Too many different Python versions on my system and causing problems

Question

During the past years, I have installed many Python libraries with various Python versions. To make them ready to work immediately, I installed them blindly without control. Currently they're causing problems when I tried to install pynest which invokes numpy, scipy and matplotlib. After struggling, I am going to clean and reinstall Python and the libraries.

After investigation, I found Python 2.5/2.6/2.7/3.2 on my system, and each of them has some copies or other things at: (my OS == Mac OS X 10.7.5 Lion)

• /Library/Frameworks/
• /opt/local/Library/Frameworks/
• /opt/local/bin/
• /Applications/
• /usr/local/bin/
• /usr/bin/
• /System/Library/Frameworks/

I know I'm crazy to have these. Now I have removed all these except the things in /System/Libarary/Frameworks (I never remove any thing from /System/Library/). After the clean work, which python now gives /usr/bin/python which links to /System/Library/Frameworks.

Now, is it a clear environment for me to reinstall python? How to double check that there's no other versions existing? How should I reinstall them to guarantee that they and their libraries won't be everywhere and have many copies again?

I want to install a clean Python 2.7 onto a proper location, and make my system know exactly where it is and never install any libraries somewhere else. Please give me some advice that how to manage it like in a professional way.

For your information, here is my current $PATH, I think it should be modified:

/opt/local/bin:/opt/local/sbin:/opt/nest/lib/python2.7/site-packages:/usr/local/lib/python2.7/site-packages:/Library/Frameworks/Python.framework/Versions/2.7/bin:/usr/texbin:/Library/Frameworks/Python.framework/Versions/3.2/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/django/bin:/usr/X11/bin:/opt/local/bin:/opt/local/sbin:/usr/local/lib/python2.7/site-packages:/Library/Frameworks/Python.framework/Versions/2.7/bin:/Library/Frameworks/Python.framework/Versions/3.2/bin 

Please let me know If you need more information. Thank you!

---

UPDATE:

I'm rethinking profoudly why it becomes so crazy. I believe it's because I installed things via:

• easy_install / macports / homebrew / fink / pip sometimes;
• .dmg sometimes;
• .pkg sometimes;
• compile source code sometimes;

and they made things at different locations. I wonder what's the mechanism behind these ways? How do they choose target location? How to prevent them from messing things up?

Answer 1

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.