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. If you already have Python installed, please install Anaconda anyway. Anaconda can be used alongside any other versions of Python. Please also make sure you install Python version 3.x (e.g., 3.5 is fine).
We will teach Python using the Jupyter notebook (also known as 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).
bash Anaconda3- and then press tab. The name of the file you just downloaded
should appear.Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
setx HOME "%USERPROFILE%"SUCCESS: Specified value was saved.This will provide you with both Git and Bash in the Git Bash program.
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). 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 (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).
You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. Please create a GitHub account if you don’t have one already. Also, it is worth considering 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 your computer as part of your Bash install (described above).
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.
If Git is not already available on your machine you can try to install it via your distro’s package manager.
For Debian/Ubuntu use the command sudo apt-get install git and for Fedora use the command sudo yum 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 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.
You’re welcome to use whatever editor you are comfortable with, or follow the instructions below for using nano.
The nano editor is a basic editor and the default that instructors use in the workshop.
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.
Note: This installer only works on 64-bit Windows. If you have 32-bit Windows (or you get an error message when running the installer), you can try following the instructions in the 5th comment here. You will need to restart or open a new bash shell before you can use nano.
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.
The nano editor 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 Text Wrangler or Sublime Text.
The nano editor 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.
Eclipse is a professional integrated development environment for Java, C, C++, Fortran, Python, R, and many other languages. It offers many features not found in text editors such as Emacs, VIM, nano, etc.
cmd application and type java -version. If you get an error or
the version is not 1.8.x then you need to install Java 8 as follows:
Terminal application and type java -version. If you get an error or
the version is not 1.8.x then you need to install Java 8 as follows:
java -version.
If you get an error or the version is not 1.8.x then you need to install Java 8. If you wish to use OpenJDK,
follow the instructions with your Linux distribution for updating the OpenJDK version. If you’d like to use
Oracles Java, do the following:
PyDev is a complete development environment for Python programs of any size. Based on the hugely popular Eclipse platform, PyDev provides a wide range of Python-specific tools, in addition to the development tools already integrated with Eclipse.
This section assems you’ve already installed Eclipse. If you haven’t install Eclipse, please do this first.
You should have a “Git SDK” icon installed on your desktop at the end of the installation. This will provide you with a Bash shell,
the make command, and a C++ compiler.
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).
For the make command and a C++ compiler, you’ll need the XCode command line tools. Run the
command xcode-select --install.
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.
Use the test process below to see if you have make and the C++
compiler installed. If the test fails, you will need to
install the corresponding packages using your systems package manager. This will depend on
on the Linux distribution you have installed. The corresponding RPM packages are:
Once you have completed the installation of these packages, do the following to test the setup:
Download setup-test.zip.
Move setup-test.zip into a directory which you can access via your bash shell.
Open a Bash shell window (“Git Bash” on Windows).
Navigate to the directory where you downloaded the file.
Unpack setup-test.zip as follows:
$ unzip setup-test.zip
On Windows, open a “Git SDK” bash shell.
Change into the setup-test directory and run make:
$ cd setup-test
$ make
If you see the output Hello world! your installation is correctly configured.