Software Carpentry: NERC / University of Bristol

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 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.

This is the first of two workshops in January aimed at the NERC community and funded by the ATSC scheme. This one is aimed at participants with some knowledge of programming who want to develop knowledge of python, and understanding of good practice in scientific computing or skills using tools such as version control. The workshop held in Leeds ten days later will be more appropriate for those with less background knowledge. If you are not sure which workshop is best for you please get in touch with us.

Where: School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ. United Kingdom. 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 J.E.Mound@leeds.ac.uk for more information.

Provisional Schedule

Day 1

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

Day 2

09:00	Recap
09:15	Python and the shell
10:30	Break
10:45	Using version control to share information
12:00	Lunch
13:00	Defensive programming with python
14:45	Break
15:00	Problem solving with Python
16:00	Sharing code: documentation and licencing
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).

Etherpad: http://pad.software-carpentry.org/2016-01-06-bristol.
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

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.

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 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).

Windows

Open http://continuum.io/downloads with your web browser.
Click on "I want Python 3.X" link.
Download this Python 3 installer.
Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Open http://continuum.io/downloads with your web browser.
Click on "I want Python 3.X" link.
Download this Python 3 installer.
Install Python 3 using all of the defaults for installation.

Linux

Open http://continuum.io/downloads with your web browser.
Click on "I want Python 3.X" link.
Download this Python 3 installer, save it in your home folder.
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.)
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).

Once you are done installing the software listed above, please go to this page, which has instructions on how to test that everything was installed correctly.

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 may 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.

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 (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/gracecox/2016-01-06-bristol-bash.git
cd 2016-01-06-bristol-bash

(typing return after each line). You should see something like "repository successfully cloned". Let us know if this does not work for you.

You can get the python material in a simmilar way, using the commands:

cd 
cd Desktop
git clone  https://github.com/andreww/2016-01-06-bristol-python.git
cd 2016-01-06-bristol-python

These repositories have been updated with material from Wednesday. To access the updates run the command:

git pull origin master

inside one of the directories.

Material for the testing lesson can be downloaded from http://andreww.github.io/2016-01-06-bristol/2016-01-06-bristol-testing.zip. The github repository can be found at https://github.com/andreww/2016-01-06-bristol-testing and the travis-ci results at https://travis-ci.org/andreww/2016-01-06-bristol-testing.

Material for the day three group project can be found at http://andreww.github.io/group-project/

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:

GitHub interactive Git tutorials
Git pretty - a flowchart about how to recover from mistakes.
Changing History, or How to Git pretty - slides relating to the above.

Python:

basemap introduction and an updated version
matplotlib examples gallery - includes source code.
SciPy Cookbook - examples of how to do useful stuff using numpy, scipy, matplotlib, interfacing, etc.
Scientific Python lecture notes

Training:

ARCHER Training - free HPC training all over the UK.
Code Academy - free online programming courses

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).