Smarter, Faster, and More Reproducible Science for Early/Mid-Career Researchers

Curtin University

May 12 - June 12 2025

3:00pm AEST

Instructors: Paul Hancock

Helpers: TBA

General Information

This workshop series was created as a collaboration between Astronomy Data And Computing Services (ADACS), and the Early Career Researcher (ECR) chapter of the Astronomical Society of Australia (ASA). The goal of the workshop is to provide Students and ECRs with training that will boost their research productivity - training that is often not part of a formal under- or post-graduate degree program. The workshop was presented online as a HOWTO series. Each of the workshops in the series were recorded and are available to view via YouTube with the links below. The workshop content itself is still being hosted on github for anyone who would like to learn at their own pace.

If you like what you see here, and would like to have a workshop developed and delivered for your research group, collaboration, or as part of a conference that you are organising please contact ADACS using this form, or via contact@adacs.org.au.

This workshop was run between May 12 - June 12 2025 and the page has now been updated as the workshop is closed and archived.

Schedule

This workshop was recorded and is available for viewing using the links below.

Workshop Title	Video
HOWTO: Automate the boring bits
HOWTO: Build on past success
HOWTO: Accelerate your research
HOWTO: Leverage GitHub for Research

Setup

To participate in a Data Carpentry workshop, you will need access to software as 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.

Before the workshop, you should visit the Setup Page to set your expectations of how this workshop will be run.

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

Two monitors: If you have two monitors, plan to have the tool you are learning up on one monitor and the video conferencing software on the other.
Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the tool you will be learning about.
Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

Python

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., 3.8 is fine).

Open https://www.anaconda.com/products/individual#download-section with your web browser.
Download the Anaconda for Windows installer with Python 3. (If you are not sure which version to choose, you probably want the 64-bit Graphical Installer Anaconda3-...-Windows-x86_64.exe)
Install Python 3 by running the Anaconda Installer, using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.

Video Tutorial

Open https://www.anaconda.com/products/individual#download-section with your web browser.
Download the Anaconda Installer with Python 3 for macOS (you can either use the Graphical or the Command Line Installer).
Install Python 3 by running the Anaconda Installer using all of the defaults for installation.

Video Tutorial

Open https://www.anaconda.com/products/individual#download-section with your web browser.
Download the Anaconda Installer with Python 3 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.)
Open a terminal window and navigate to the directory where the executable is downloaded (e.g., `cd ~/Downloads`).
Type
```
bash Anaconda3-
```
and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
Press Enter (or Return depending on your keyboard). You will follow the text-only prompts. To move through the text, press Spacebar. Type yes and press enter to approve the license. Press Enter (or Return) to approve the default location for the files. Type yes and press Enter (or Return) to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
Close the terminal window.

The Bash Shell

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

Download the Git for Windows installer.
Run the installer and follow the steps below:
1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
2. From the dropdown menu, "Choosing the default editor used by Git", select "Use the Nano editor by default" (NOTE: you will need to scroll up to find it) and click on "Next".
3. On the page that says "Adjusting the name of the initial branch in new repositories", ensure that "Let Git decide" is selected. This will ensure the highest level of compatibility for our lessons.
4. Ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
5. Select "Use bundled OpenSSH".
6. Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
7. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
8. Ensure that "Use Windows' default console window" is selected and click on "Next".
9. Ensure that "Default (fast-forward or merge) is selected and click "Next"
10. Ensure that "Git Credential Manager" is selected and click on "Next".
11. Ensure that "Enable file system caching" is selected and click on "Next".
12. Click on "Install".
13. Click on "Finish" or "Next".
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.

Video Tutorial

The default shell in Mac OS X Ventura and newer versions is Zsh, but 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 Return key. If the message printed does not end with '/bash' then your default is something else, you can change your current shell to Bash by typing bash and then pressing Return. To check your current shell type echo $0 and press Return.

To change your default shell to Bash type chsh -s /bin/bash and press the Return key, then reboot for the change to take effect. To change your default back to Zsh, type chsh -s /bin/zsh, press the Return key and reboot. To check available shells, type cat /etc/shells.

Video Tutorial

The default shell is usually Bash and there is usually no need to install anything.