Jan 18-20, 2017
9:00 am - 5:00 pm
Instructors: Andrew Walker, Martin Callaghan, Grace Cox
Helpers: Neil Wilkins
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 Andrew Walkeer for further information. Some funding to cover travel and accommodation costs of these participants is available. Any unallocated spaces will be made generally available in 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 held in very early January in Bristol 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 Sciences, University of Bristol, Wills Memorial Building, Queens Road,Bristol BS8 1RJ. 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.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers have checked that:
Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch and we will attempt to provide them.
Contact: Please mail a.walker@leeds.ac.uk for more information.
Surveys
Please be sure to complete these surveys before and after the workshop.
| 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) |
| 12:30 | Lunch (provided) |
| 13:30 | Using version control to manage information |
| 15:00 | Break |
| 15:15 | An introduction to python (2) |
| 17:00 | Close |
| 09:00 | Recap |
| 09:15 | Using the shell to do more in less time (2) |
| 10:30 | Break |
| 10:45 | An introduction to python (3) |
| 12:30 | Lunch |
| 13:00 | Using version control to share information |
| 15:00 | Break |
| 15:15 | Open science and good programming practice |
| 17:00 | Close |
| 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 | Pulling it all together |
| 16:00 | Close |
Etherpad: http://pad.software-carpentry.org/2017-01-18-bristol.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
add, commit, ...status, diff, ...clone, pull, push, ...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.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
cmd and press [Enter])setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.exit then pressing [Enter]This will provide you with both Git and Bash in the Git Bash program.
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.
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 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.
Git should be installed on your computer as part of your Bash install (described above).
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.
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.
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.
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).
bash Anaconda3-and then press tab. The name of the file you just downloaded should appear.
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).
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.
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
cd Desktop
git clone https://github.com/gracecox/2017-01-18-bristol-bash.git
cd 2017-01-18-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.
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.
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).
Scopatz, A. and Huff, K. D. (2015) Effective computation in physics, O'Reilly.