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Your question is not at all uncommon. I’ve seen PhD graduates struggle with the exact same issues! While Python is a beautiful programming language with a very friendly community, getting started with the scientific Python stack can be quite a hassle.
There are two nice options for Python on Mac OS X, depending on how much time you want to invest into learning a particular set of tools. Both sets of tools are excellent and are well worth your time, but have a few tradeoffs. They are similar, though, in that they both will require you to spend some time in the terminal; I would recommend installing iTerm2 as your first step, if you haven’t already.
Option 1: Homebrew
This option might be a bit more complicated, and may require more time invested up-front, but in the end can save you time and headaches because you have more control and freedom with how you want to set up Python and other command-line tools.
The first step is to install Homebrew. Currently, this is done with a single terminal command that will guide you through the installation process.
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
As part of it, you will have to install XCode (free from the App Store) and its associated command line tools. This is what makes this option time consuming.
Once you’ve installed Homebrew, you have access to a new command in the terminal, brew. You can use this command to install Python 3, NumPy, and Matplotlib.
# Install Python 3 that will be managed by Homebrew
brew install python3
# Get access to the scientific Python formulas
brew tap Homebrew/python
# Install Numpy and Matplotlib
brew install numpy --with-python3
brew install matplotlib --with-python3
Then you’re good to go! This option gives you access to some powerful tools, like pip and brew. It means that in the future, when you want to install a new Python package, you should be able to pip install <that package>. Other command line tools, like for example git, can be installed with brew install git. It will make programming on Mac OS X a lot easier, in the end!
For some more information, see the Homebrew and Python wiki page.
Option 2: Anaconda
Anaconda is an all-in-one solution that will set up Python and all of the scientific Python tools all at once. All you have to do is download and install it!
Once installed, you should be able to run Python code that uses Numpy and Matplotlib. If you need a new Python package, you should be able to open up a terminal and do pip install <that package>. Some command-line tools and libraries are set up to install with conda install <tool>, but not nearly as many packages are available with conda as are available with brew. But, that might not be a big issue — it depends what you end up using in the future!
The quick start guide is a good resource for the most common issues with Anaconda.