information
15:00 Break
15:15 Open science and good programming practice
17:30 Close

Day 3

09:00 Recap
09:30 Python and environmental data
10:30 Break
10:45 Mini-project
12:00 Lunch
13:00 Mini-project
15:00 Break
15:15 Mini-project
16:30 Pulling it all together
17:00 Close

We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.


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...


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.


Download the Git for Windows installer. Run the installer. Important: on the 6th page of the installation wizard (the page titled `Configuring the terminal emulator...`) select `Use Windows' default console window`. 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. 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.


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 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 You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).


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.


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.


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.


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 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 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).


  1. Open with your web browser.
  2. Click on "I want Python 3.X" link.
  3. Download this Python 3 installer.
  4. Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

  1. Open with your web browser.
  2. Click on "I want Python 3.X" link.
  3. Download this Python 3 installer.
  4. Install Python 3 using all of the defaults for installation.


  1. Open with your web browser.
  2. Click on "I want Python 3.X" link.
  3. Download this Python 3 installer, save it in your home folder.
  4. 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.)
  5. Open a terminal window.
  6. Type
    bash Anaconda-
    and then press tab. The name of the file you just downloaded should appear.
  7. 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).

During and after the workshop

We have gathered together the various links you will need and useful information below. These will remain accessable after the workshop and we will add to this list as the workshop progresses. Please read and abide by the code of conduct.

We will make use of this etherpad during the workshop. Please use this to keep collaborative notes and ask (and answer) each others questions. Feel free to tweet from the workshop using #SWCLeeds.

Workshop material

Much of the material we will be using during the workshop can be found online and you will need copies of this on your laptop. In order to download the material for the first session on bash (and to check you have a working system with internet access) please start a new shell and type the following commands:

cd Desktop
git clone
cd 2016-01-18-leeds-bash
(typing return after each line). You should see something like "repository successfully cloned". Let us know if this does not work for you.

The python material is is avalable in the same way. To get hold of the data (and the files we created during the workshop) type:

cd Desktop
git clone
cd 2016-01-18-leeds-pystudents

Stuck somewhere new?

If you find yourself in a shell that you don't recognise, or in an editor that you can't get out of then see recognising prompts and how to exit.

Useful links

Software Carpentry online lessions:





Wilson G, Aruliah DA, Brown CT, Chue Hong NP, Davis M, et al. (2014) Best Practices for Scientific Computing. PLoS Biol 12(1): e1001745. doi:10.1371/journal.pbio.1001745.

Sandve GK, Nekrutenko A, Taylor J, Hovig E (2013) Ten Simple Rules for Reproducible Computational Research. PLoS Comput Biol 9(10): e1003285. doi:10.1371/journal.pcbi.1003285.

Noble WS (2009) A Quick Guide to Organizing Computational Biology Projects. PLoS Comput Biol 5(7): e1000424. doi:10.1371/journal.pcbi.1000424.

Ram K (2013) "git can facilitate greater reproducibility and increased transparency in science", Source Code for Biology and Medicine 2013, 8:7 doi:10.1186/1751-0473-8-7.

Glass, R. (2002) Facts and Fallacies of Software Engineering, Addison-Wesley, 2002. (PDF).