Software Carpentry workshop - University of Leeds

August 2015

By C.Scott Watson

Software Carpentry workshops are designed for PhD students and early career researchers wanting to develop programming skills to increase productivity. With a NERC funded workshop running on my doorstep as part of the Advanced Training Short Courses programme, I couldn't miss the opportunity to finally learn some coding.

I'd wanted to develop some Python skills since starting my PhD, and with no prior programming experience, this was the ideal opportunity. The workshop ran over three days, firstly introducing us to the Shell (Bash), before moving onto programming in Python and using version control in Git. The third day gave us the opportunity to work in small groups to put our new skills into practice on a small project. 

Day 1 summary

• Navigating around directories using Bash and manipulating files

• This led nicely onto using version control in Bash.

• Version control is vaguely similar to using tracked changes on a work document but can track whole repositories of files and show the history of changes. It's particularly useful for collaborative projects where several people may be working on developing code.

• Anyone working on the files can pull these repositories to their own computer, make changes to files and code for example, and then push those files back up to the repository so that other collaborators can access them.

• Functions of Python relevant to environmental Scientists using IPython notebooks and how to document code so that it can be used by other people, or to remind you how it works months after you wrote it.

• Leading on from this we the looked at how to build testing functions into the code to make sure it works as desired and produces the correct output.

The IPython notebook is a useful way of writing, testing, and documenting code before finalising it in a script:

Day 2 summary

• More coding in Python including Matplotlib Basemap, which is useful for everything from making a simple overview map to plotting raster or vector data.

• Using GitHub, which is the online interface for the version control we had been using in the Shell.

• Looking at documenting code and choosing an appropriate license so that other can  use and modify the code.

Day 3 summary Our group project aim was to use Python to compare point and gridded rainfall data and we decided to use historical Met Office data, thinking this would be nice and easy to manipulate...only it turned out to be a bit of a nightmare. 

Our first task was using Python to download the text files containing the data for available weather stations using the Met Office URL. We then had to clean these text files to remove weird characters and replace no data values, before conducting some basic analysis and plotting up time series graphs. The mini project certainly put the time demands of apparently simple projects into perspective and got us using our newfound skills, including all collaborating through a Git repository.


The shell:

Plotting up our Met stations in Basemap:

Overall the workshop was a great three days and wasn't overwhelming for someone with no programming experience, but equally it seemed useful for those that already programmed in different languages or were coding on a daily basis as part of their PhD. All the instructors and assistants made sure the workshop ran as smooth as it could and the lessons were hands-on and run interactively on the projected displays, so it was generally easy to follow on your own laptop.

Alpine preparation - Plas Y Brenin

Alpine preparation - Plas Y Brenin

April 2015 

By C. Scott Watson

To learn/improve our ropework and glacier travel skills, three of us headed down to Capel Curig for a two day Alpine Preparation course run at the National Mountain Sports Centre. Our instructor for the two day course was a British Mountain Guide called Owen. The course served a dual purpose for me, on one hand I'm going out to the Himalaya later this year to conduct research on the Khumbu Glacier, on the other I'm heading out to the Alps with some friends this summer for a spot of mountaineering. As a UK Mountain Leader and climbing instructor my ropework skills are generally pretty good, but I don't have any Alpine experience so there was plenty to learn over the two days.

The first day focused on glacier techniques, starting with a short classroom lesson on Alpine kit and hazards. For the rest of the day we headed out into the National Park to practice ropework techniques, including simulating glacier travel on the grassy slopes of Llyn Idwal and practicing abseiling. We also took turns to conduct 'crevasse' rescues to on our buddies, in this case our simulated crevasse was a small rock outcrop.

The second day focused on ropework techniques for travel over rocky Alpine terrain and taught us how to protect ourselves whilst moving efficiently over scrambling territory - Y Gribin ridge was our training venue and the weather was equally glorious. Back at base we finished with some map work, tips when using guidebooks, and recommended route choices for our first alpine adventure. Our guide was brilliant and I'd definitely recommend the course as an introduction to Alpine techniques.

Practicing travelling as a group of three along ridges - Alpine style

 

 Ridge scrambling on the second glorious day

Hoisting our buddies out of a 'crevasse' 

 Photo credits: Owen Samuel

Windsor workshop

Windsor Workshop 

December 2014

By C. Scott Watson

Back in December Owen and I travelled down to Windsor for the annual workshop run by the British Society for Geomorphology designed for first year PhD students. Accommodation is provided in the 17th-century Cumberland Lodge, located in the grounds of Windsor Great Park...don't forget your running shoes.

The course provides an introduction to undertaking a PhD and includes skills based training elements such as project design, conducting fieldwork, publishing, modelling, and python coding. We met PhD students from across Europe and had the chance to design a PhD independent from our own work and think about the timescales involved. The opportunity to present your own research ideas to small groups and receive feedback from academics other than your supervisors was also a very useful experience  when thinking about the best way to approach your research.

Overall the workshop provided a great introduction to what you should expect during a PhD but meeting fellow PhD newbies (with completely different research topics) and hearing about their ideas and  research techniques was one of the most memorable parts. The workshop comes highly recommended!

A few snaps:
 

A spot of deer stalking

 

The view to Windsor Castle

A Structure-from-Motion derived Duke of Edinburgh