Jan 4-6, 2017
9:00 am - 5:00 pm
Instructors: Andrew Walker, Martin Callaghan
Helpers: Alan Baird, 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 Walker for further information. Some funding to cover travel and accommodation costs of these participants is available. Any unallocated spaces will be made generally avalable in early June.
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 Bristol two weeks 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.
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 firstname.lastname@example.org for more information.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
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|
|10:45||Python and good programming practice (1)|
|13:30||Using version control to manage information|
|15:15||Python and good programming practice (2)|
|09:30||Using version control to share information|
|11:00||Testing and Continuous Integration with Python (1)|
|13:30||Python and the command line|
|15:15||Testing and Continuous Integration with Python (2)|
|16:15||Preperation for 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).
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.
cmdand press [Enter])
setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.
exitthen 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
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
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
After installing Git, there will not be anything in your
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"
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.
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.
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.
yesand press enter to approve the license. Press enter to approve the default location for the files. Type
yesand 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.
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.
If you haven't already, please register for free accounts to
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, you wil need to take 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.
Finally, please compleate the pre-workshop survay here
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.
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:
(typing return after each line). You should see something like "repository successfully cloned". Let us know if this does not work for you.
cd cd Desktop git clone https://github.com/callaghanmt/shell-training.git cd shell-training
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 cd Desktop git clone https://github.com/andreww/2017-01-04-python1.git cd 2017-01-04-python1
The testing material is is avalable in the same way:
cd cd Desktop git clone https://github.com/andreww/2017-01-04-testing.git cd 2017-01-04-python1
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.