Why are all Python packages suddenly gone?

Question

Today I wanted to run a (self written) Python script on my OSX laptop, but all of a sudden, all the imports returned an ImportError. The script was running fine about a month ago and in the meantime I didn't change anything to Python. Furthermore I'm sure that I didn't use a virtualenv back then.

So I just started reinstalling all the packages again (even pip needed a reinstall). I also need OpenCV, for which I run brew install opencv3, but that gives me:

Warning: homebrew/science/opencv3 3.2.0 is already installed

even though I still can't import it in Python:

>>> import cv2
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named cv2

I can of course uninstall and reinstall OpenCV, but it really makes me wonder; how can this have happened? What could possibly erase all Python packages?

All tips are welcome!

EDIT

Ok, I just found out that before I was using the Python installed by brew, but that the python command somehow linked back to /usr/bin/python instead of /usr/local/Cellar/python/2.7.13_1/bin/python2 in which all packages are still installed correctly. So to link python back to the brew version I ran brew unlink python && brew link python, but which python still refers to /usr/bin/python

Which brilliant soul can guide me back to using the brew Python?

EDIT2

I just checked out this list of suggestions to link python to the brew version again, but nothing seems to work. Let me show you what I did:

$ echo $PATH
/usr/local/opt/opencv3/bin:/opt/local/bin:/opt/local/sbin:/usr/local/heroku/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/bin:/Users/hielke/Library/Android/sdk:/Users/hielke/Library/Android/sdk/tools:/Users/hielke/Library/Android/sdk/platform-tools:/usr/local/mysql/bin:/Users/hielke/.composer/vendor/bin
# which shows `/usr/local/bin` before `/usr/bin`

$ brew link --overwrite python
Warning: Already linked: /usr/local/Cellar/python/2.7.13_1
To relink: brew unlink python && brew link python
$ which python
/usr/bin/python  # <= STILL RUNNING THE SYSTEM PYTHON
$ brew unlink python && brew link python
Unlinking /usr/local/Cellar/python/2.7.13_1... 26 symlinks removed
Linking /usr/local/Cellar/python/2.7.13_1... 26 symlinks created
$ which python
/usr/bin/python  # <= STILL RUNNING THE SYSTEM PYTHON

$ cat /etc/paths
/usr/local/bin
/usr/bin  # THIS SEEMS TO BE CORRECT
/bin
/usr/sbin
/sbin

I then restarted the terminal, but which python still gives me /usr/bin/python.

So then I restarted the whole OS, but frustratingly which python still gives me /usr/bin/python.

Who can get me out of this brew mess?!

Print the `sys.path` and find if opencv package is in the path — aristotll, Jul 22 '17 at 16:54
@aristotll - Turns out I was using the wrong Python. I was suddenly using the system installed python instead of the brew installed Python (which is the one in which all packages are installed). I edited my question to it. Would you have any idea how I can link `python` to the brew version again? — kramer65, Jul 22 '17 at 17:05
@kramer65 `echo $PATH` and see if `/usr/local/bin` is before `/usr/bin` — aristotll, Jul 22 '17 at 17:14
@aristotll - I just followed pretty much all tips from this list of answers https://stackoverflow.com/questions/5157678/python-homebrew-by-default but nothing seems to work. I edited my question to include all the things I've tried. Do you have any other ideas? — kramer65, Jul 22 '17 at 17:24

score 2 · Accepted Answer · answered Jul 22 '17 at 17:48

Ok, after a lot of messing around, I found that the folder /usr/local/Cellar/python/2.7.13_1/bin/ didn't contain a symlink called python, just python2 and python2.7.

So finally I solved it by creating a new symlink in /usr/local/Cellar/python/2.7.13_1/bin/ like this:

ln -s ../Frameworks/Python.framework/Versions/2.7/bin/python python

After that I ran

brew unlink python && brew link python

which solved all my problems.

Thanks for your attention and continuous inspiration!

ps. Although this was a solution to my troubles, I'm still unsure how this could have happened. If anybody can enlighten me that is of course still very welcome!

Sounds like it was due to this issue: https://github.com/Homebrew/homebrew-core/issues/15746 There's lot of comments on that issue so it's hopefully helpful to anyone else struggling with this — pir, Jul 20 '20 at 01:28

score 0 · Answer 2 · answered Nov 25 '22 at 00:56

In my case the installed modules seemed to disappear because macOS installed a new minor version and the python3 symlink was updated to point to that new version.

This can be checked by running: ls -laFG /usr/local/bin. As you can see, python3 is pointing to v3.11:

...which is the new version without any modules installed:

However, by explicitly pointing to the old version, we can see all the modules are still there:

Why are all Python packages suddenly gone?

2 Answers2