Introduction to Python - Software Carpentry
N53 0.57 Nathan Campus, Griffith University

15th-17th April

9am to 5pm

Instructors: Masami Yamaguchi, Ido Bar, Heidi Perrett, Amanda Miotto

Helpers: Masami Yamaguchi, Ido Bar



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 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.


Surveys

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

Pre-workshop Survey

Post-workshop Survey


Schedule

Day 1

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

Day 2

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

Day 3

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

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...

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/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



Second lesson: Python

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


Third lesson: Git

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.



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.

The Bash Shell

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

Windows

Today we will be using the Windows Subsystem Linux (Ubuntu flavor). Please install as per this site Install Win 10 If you would like to use a different terminal system, or are operating on Windows 7, please see the install for Git for Windows on the Setup for Bash Software Carpentry page . If you are using Git for Windows, you will not need to install Git separately.

macOS

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.

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.

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.

Windows

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.

macOS

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.

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 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, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

Windows

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.

macOS

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.

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 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).

Windows

Video Tutorial
  1. Open https://www.anaconda.com/download/#windows 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 Add Anaconda to my PATH environment variable.

macOS

Video Tutorial
  1. Open https://www.anaconda.com/download/#macos 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 https://www.anaconda.com/download/#linux 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 Return. 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 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.