C24 Sackville St Building, 60 Sackville St, Manchester M1 3WE
2-3 March 2017, 9:00 am - 5:00 pm
Instructors: Mario Antonioletti, David Jones, Aleksandra Nenadic
Helpers: Mario Antonioletti, David Jones, Aleksandra Nenadic
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 the 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.
When: 2-3 March 2017, 9:00 am - 5:00 pm.
Where: C24 Sackville St Building, 60 Sackville St, Manchester M1 3WE. Get directions with OpenStreetMap or Google Maps.
Etherpad: http://pad.software-carpentry.org/2017-03-02-manchester.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code during the workshop.
Contact: Please email Jenefer.Cockitt@manchester.ac.uk or a.nenadic@manchester.ac.uk for more information.
Surveys
Please be sure to complete these surveys before and after the workshop.
| Time | Content | References |
| 09:00 | Welcome and introduction |
|
| 09:45 | Automating tasks with the Unix Shell (1) | |
| 11:00 | Coffee | |
| 11:15 | Automating tasks with the Unix Shell (2) | |
| 12:30 | Lunch break | |
| 13:15 | Data organization and cleaning (best practices) |
|
| 15:00 | Coffee | |
| 15:15 | Version control with Git (1) |
|
| 17:00 | Wrap-up |
| Time | Content | References |
| 09:00 | Recap of Day 1 | |
| 09:15 | Version control with Git (2) |
|
| 10:30 | Coffee | |
| 11:00 | Programming in Python (1) | |
| 12:30 | Lunch break | |
| 13:15 | Programming in Python (2) |
|
| 14:45 | Coffee | |
| 15:30 | Programming in Python (3) |
|
| 16:30 | Feedback and wrap-up |
|
Below are links to all the lessons taught at the course.
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 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., 3.4 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).
OpenRefine (previously Google Refine) is a tool for data cleaning that runs through a web browser, and any browser - Safari, Firefox, Chrome, Explorer - should work fine. You will need to download Google Refine and install it, and when you open it, it will run through the browser, but you don't need an internet connection, and the data will all be stored on your computer.
Go to the OpenRefine download page, and click on Windows kit to download the install file.
To use it, unzip, and double-click on openrefine.exe (if you're having issues with openrefine.exe try refine.bat instead). OpenRefine will then open in your web browser.
If it doesn't open automatically, open a web broswer after you've started the program and go to the URL http://localhost:3333 and you should see OpenRefine.
Go to the OpenRefine download page, and click on Mac kit to download the install file.
Open the downloaded .dmg file and drag the icon in to the Applications folder. Double click on the icon and Google Refine will then open in your web browser.
If it doesn't open automatically, open a web broswer after you've started the program and go to the URL http://localhost:3333 and you should see OpenRefine.
Go to the OpenRefine download
page. Click on Linux kit to download the install file. Extract the file and
type ./refine in your terminal and Google Refine will then
open in your web browser. If it doesn't open automatically, open a web broswer after you've started
the program and go to the URL http://localhost:3333 and you should
see OpenRefine.