Too many different Python versions on my system and causing problems

Why did it get messed up?

There're a couples of different way to install Python, as the update of OP says, and they locate files in different locations. For example, macports puts things into /opt/local/, while homebrew puts things into /usr/local/. Also, Mac OS X brings a few python versions with itself. So, if you install python many times via different ways, you will get many python versions existing independently on your system.

What problem does it cause?

I don't know exactly. I guess the problem is that if you have many versions of python, then which one to use and where to find packages will be determined by the path order in your system PATH and the PYTHONPATH respectively. So you may lose control of where to install python modules. Consider that if you run sudo python setup.py install to install a module (it finds python by the root's PATH) and then try to import the module by python -c "import it" (this time it finds python by your PATH), maybe something will go wrong. This is my guess, I didn't validate it. But in my own case, something did go wrong.

How to avoid this?

I think the principle would be that be aware of that different ways and tools install things independently to different locations, so use them mindfully.

• Unless you intend to, don't install the same thing twice via different ways. (If you intend to do it for python, you might want to check out virtualenv)
• Keep an eye on the path order in your PATH and consider if it's correct.
• When installing modules, be clear which python (or pip) is running and where the module is installed.

So, how did I solve my own case?

Since it had been messing up already and seemed to be very hard to cure, so finally I solved this question by a full OS re-installation, and started to follow the DOs-and-DONTs above. For the installation of the scientific environment with python (numpy/scipy/matplotlib, which had shown problems to make me ask this question), I found this tutorial was extremely helpful. So, problem solved finally.

Here is what was confusing me and how I solved it.

$ which python
/usr/bin/python 

$ which python3
/usr/local/bin/python3

$ ls /usr/local/bin/python
ls: /usr/local/bin/python: No such file or directory

So notice I didn't have a HomeBrew installation of python2.7, but did have the python3 installation. The version under /usr/bin/python is using the system default. You can tell based on the module search path:

$ /usr/bin/python
Python 2.7.10 (default, Feb  7 2017, 00:08:15) 
[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.34)] on darwin
`enter code here`Type "help", "copyright", "credits" or "license" for 
more information.
>>> import sys
>>> sys.path
['', '/Library/Python/2.7/...

Notice the '/Library/Python'... that's Mac OS's version of python. But I want to stay strictly on a user installed version (i.e. HomeBrew).

So here's what I did to fix this:

$ brew install python
...
Warning: python 2.7.13 is already installed, it's just not linked.
You can use `brew link python` to link this version.

$ brew link --overwrite python

$ which python
/usr/local/bin/python

$ python
Python 2.7.10 (default, Feb  7 2017, 00:08:15) 
[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.34)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.path
['', '/usr/local/Cellar/python/2.7.13...

Its no longer /Library/.. but /usr/local.

Now its finding all of my pip installed modules! Problem solved!

---

UPDATE:

After updating brew to version 1.5.4, it seems the symbolic links were removed. And now you have to add this to your path:

export PATH="/usr/local/opt/python/libexec/bin:$PATH"

Read the Caveats section in 'brew info python':

==> Caveats
This formula installs a python2 executable to /usr/local/bin.
If you wish to have this formula's python executable in your PATH then add
the following to ~/.bash_profile:
  export PATH="/usr/local/opt/python/libexec/bin:$PATH"

Pip and setuptools have been installed. To update them
  pip2 install --upgrade pip setuptools

You can install Python packages with
  pip2 install <package>

They will install into the site-package directory
  /usr/local/lib/python2.7/site-packages

See: https://docs.brew.sh/Homebrew-and-Python.html