python - conda environment has access to system modules, how to prevent?

Question

I noticed that when I create a new enviornment with conda, I can import python modules in that environment that were NOT installed there.

Example with keras: Although the module is NOT in that enviornment:

(py2) user@user-Precision-7920-Tower:~$ conda list keras
# packages in environment at /home/user/anaconda3/envs/py2:
#
# Name                    Version                   Build  Channel

I can still import it, apparently from the system (user) install, outside conda!

(py2) user@user-Precision-7920-Tower:~$ python
Python 2.7.15 | packaged by conda-forge | (default, Mar  5 2020, 14:56:06) 
[GCC 7.3.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.

>>> import keras
Using TensorFlow backend.
>>> keras.__file__
'/home/user/.local/lib/python2.7/site-packages/keras/__init__.pyc'

In fact, python inside conda has access to non-conda paths!

>>> import sys
>>> 
>>> sys.stdout.write("
".join(sys.path))

/home/user/anaconda3/envs/py2/lib/python27.zip
/home/user/anaconda3/envs/py2/lib/python2.7
/home/user/anaconda3/envs/py2/lib/python2.7/plat-linux2
/home/user/anaconda3/envs/py2/lib/python2.7/lib-tk
/home/user/anaconda3/envs/py2/lib/python2.7/lib-old
/home/user/anaconda3/envs/py2/lib/python2.7/lib-dynload
/home/user/.local/lib/python2.7/site-packages               <-- 
/home/user/anaconda3/envs/py2/lib/python2.7/site-packages>>> 

Conda is supposed to keep things isolated. How did this path endd up in here, and how to avoid this from happening?

UPDATE:

My user-level python is 2.7, and I noticed this behavior always happen when I create a new conda environment with python 2.7, this just automatically adds the .local/lib/python2.7/site-packages to PYTHONPATH.

If I create new conda environments with python3.x , this does not happen.

Does this mean that one cannot create a separate isolated conda environment for the same python version as the user-level python?

Answer 1

In addition to what @VikashB mentioned, these can result from packages installed with pip install --user. As @TimRoberts alluded to in the comments, the site module, which populates the sys.path variable, searches paths like ~/.local/lib/python*/site-packages by default.

If you need to keep these packages for some reason, you'll need to move them to a non-default location so the site module doesn't find them. For example,

mkdir ~/.local/lib/py_backup
mv ~/.local/lib/python* ~/.local/lib/py_backup

This will effectively hide them, and they could still be used through PYTHONPATH if necessary.

Otherwise, just remove them, i.e.,

rm -r ~/.local/lib/python*

For reference, Conda users are discouraged from using the --user flag in the Conda documentation. Conda environments assume full isolation of environments, so leakage such as OP reports can lead to undefined behavior.