15th-17th April
9am to 5pm
Instructors: Masami Yamaguchi, Ido Bar, Heidi Perrett, Amanda Miotto
Helpers: Masami Yamaguchi, Ido Bar
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: N53 0.57 Nathan Campus, Griffith University. Get directions with OpenStreetMap or Google Maps.
When: 15th-17th April. 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 hackyhour@griffith.edu.au for more information.
Please be sure to complete these surveys before and after the workshop.
| Before | Pre-workshop survey |
| 09:00 | Automating tasks with the Unix shell |
| 10:30 | Morning break |
| 12:00 | Lunch break |
| 13:00 | Introduction to Python- Lessons 1-4 |
| 14:30 | Afternoon break |
| 16:00 | Wrap-up |
| 16:30 | END |
| 09:00 | Introduction to Python- Lessons 5-8 |
| 10:30 | Morning break |
| 12:00 | Lunch break |
| 13:00 | Introduction to Python- Lessons 9-13 |
| 14:30 | Afternoon break |
| 16:00 | Wrap-up |
| 16:30 | Post-workshop Survey |
| 16:40 | END |
| 09:00 | Introduction to Python- Lessons 14-18 |
| 10:30 | Morning break |
| 12:00 | Lunch break |
| 13:00 | Introduction to Git |
| 14:30 | Afternoon break |
| 16:00 | Wrap-up |
| 16:30 | Post-workshop Survey |
| 16:40 | END |
add, commit, ...status, diff, ...clone, pull, push, ...Below are all the links to the lessons and the data used in them
Lessons online : http://swcarpentry.github.io/shell-novice/
Data to download: http://swcarpentry.github.io/shell-novice/data/data-shell.zip
Please unzip after downloading. If you are in Mac or Linux, you can use the following commands:
Windows: Install Windows For Linux Subsystem then use the following commands in the program:
wget http://swcarpentry.github.io/shell-novice/data/data-shell.zip
Mac:
curl -O http://swcarpentry.github.io/shell-novice/data/data-shell.zip
unzip shell-novice-data.zip
Linux:
wget http://swcarpentry.github.io/shell-novice/data/data-shell.zip
unzip shell-novice-data.zip
Lessons online : https://swcarpentry.github.io/python-novice-gapminder/
Data to download: https://swcarpentry.github.io/python-novice-gapminder/files/python-novice-gapminder-data.zip
You need to download to your computer, use the following...
Please unzip after downloading. If you are in Mac or Linux, you can use the following commands:
Windows: you can download it and move it to the folder you plan on working in, then unzip it by right clicking
Mac:
curl -O https://swcarpentry.github.io/python-novice-gapminder/files/python-novice-gapminder-data.zip/p>
unzip python-novice-gapminder-data.zip
Linux:
wget https://swcarpentry.github.io/python-novice-gapminder/files/python-novice-gapminder-data.zip
unzip python-novice-gapminder-data.zip
Lessons online : http://swcarpentry.github.io/git-novice/
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.
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.
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 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 in Ubuntu/Windows Linux Subsystem (described above).
Please open the Terminal app, type sudo apt install git and press
Enter
It will ask you "Do you want to continue?" - Please press Yes.
Please open the Terminal app, type git --version and press
Enter/Return. If it's not installed already,
follow the instructions to Install the "command line
developer tools". Don't click "Get Xcode", because that will
take too long and is not necessary for our Git lesson.
After installing these tools, there won't be anything in your /Applications
folder, as they and Git are command line programs.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
available here.
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 in the pop-up dialog. You can watch
a video tutorial about this case.
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.
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. Once it is installed, we will be using Spyder as the IDE to run Python.
Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine).
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 DownloadsThen, try again.
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).