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Chris Lamb Training Theatre, John Innes Centre

June 1st and 2nd, 2016

09:30 am - 4:00 pm

Instructors: Dan MacLean

Helpers: Martin Page

General Information

TSL uses Software Carpentry Training Courses. 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, 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. Please note that this is not a full SWC workshop, we will be leaving out the Git version control section (in response to previous feedback and time constraints) in favour of concentrating more on the Python section.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at TSL researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Norwich Research Park. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants are encouraged to 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). If you do not have access to one, then you can use the JIC machines in the training theatre. Participants 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:

  • The room is wheelchair / scooter accessible.
  • Accessible restrooms are available.

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 dan.maclean@tsl.ac.uk for more information.

Schedule

Day 1

09:30 Automating tasks with the Unix shell
10:30 Coffee
12:00 Lunch break
13:30 Building programs with Python
14:30 Coffee
16:00 Wrap-up

Materials for this day can be found here: Shell Novice and here Python

Day 2

09:30 Building programs with Python
10:30 Coffee
12:00 Lunch break
13:00 Building programs with Python
14:30 Coffee
16:00 Wrap-up

Materials for this day can be found here:Python

Syllabus

The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things
  • Reference...

Programming in Python

  • Using libraries
  • Working with arrays
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Defensive programming
  • Using Python from the command line
  • Reference...

Setup

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.

The instructions below will install everything you need, one-by-one and the software will be available on your machine after the workshop - but it is a lot of installing. If you'd rather use a virtual machine that can be disposed of after the workshop please see the instructions here: Virtual Machine Install Instructions

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.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on "Next".
    2. Click on "Next".
    3. Click on "Next".
    4. Click on "Next".
    5. Click on "Next".
    6. Select "Use Git from the Windows Command Prompt" and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    7. Click on "Next". Keep "Checkout Windows-style, commit Unix-style line endings" selected.
    8. Select "Use Windows' default console window" and click on "Next".
    9. Click on "Next".
    10. Click on "Finish".

This will provide you with both Git and Bash in the Git Bash program.

Mac OS X

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.

Linux

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.

Text Editor

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.

Windows

Video Tutorial

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.

Mac OS X

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.

Linux

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

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).

Windows

Video Tutorial
  1. Open http://continuum.io/downloads with your web browser.
  2. Download the Python 3 installer for Windows.
  3. Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Video Tutorial
  1. Open http://continuum.io/downloads with your web browser.
  2. Download the Python 3 installer for OS X.
  3. Install Python 3 using all of the defaults for installation.

Linux

  1. Open http://continuum.io/downloads with your web browser.
  2. Download the Python 3 installer for Linux.
  3. Install Python 3 using all of the defaults for installation. (Installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  4. Open a terminal window.
  5. Type 
    bash Anaconda3-
    and then press tab. The name of the file you just downloaded should appear.
  6. Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. Type 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).

Virtual Machine

You may prefer to use a virtual machine (VM) rather than install lots of software on your own computers. Use these instructions for this option.

  1. Install VirtualBox.
  2. Download our VM image. Warning: this file is > 2 GByte, so please download it before coming to your workshop.
  3. Load the VM into VirtualBox by selecting "Import Appliance" and loading the .ova file.
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