pdm run don't exclude all site-packages in PYTHONPATH

[dev590t]

• I have searched the issue tracker and believe that this is not a duplicate.

Steps to reproduce

pdm init
pdm run python3 -c "import sys; print(sys.path)"

Actual behavior

(base) echo $PYTHONPATH
/home/dev_1/.local/share/pdm/venv/lib/python3.8/site-packages/pdm/pep582:/home/dev_1/.local/lib/python3.8/site-packages:/home/dev_1/.guix-profile/lib/python3.8/site-packages
(base) pdm run python3 -c "import sys; print(sys.path)"
['', '/home/dev_1/.guix-profile/lib/python3.8/site-packages', '/gnu/store/abznl1yzi6isa57mh1mj3fsdylksqd7m-python-3.8.2/lib/python38.zip', '/gnu/store/abznl1yzi6isa57mh1mj3fsdylksqd7m-python-3.8.2/lib/python3.8', '/gnu/store/abznl1yzi6isa57mh1mj3fsdylksqd7m-python-3.8.2/lib/python3.8/lib-dynload', '/tmp/pdm/__pypackages__/3.8/lib']

/home/dev_1/.guix-profile/lib/python3.8/site-packages is still in sys.path. My project load the system numpy instead of my pypackages numpy.

Environment Information

# Paste the output of `pdm info && pdm info --env` below:
(base) pdm info && pdm info --env
PDM version:        1.12.2
Python Interpreter: /home/dev_1/.guix-profile/bin/python3 (3.8)
Project Root:       /tmp/pdm
Project Packages:   /tmp/pdm/__pypackages__/3.8
{
  "implementation_name": "cpython",
  "implementation_version": "3.8.2",
  "os_name": "posix",
  "platform_machine": "x86_64",
  "platform_release": "5.9.3-gnu",
  "platform_system": "Linux",
  "platform_version": "#1 SMP 1",
  "python_full_version": "3.8.2",
  "platform_python_implementation": "CPython",
  "python_version": "3.8",
  "sys_platform": "linux"
}

additional information

I have try to remove /home/dev_1/.guix-profile/lib/python3.8/site-packages from PYTHONPATH, but it seems pdm depend it to run.
I have try to search a configuration in pdm to explicit exclude this path, but not found.
related issue #100

[frostming]

You shouldn't include any site-packages in PYTHONPATH, they are loaded every time, even if you are using incompatible Python versions.

I don't know why you say PDM depends on that, it shouldn't.

[dev590t]

You shouldn't include any site-packages in PYTHONPATH, they are loaded every time, even if you are using incompatible Python versions.
I don't know why you say PDM depends on that, it shouldn't.

You can see if I remove some site-packages from my PYTHONPATH, pdm will not run

(base) echo $PYTHONPATH 
/home/dev_1/.local/share/pdm/venv/lib/python3.8/site-packages/pdm/pep582:/home/dev_1/.local/lib/python3.8/site-packages:/home/dev_1/.guix-profile/lib/python3.8/site-packages
(base) pdm -V
Python Development Master (PDM), version 1.12.2
(base) export PYTHONPATH=/home/dev_1/.local/share/pdm/venv/lib/python3.8/site-packages/pdm/pep582
(base) pdm -V
Traceback (most recent call last):
  File "/home/dev_1/.local/bin/pdm", line 5, in <module>
    from pdm.core import main
  File "/home/dev_1/.local/share/pdm/venv/lib/python3.8/site-packages/pdm/__init__.py", line 5, in <module>
    from pdm.cli.commands.base import BaseCommand
  File "/home/dev_1/.local/share/pdm/venv/lib/python3.8/site-packages/pdm/cli/commands/base.py", line 5, in <module>
    from pdm.cli.options import Option, global_option, project_option, verbose_option
  File "/home/dev_1/.local/share/pdm/venv/lib/python3.8/site-packages/pdm/cli/options.py", line 7, in <module>
    from click import secho
ModuleNotFoundError: No module named 'click'

In a new shell

(base) python3 -c "import click;print(click.__path__)"
['/home/dev_1/.local/lib/python3.8/site-packages/click']

I have installed pdm with

curl -sSL https://raw.githubusercontent.com/pdm-project/pdm/main/install-pdm.py | python3 -

[frostming]

Make sure PYTHONPATH is /home/dev_1/.local/share/pdm/venv/lib/python3.8/site-packages/pdm/pep582 and run

/home/dev_1/.local/share/pdm/venv/bin/python -m pip list

To show whether click is installed

[dev590t]

(base) export PYTHONPATH=/home/dev_1/.local/share/pdm/venv/lib/python3.8/site-packages/pdm/pep582
(base) /home/dev_1/.local/share/pdm/venv/bin/python -m pip list
Package    Version
---------- -------
pdm        1.12.2
pip        21.3.1
setuptools 41.2.0

I have installed pdm following recommended-installation-method. Why the script haven't installed the dependancies of pdm into pdm 's site-packages?

[frostming]

Run /home/dev_1/.local/share/pdm/venv/bin/python -m pip install -I --force-reinstall pdm to see what it outputs, it may give some hints why it thinks the dependencies don't need to be installed.

[dev590t]

Thanks! That runs. I remove pdm, and reinstalled it with

curl -sSL https://raw.githubusercontent.com/pdm-project/pdm/main/install-pdm.py | python3 -

And this time, it is installed correctly

(base) /home/dev_1/.local/share/pdm/venv/bin/python -m pip list
Package         Version
--------------- -------
attrs           21.4.0
blinker         1.4
cached-property 1.5.2
click           8.0.3
..

I have try to reinstall it few times before, I don't why, but this time it is correctly installed

[dev590t]

Additional information, I have replace in .bashrc

if [ -n "$PYTHONPATH" ]; then
    export PYTHONPATH='/home/dev_1/.local/share/pdm/venv/lib/python3.8/site-packages/pdm/pep582':$PYTHONPATH
else
    export PYTHONPATH='/home/dev_1/.local/share/pdm/venv/lib/python3.8/site-packages/pdm/pep582'
fi

by

export PYTHONPATH='/home/dev_1/.local/share/pdm/venv/lib/python3.8/site-packages/pdm/pep582'

to remove all site-packages.

I think the documentation should precise "don't include any site-packages in PYTHONPATH". Because this line export PYTHONPATH='/home/dev_1/.local/share/pdm/venv/lib/python3.8/site-packages/pdm/pep582':$PYTHONPATH from pdm --pep582 will include it. I can make a PR for that.

[frostming]

Good, go for it!