NERC / University of Leeds

School of Earth and Environment, University of Leeds, Leeds, LS2 9JT
Jan 14-16, 2015
9:00 am - 5:30 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. This three-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 workshop is funded by NERC as part of the Advanced Training Short Courses programme (the application can be found here). Priority will thus be given to NERC-funded PhD students and early career researchers from the environmental sciences who should contact Andrew Walker for booking information. Some funding to cover travel and accommodation costs of these participants is avalable. Any unallocated spaces will be made generally avalable in mid December.

Instructors: Martin Callaghan, Aleksandra Pawlik, Andrew Walker, Aaron O'Leary, Peter Willetts

Helpers: Jo Leng, Grace Cox

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. Priority will be given to NERC-funded PhD students and early career researchers from the environmental sciences.

Where: School of Earth and Environment, University of Leeds, Leeds, LS2 9JT. 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 a.walker@leeds.ac.uk for more information.

Schedule

Day 1

09:00 Arrival and Welcome
09:30 Using the shell to do more in less time
10:30 Break
10:45 Using version control to manage information
12:00 Lunch (provided)
13:00 Using version control to share information
15:00 Break
15:15 Introduction to Python for Environmental Scientists
16:30 Sharing code: documentation and licencing
17:30 Close

Day 2

09:00 Recap
09:30 Python and good programming practice
10:30 Break
10:45 Defensive programming
12:00 Lunch
13:00 Problem solving with Python
14:45 Break
15:15 Handling and displaying environmental data with Python
16:15 Python and the shell
17:00 Pulling it all together
17:30 Close

Day 3

The third day will attendees to begin to work together in small groups to develop useful tools for their own research. We will start with an introduction to the day at 09:00 and have a wrap-up session including time for groups show their progress from about 15:00. We will finish by 17:00 (lunch and breaks will be provided as detailed above).

Syllabus

The Unix Shell

  • Files and directories: pwd, cd, ls, mkdir, ...
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things: grep, find, ...
  • Reference...

Programming in Python

  • Using libraries
  • Working with arrays
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals: for, if, else, ...
  • 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 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 workshop.

Overview

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.

The Bash Shell

Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.

Git

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.

Python

Python is becoming very popular in scientific computing, and it's a great language for teaching general programming concepts due to its easy-to-read syntax. We teach with Python version 2.7, since it is still the most widely used. Installing all the scientific packages for Python individually can be a bit difficult, so we recommend an all-in-one installer.

Windows

Python

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

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.

Software Carpentry Installer

This installer requires an active internet connection

After installing Python and Git Bash:

  • Download the installer.
  • If the file opens directly in the browser select File→Save Page As to download it to your computer.
  • Double click on the file to run it.

Editor

nano is the editor installed by the Software Carpentry Installer, it is a basic editor integrated into the lesson material.

Notepad++ 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.

Mac OS X

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.

Editor

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

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.

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 workshop.)

  1. Download the installer that matches your operating system and save it in your home folder.
  2. Open a terminal window.
  3. Type 
    bash Anaconda-
    and then press tab. The name of the file you just downloaded should appear.
  4. 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).

Virtual Machine

Sometimes the instructions above don't work. One way around this is to use a virtual machine (VM) rather than install software on their own computers. If all else fails you can try this using the following instructions:

  1. Install VirtualBox.
  2. Download our VM image. Warning: this file is 1.7 GByte, so please download it before coming to your workshop.
  3. Load the VM into VirtualBox by selecting "Import Appliance" and loading the .ova file.

Before the workshop

There are a three extra tasks to undertake before the workshop in order to help make sure things run smoothly. Please try to do the following.

1. Grab free accounts

If you haven't already, please register for free accounts to

  • Make use of Github. Register here and don't forget your password. We will use this service as part of the lesson on version control.
  • Use the Met Office datapoint API. Register for an account here. We will use this as a data source for some of the exercises.

2. Take a look at Bash, and maybe look at Python

We would like to get started with bash quickly at the start of the workshop. It would be useful if everybody could take a look at the first three shell lessons, found here, here, and here, to either remind yourself of how a shell works, or to have a first look if this is new to you.

If you are new to Python, or you fear that your Python is rusty, it may be worth taking a look at an online introduction. Christopher Woods has a nice short introduction here. If you can follow this as far as "conditions", you are good to go. We will be reviewing this material anyway, so don't worry if you get stuck.

3. Check your setup

Finally, if you are confident, it may be worth checking your setup, following the steps outlined below. These tools can be useful in helping to diagnose problems either at, or before, the workshop.

  • Download swc-installation-test-1.py
  • Open up a bash shell
  • Change into the directory where you put the script
  • Run the script: 
    python swc-installation-test-1.py

To check you have the necessary software and tools:

  • Download swc-installation-test-2.py
  • Open up a bash shell
  • Change into the directory where you put the script
  • Run the script: 
    python swc-installation-test-2.py

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 at github.com/andreww/SWC-leeds-intro. You will need this on your laptop. In order to download the material (and to check you have a working system with internet access) please start a new shell and type the following commands: 

cd 
cd Desktop
git clone https://github.com/andreww/SWC-leeds-intro
(typing return after each line). You should see something like "repository successfully cloned". Let us know if this does not work for you.

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:

Git:

Python:

Training:

Papers

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).

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