Macos – Removing all but original system-default python on macOS

homebrewmacospippython

I am trying to clean up the various Python installations on my MacBook Pro (macOS 10.13.4) by removing everything except the original system python (2.7.2 for the current version of macOS). I have had installations from python.org, macports, and homebrew at one time or another, and I think I have been able to delete everything these installations touched, but my system python still yells at me when I try to install a module.

After removing the homebrew python and pip installations, and deleting old folders from the macports install, I updated my ~/.bash_profile to contain just my .bashrc config and iTerm2 utilities. I then installed PIP for the system python using easy_install. However, when I try to install a package, for instance voltron, I get the following errors, and the installation does not finish.

matplotlib 1.3.1 requires nose, which is not installed.
python-dateutil 2.6.1 has requirement six>=1.5, but you'll have six 1.4.1 which is incompatible.
prompt-toolkit 1.0.15 has requirement six>=1.9.0, but you'll have six 1.4.1 which is incompatible.
blessed 1.14.2 has requirement six>=1.9.0, but you'll have six 1.4.1 which is incompatible.
matplotlib 1.3.1 has requirement numpy>=1.5, but you'll have numpy 1.8.0rc1 which is incompatible.

which python returns /usr/bin/python and which pip returns /usr/local/bin/pip

I would like to get my computer back to the state it was in when it came out of the box, but I do not want to do a wipe-and-reinstall. I have tried using macOS Recovery Mode to reinstall macOS, but it didn't change the error, so it seems there are some lingering references to these packages somewhere. How can I restore the original state of Python?

$> pip -V
pip 10.0.0b2 from /Library/Python/2.7/site-packages/pip-10.0.0b2-py2.7.egg/pip (python 2.7)

Looks like it actually did end up installing Voltron, but it is still showing an error for the missing dependencies. Here is what happens when I try installing one of them (six, in this case)

$> pip install --user six
Requirement already satisfied: six in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (1.4.1)
python-dateutil 2.6.1 has requirement six>=1.5, but you'll have six 1.4.1 which is incompatible.
prompt-toolkit 1.0.15 has requirement six>=1.9.0, but you'll have six 1.4.1 which is incompatible.
blessed 1.14.2 has requirement six>=1.9.0, but you'll have six 1.4.1 which is incompatible.
matplotlib 1.3.1 has requirement numpy>=1.5, but you'll have numpy 1.8.0rc1 which is incompatible.

Update – value of sys.path

$> python -c "import os, sys; print(os.linesep.join(sys.path))"

/Library/Python/2.7/site-packages/pip-10.0.0b2-py2.7.egg
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload
/Users/emroch/Library/Python/2.7/lib/python/site-packages
/Library/Python/2.7/site-packages
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/PyObjC

Best Answer

I was having a similar issue when installing pacages with PIP and seems that the cause of the problem is this https://github.com/pypa/pip/issues/5196

I could solve the issue following what is proposed here https://stackoverflow.com/questions/27630114/matplotlib-issue-on-os-x-importerror-cannot-import-name-thread

sudo pip uninstall python-dateutil
sudo pip install python-dateutil==2.2

from @oriol-nieto answer

python was using an old version of six, which I removed by typing:

rm -rf /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/six.*

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Ubuntu – Any way to (easily) upgrade Python in Ubuntu

I think you need to set PYTHONPATH after changing the links. On a fresh install of Ubuntu 10.10 I just did, I have:

evadeflow(57)% echo $PYTHONPATH 
/home/evadeflow/lib/python2.6/site-packages:/usr/lib/python2.6/site-packages

You should set this in your environment so it points to the version you want to use (i.e., change the 2.6 to 2.7...)

The suggested way to handle pip(easy_install) with homebrew

Maybe it is time to consider using virtualenv. Virtualenv creates self-contained python environments using the python version you specify. After activating the new virtual environment, everything you install using pip goes under that environment. This helps avoid situations like the one you described.

E.g. create and activate a new python environment using the default python:

# create environment
$ virtualenv --distribute myproject
New python executable in myproject/bin/python
Installing distribute...done.
Installing pip...done.

# activate environment
$ . ./myproject/bin/activate

# check default python
(myproject)$ which python
/Users/me/myproject/bin/python

It is suggested to use the --distribute options to indicate that distribute should be used for installing packages in the new environment instead of (the older) setuptools. After activation your command prompt changes to indicate which python environment is active.

Now install some package. The files will go into myproject directory:

# install django
(myproject)$ pip install django
...

# search for django dir
(myproject)$ find myproject -iname django
myproject/lib/python2.7/site-packages/django

Finally, deactivate:

# deactivate and check for default python
(myproject)$ deactivate
$ which python
/usr/bin/python

To create an environment using a non-default version of python:

$ virtualenv --distribute -p /path/to/custom/python mynewproject

By default virtualenv will copy to the new environment any packages installed for the python version you use to bootstrap it. To prevent this and create an empty environment use the --no-site-packages option. This is especially useful to create environments which can be exactly replicated e.g. from development to production.

Update: As of version 1.7 --no-site-packages has become the default behaviour of virtualenv.

If you want more details, there are plenty of tutorials and blog posts online. E.g.:

Notes on using pip and virtualenv with Django. (most of the post is not django-specific)
Working with virtualenv.

Give it a try and I'm sure you'll stick with it.

Note: Make sure that your executable scripts do not have the python interpreter hardcoded. I.e. their first line should be #!/usr/bin/env python and not something like #!/usr/bin/python.

Update – value of sys.path

Best Answer

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Ubuntu – Any way to (easily) upgrade Python in Ubuntu

The suggested way to handle pip(easy_install) with homebrew

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