Software Carpentry: Griffith University

If you are looking for Software Carpentry - R, please find it here: https://bio-swc-bne.github.io/2016-09-28-GriffithUni-R/

General Information

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, 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: Nathan Campus, Queensland, QLD. Get directions with OpenStreetMap or Google Maps. A campus map for Nathan can also be found here Campus Map

Requirements: Participants must 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). 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 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 a.miotto@griffith.edu.au for more information.

Schedule

Surveys

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

Pre-workshop Survey

Post-workshop Survey

Day 1

08:30	Automating tasks with the Unix shell
10:15	Coffee
10:30	Automating tasks with the Unix shell
12:00	Lunch break
12:45	Version control with Git
14:00	Hacky Hour (Optional)

Day 2

08:30	Intro to Python
10:30	Coffee
10:45	Intro to Python (continued)
12:00	Lunch break
13:00	Building programs with Python (continued)
14:00	Coffee Break
14:15	Building programs with Python (continued)
17:00	Finish

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...

Version Control with Git

Creating a repository
Recording changes to files: add, commit, ...
Viewing changes: status, diff, ...
Ignoring files
Working on the web: clone, pull, push, ...
Resolving conflicts
Open licenses
Where to host work, and why
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.

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.

Links for classes

Below are all the links to the lessons and the data used in them

First lesson: The Unix Shell (Bash)

Lessons online : http://swcarpentry.github.io/shell-novice/

Data to download: http://swcarpentry.github.io/shell-novice/shell-novice-data.zip

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 http://swcarpentry.github.io/shell-novice/data/shell-novice-data.zip

unzip shell-novice-data.zip

Linux:

wget http://swcarpentry.github.io/shell-novice/data/shell-novice-data.zip

unzip shell-novice-data.zip

Second lesson: Python

Lessons online : http://swcarpentry.github.io/python-novice-inflammation/

Data to download: https://github.com/swcarpentry/python-novice-inflammation/raw/gh-pages/data/python-novice-inflammation-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://github.com/swcarpentry/python-novice-inflammation/raw/gh-pages/data/python-novice-inflammation-data.zip/p>

unzip python-novice-inflammation-data.zip

Linux:

wget https://github.com/swcarpentry/python-novice-inflammation/raw/gh-pages/data/python-novice-inflammation-data.zip

unzip python-novice-inflammation-data.zip

Third lesson: Git

Lessons online : http://swcarpentry.github.io/git-novice/

Data to download: None needed!

Github Sign-up: Create an account here https://github.com/join?source=button-home

The Bash Shell

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

Windows

Download the Git for Windows installer.
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). 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.

Git

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).

Windows

Git should be installed on your computer as part of your Bash install (described above).

Mac OS X

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.

Linux

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.

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

Sublime is the editor we will be using Sublime Text.

Mac OS X

Sublime is the editor we will be using Sublime Text.

Linux

Sublime is the editor we will be using 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., 3.5 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

Open http://continuum.io/downloads with your web browser.
Download the Python 3 installer for Windows.
Install Python 3 using all of the defaults for installation . Please ensure you check Make Anaconda as the default Python.

Mac OS X

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

Linux

Open http://continuum.io/downloads with your web browser.
Download the Python 3 installer for Linux.
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.)
Open a terminal window.
Type
```
bash Anaconda-
```
and then press tab. The name of the file you just downloaded should appear.
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).

Once you are done installing the software listed above, please go to this page, which has instructions on how to test that everything was installed correctly.

If all else fails- ResBaz Cloud

If you have issues with these installations, please arrive to class early and an instructor can assist you in installation. Failing that, available are the ResBaz Cloud that we can use to do this work via a web browser. Please find the site below, log in via the Australia Access Federation then ask an instructor for the password. ResBaz Cloud.