Tuesday Jan 21, Jan 28, Feb 4, Feb 11 & Feb 18 2020
9:00 am - 12:00 noon
Instructors: Antonia Mey, David McKain, Ruairidh MacLeod
Helpers: Wilson Wu, Mario Antonioletti, Sofia Bariami, Ezra Kitson, Rafal Szabla, Jordi Juarez Jimenez, Bianca Prodan, Fiona Bissett, Jen Daub, Holly Judge
Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. 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".
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.
Where: Teaching Studio G.09, Murchison House, King's Buildings, Max Born Crescent, Edinburgh. Get directions with OpenStreetMap or Google Maps.
When: Tuesday Jan 21, Jan 28, Feb 4, Feb 11 & Feb 18 2020. Add to your Google Calendar.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers 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 (using contact details below) and we will attempt to provide them.
Contact: Please email david.mckain@ed.ac.uk or antonia.mey@ed.ac.uk for more information.
Registration: Please register if you would like to attend. You will need to book individually for each week of the workshop. The following links take you directly to the booking pages for each week:
Everyone who participates in Carpentries activities is required to conform to the Code of Conduct.This document also outlines how to report an incident if needed.
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
Please be sure to complete these surveys before and after the workshop.
| Before | Pre-workshop survey |
| 09:00 | Plotting and Programming in Python (Part 1) |
| 10:30 | Break |
| 10:45 | Plotting and Programming in Python (Part 1 - Continued) |
| 12:00 | END |
| 09:00 | Plotting and Programming in Python (Part 2) |
| 10:30 | Break |
| 10:45 | Plotting and Programming in Python (Part 2 - Continued) |
| 12:00 | END |
| 09:00 | Automating Tasks with the Unix Shell (Part 1) |
| 10:30 | Morning break |
| 10:45 | Automating Tasks with the Unix Shell (Part 1 - Continued) |
| 12:00 | END |
| 09:00 | Automating Tasks with the Unix Shell (Part 2) |
| 10:30 | Morning break |
| 10:45 | Automating Tasks with the Unix Shell (Part 2 - Continued) |
| 12:00 | END |
| 09:00 | Version Control with Git |
| 10:30 | Morning break |
| 10:45 | Version Control with Git (Continued) |
| 11:45 | Post-workshop Survey |
| 12:00 | END |
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.
Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research 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., 3.6 is fine).
We will teach Python using JupyterLab, a programming environment that runs in a web browser. (JupyterLab will be installed by Anaconda, and we will do this together during the workshop). For this to work you will need a reasonably up-to-date browser. Current versions of the Chrome, Safari and Firefox browsers are all supported, Internet Explorer and Edge are not supported.
bash Anaconda3-and then press Tab to autocomplete the full file name. The name of 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).
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 some versions of macOS is Bash, and
Bash is available in all versions, 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.
To see if your default shell is Bash type echo $SHELL in
Terminal and press the enter/return key. If the message printed does
not end with '/bash' then your default is something else and you can run
Bash by typing bash.
The default shell is usually Bash and there is usually no need to install anything.
To see if your default shell is Bash type echo $SHELL in
a terminal and press the enter/return key. If the message printed does
not end with '/bash' then your default is something else and you can run
Bash by typing bash.
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.
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.
Because this installer is not signed by the developer, you may have to
right click (control click) on the .pkg file, click Open, and click
Open on the pop up window.
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 dnf 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 macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc 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. It is installed along with Git.
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 BBEdit 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.