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COMP0233: Research Software Engineering With Python

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Mac

Upgrade OSX

We do not recommend following this training on older versions of OSX without an app store: upgrade to at least OSX Mavericks.

Git

On a terminal you can install git by trying to run it:

git --version

If that throws you an error message, then most likely you will need to install XCode.

XCode and Command line tools

Install the XCode command-line-tools by opening a terminal and run the following.

xcode-select --install

And follow the on screen instructions.

You may also install Xcode from the Mac app store if you wish, but it is not needed.

Pre Mavericks:

Install XCode using the Mac app store.

Then, go to Xcode…Preferences…Downloads… and install the command line tools option.

Homebrew

Homebrew is a package manager for OSX which enables the installation of a lot of software useful for scientific computing. It is required for some of the installations below. But not essential for Software Carpentry. Homebrew requires the Xcode tools above.

Install Homebrew via typing this at a terminal:

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

and then type.

brew doctor

And read the output to verify that everything is working as expected.

If you are already running MacPorts or another package manager for OSX we don’t recommend installing homebrew.

Python

We recommend installing a complete scientific python distribution. One of these is Anaconda.

Please download and install Anaconda (Python 3.7 version).

Python from Homebrew

Alternatively if you wish to install python manually you can use Homebrew. OSX ships with python and some packages. However this has known limitations and we do not recommend it. You can install a new version of python from Homebrew with the following. Please follow the instructions above to install the Xcode tools and Homebrew before attempting this.

brew install python3

In order to ensure that this version of python is selected over the OSX default version you should execute the following command:

echo export PATH='/usr/local/bin:$PATH' >> ~/.bash_profile

and reopen the terminal. Verify that this is correctly installed by executing

python --version

Which should print:

Python 3.7.x

This will result in an installation of python3 and pip3 which you can use to have access to the latest python features which will be taught in this course.

Then install additional python packages by executing the following.

brew install [package-name]

  • pkg-config
  • freetype
  • gcc

pip3 install [package-name]

  • numpy
  • scipy
  • matplotlib
  • jupyter
  • ipython[all]

The following packages should be installed automatically as dependencies. But we recommend installing them manually just in case.

  • tornado
  • jinja2
  • pyzmq
  • pytest

Editor and shell

The default text editor on OS X textedit should be sufficient for our use. Alternatively we recommend to use Visual Studio Code. Check their setup page for detailed instructions.

For a better git integration we suggest the git graph plugin.

To setup git to use textedit executing the following in a terminal should do.

git config --global core.editor /Applications/TextEdit.app/Contents/MacOS/TextEdit

For VS Code:

git config --global core.editor "code --wait"

The default terminal on OSX should also be sufficient. If you want a more advanced terminal iTerm2 is an alternative.