Macquarie University

July 3-4, 2018

9:45 am - 5:00 pm

Instructors: Xavier Ho, Anastasios Papaioannou, James Tocknell, Wilfred Gee

Helpers: Cormac Purcell, Gustavo Thomas, Malcom Ramsay

General Information

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 workshop is part of the Research Bazaar Sydney 2018 event. This hands-on workshop will cover: useful software development skills and tools, including debugging, testing, and task automation; visualisation of datasets via the web; and data analysis and reduction using seaborn and pandas. 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 who have already completed a Software Carpentry course in Python. You do not need to have used pytest, seaborn, pandas or D3.js previously.

Where: E3B 217 (8SCO 217), Macquarie University, Sydney, Australia. Get directions with OpenStreetMap or Google Maps.

When: July 3-4, 2018. 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). 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 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 for more information.


Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Day 1

Before Pre-workshop survey
09:45 Python Testing and Continuous Integration
11:00 Coffee
13:00 Lunch break
15:15 Coffee
16:50 Wrap-up
17:00 END

Day 2 (stream A), 08SCO Room 217

09:45 Visualising your data on the web using D3
11:00 Coffee
13:00 Lunch break
15:15 Coffee
16:40 Wrap-up
16:50 Post-workshop Survey
17:00 END

Day 2 (stream B), 08SCO Room 218

09:45 Data Manipulation using Pandas
11:00 Coffee
13:00 Lunch break
14:00 Data Visualisation using Seaborn
15:15 Coffee
16:40 Wrap-up
16:50 Post-workshop Survey
17:00 END

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


Python Testing and Continuous Integration

  • Basics of Testing
  • Exceptions, Status Values and Backtraces
  • Unit Tests
  • Edge and Corner Cases
  • Test Driven Development
  • Continuous Integration
  • Reference...

Visualising your data on the web using D3

  • HTML
  • CSS
  • Images and SVG
  • Publishing with Github
  • JavaScript
  • JSON data format
  • D3 Setup
  • D3 Into the data
  • D3 Add and remove
  • D3 Transitions
  • Reference...

Data Manipulation and Data Visualisation in Python

  • We teach using Jupyter notebooks, which allow program code, results, visualisations and documentation to be blended seamlessly.
  • Getting started with dataframes using the Pandas library.
  • Indexing, Slicing and Subsetting Dataframes.
  • Data types and formats.
  • Combine and join dataframes using Pandas.
  • Visualisation in Python using the Seaborn and the Matplotlib libraries.


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.

The Bash Shell

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


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. Keep "Use Git from the Windows Command Prompt" selected 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.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Keep "Use Windows' default console window" selected and click on "Next".
    7. Click on "Install".
    8. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing 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 macOS 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 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 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).


Video Tutorial

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 dnf install git.

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 macOS 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.


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.


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., 3.6 is fine).

We will teach Python using the Jupyter 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).


Video Tutorial
  1. Open 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.


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


  1. Open with your web browser.
  2. Download the Python 3 installer for Linux.
    (The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  3. Open a terminal window.
  4. Type
    bash Anaconda3-
    and then press tab. The name of the file you just downloaded should appear. If it does not, navigate to the folder where you downloaded the file, for example with:
    cd Downloads
    Then, try again.
  5. Press enter. You will follow the text-only prompts. To move through the text, press the space key. 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).
  6. Close the terminal window.


pytest is the most widely used testing tool used with Python.

Anaconda Users

If you have used Anaconda to install Python, then the best way of installing pytest is to open the Anaconda Navigator, select the Environments tab, and search for pytest. If there is a green tick in the checkbox for pytest, then pytest is installed, otherwise click the checkbox and follow the prompts.

Once pytest is installed, go the "Checking pytest works" section


If you have installed Python via some other method, then install pytest via pip:

python -m pip install pytest
Furthur information about using pip can be found at

Once pytest is installed, go the "Checking pytest works" section

Checking pytest works

To check that pytest works, run

pytest --version
inside the bash shell. This should produce output similar to
This is pytest version 3.6.2, imported from /usr/lib/python3/site-packages/pytest/__init__.pyc