00 Installing the environment
12 Jan 2016The instructions were taken from Software Carpentry, in particular David Dotson's recent workshop at ASU.
Overview
You will need to install
- The Bash Shell
- Git
- a text editor (by default,
nano
) - Python (including a number of additional packages required for scientific computing)
In each section, find the instructions for your operating system (Windows, Mac OS X, or Linux).
Once you have installed everything, test your installation.
Setup
To participate in a the class, you will need access to the software described below. In addition, you will need an up-to-date web browser.
SoftwareCarpentry maintains 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
- Download the Git for Windows installer.
- Run the installer and follow the steps bellow:
- Click on "Next".
- Click on "Next".
- Click on "Next".
- Click on "Next".
- Click on "Next".
- 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.
- Click on "Next". Keep "Checkout Windows-style, commit Unix-style line endings" selected.
- Select "Use Windows' default console window" and click on "Next".
- Click on "Next".
- 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
nano is a basic editor and the default that is used in the class. 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.
Mac OS X
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 Text Wrangler 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 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., 3.4 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 except make sure to check Make Anaconda 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
</p>- 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. Typeyes
and press enter to prepend Anaconda to yourPATH
(this makes the Anaconda distribution the default Python).
Testing
Bash shell
Open a terminal (Mac OS X, Linux) or open Git Bash (under All Programs/Git/Git Bash) in Windows.
Type
Should show /bin/bash
or /usr/bin/bash
(or similar).
We use "shell" and "terminal" (and "console") pretty interchangeably.
Git
In the shell, type
which should show something like git version 2.7.0
.
nano
In the shell, type
You should see GNU nano 2.0.6
(or similar in the top line) and at
the bottom of the screen ^X Exit ^J Justify
(and more). Quit
nano by holding down the control
key together with X
,
i.e. control + X
. In Unix keystrokes, the control key is typically
indicated with the caret character ^
.
Python
In the shell, type
which should give something similar to 3.5.1 |Anaconda 2.4.1
(64-bit); (default, Dec 7 2015, 15:00:12)
(and more
stuff). Important: you should have Python 3, i.e., a version like
3.4. or 3.5.