pip breaks installed packages unrelated to the one installed (or their dependencies)

[davidedelvento]

Environment

• pip version: 19.1.1
• Python version: 3.5
• OS: CentOS Linux release 7.4.1708

In the NVIDIA-provided 18.10-py3 container

> python --version
Python 3.5.2
> pip --version
pip 19.1.1 from /home/ddvento/.local/lib/python3.5/site-packages/pip (python 3.5)

Description
I need to add packages (describing just one for the sake of the issue) to my environment. Since the NVIDIA container does not provide venv I am using pip's -t option instead.

> python -m venv my_env
The virtual environment was not created successfully because ensurepip is not
available.  On Debian/Ubuntu systems, you need to install the python3-venv
package using the following command.

    apt-get install python3-venv

You may need to use sudo with that command.  

I don't have root on this machine (not even in the container) so I do:

> export PYTHONPATH=/tmp/test_env/
> pip install patsy -t $PYTHONPATH 

Expected behavior
Running the previous should either install patsy and its dependencies, or not. Hopefully the former. Instead it breaks a third package.

How to Reproduce

> pip show numpy
Name: numpy
Version: 1.14.5
Summary: NumPy: array processing for numbers, strings, records, and objects.
Home-page: http://www.numpy.org
Author: Travis E. Oliphant et al.
Author-email: None
License: BSD
Location: /usr/local/lib/python3.5/dist-packages
Requires: 
Required-by: tensorflow-gpu, tensorboard, scipy, scikit-learn, resampy, pandas, numba, matplotlib, librosa

> pip show tensorflow-gpu
Name: tensorflow-gpu
Version: 1.10.0+nv
Summary: TensorFlow is an open source machine learning framework for everyone.
Home-page: https://www.tensorflow.org/
Author: Google Inc.
Author-email: opensource@google.com
License: Apache 2.0
Location: /usr/local/lib/python3.5/dist-packages
Requires: numpy, grpcio, astor, six, tensorboard, termcolor, protobuf, gast, wheel, setuptools, absl-py
Required-by: 

> pip show patsy

> 

Notice how patsy is not originally installed.

Output

> pip install patsy -t $PYTHONPATH 
Collecting patsy
  Using cached https://files.pythonhosted.org/packages/ea/0c/5f61f1a3d4385d6bf83b83ea495068857ff8dfb89e74824c6e9eb63286d8/patsy-0.5.1-py2.py3-none-any.whl
Collecting six (from patsy)
  Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting numpy>=1.4 (from patsy)
  Using cached https://files.pythonhosted.org/packages/f6/f3/cc6c6745347c1e997cc3e58390584a250b8e22b6dfc45414a7d69a3df016/numpy-1.16.3-cp35-cp35m-manylinux1_x86_64.whl
ERROR: tensorflow-gpu 1.10.0+nv has requirement numpy<=1.14.5,>=1.13.3, but you'll have numpy 1.16.3 which is incompatible.
Installing collected packages: six, numpy, patsy
Successfully installed numpy-1.16.3 patsy-0.5.1 six-1.12.0

This is related to #5178 and probably #988 (the mother of all my anger about pip)

[chrahunt]

As mentioned in #5178, -t also unfortunately implies --ignore-installed. Since this is just a side-effect of the issue described there (and you have contributed the same information on that issue), I will close this one. Please also check out #4575 where some of the details of the relationship between --target and the other types of environments pip installs into are being discussed.