pip install --user -e . fails

Description

The setup.py call is appended with --prefix= - which breaks installation, bailing on not being able to write to /usr/local - or, even worse, if it is writable, put’s the files there rather then in $HOME.

Using --prefix=~/.local instead of --user works as expected.

Expected behavior

Respect --user and install to $HOME

pip version

pip 21.3.1

Python version

python3-3.9.6-2.fc34.x86_64

OS

Fedora 34

How to Reproduce

1. git clone https://github.com/dschwoerer/xemc3
2. pip install --user -e xemc3

(Full instructions below)

Output

Starting on a clean fedora:34 image:
$ dnf install git
$ python3 -m ensurepip
$ pip install -U pip
$ useradd test
$ su test
$ cd
$ git clone https://github.com/dschwoerer/xemc3
Cloning into 'xemc3'...
remote: Enumerating objects: 1090, done.
remote: Counting objects: 100% (450/450), done.
remote: Compressing objects: 100% (260/260), done.
remote: Total 1090 (delta 261), reused 218 (delta 184), pack-reused 640
Receiving objects: 100% (1090/1090), 296.48 KiB | 4.17 MiB/s, done.
Resolving deltas: 100% (709/709), done.
$ pip install -e xemc3 --user
Obtaining file:///home/test/xemc3
  Installing build dependencies ... done
  Checking if build backend supports build_editable ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting xarray>=0.16.0
  Downloading xarray-0.19.0-py3-none-any.whl (827 kB)
     |████████████████████████████████| 827 kB 3.2 MB/s            
Collecting eudist
  Downloading eudist-0.1.3-cp39-cp39-manylinux2014_x86_64.whl (330 kB)
     |████████████████████████████████| 330 kB 13.2 MB/s            
Collecting numpy>=1.13.0
  Downloading numpy-1.21.3-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
     |████████████████████████████████| 15.7 MB 427 kB/s            
Collecting matplotlib!=3.3.0,!=3.3.1,!=3.3.2,>=3.1.1
  Downloading matplotlib-3.4.3-cp39-cp39-manylinux1_x86_64.whl (10.3 MB)
     |████████████████████████████████| 10.3 MB 12.7 MB/s            
Collecting netcdf4>=1.4.0
  Downloading netCDF4-1.5.7-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.7 MB)
     |████████████████████████████████| 4.7 MB 14.5 MB/s            
Collecting pyparsing>=2.2.1
  Using cached pyparsing-3.0.1-py3-none-any.whl (96 kB)
Collecting pillow>=6.2.0
  Downloading Pillow-8.4.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
     |████████████████████████████████| 3.1 MB 6.7 MB/s            
Collecting cycler>=0.10
  Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.3.2-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB)
     |████████████████████████████████| 1.6 MB 8.7 MB/s            
Collecting python-dateutil>=2.7
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
     |████████████████████████████████| 247 kB 9.7 MB/s            
Collecting cftime
  Downloading cftime-1.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (228 kB)
     |████████████████████████████████| 228 kB 13.3 MB/s            
Collecting pandas>=1.0
  Downloading pandas-1.3.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.5 MB)
     |████████████████████████████████| 11.5 MB 6.6 MB/s            
Requirement already satisfied: setuptools>=40.4 in /usr/local/lib/python3.9/site-packages (from xarray>=0.16.0->xemc3==0.1.0) (53.0.0)
Collecting six
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting pytz>=2017.3
  Downloading pytz-2021.3-py2.py3-none-any.whl (503 kB)
     |████████████████████████████████| 503 kB 11.0 MB/s            
Installing collected packages: six, pytz, python-dateutil, numpy, pyparsing, pillow, pandas, kiwisolver, cycler, cftime, xarray, netcdf4, matplotlib, eudist, xemc3
  Running setup.py develop for xemc3
    ERROR: Command errored out with exit status 1:
     command: /usr/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/test/xemc3/setup.py'"'"'; __file__='"'"'/home/test/xemc3/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps --user --prefix=
         cwd: /home/test/xemc3/
    Complete output (35 lines):
    /tmp/pip-build-env-rexipg1m/overlay/lib/python3.9/site-packages/setuptools/__init__.py:148: SetuptoolsDeprecationWarning: setup_requires is deprecated. Supply build dependencies using PEP 517 pyproject.toml build-requires.
      warnings.warn(
    running develop
    /tmp/pip-build-env-rexipg1m/overlay/lib/python3.9/site-packages/setuptools/command/easy_install.py:156: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
      warnings.warn(
    WARNING: The user site-packages directory is disabled.
    /tmp/pip-build-env-rexipg1m/overlay/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
      warnings.warn(
    Checking .pth file support in /usr/local/lib/python3.9/site-packages/
    error: can't create or remove files in install directory
    
    The following error occurred while trying to add or remove files in the
    installation directory:
    
        [Errno 13] Permission denied: '/usr/local/lib/python3.9/site-packages/test-easy-install-145.pth'
    
    The installation directory you specified (via --install-dir, --prefix, or
    the distutils default setting) was:
    
        /usr/local/lib/python3.9/site-packages/
    
    Perhaps your account does not have write access to this directory?  If the
    installation directory is a system-owned directory, you may need to sign in
    as the administrator or "root" account.  If you do not have administrative
    access to this machine, you may wish to choose a different installation
    directory, preferably one that is listed in your PYTHONPATH environment
    variable.
    
    For information on other options, you may wish to consult the
    documentation at:
    
      https://setuptools.readthedocs.io/en/latest/deprecated/easy_install.html
    
    Please make the appropriate changes for your system and try again.
    
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/test/xemc3/setup.py'"'"'; __file__='"'"'/home/test/xemc3/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps --user --prefix= Check the logs for full command output.

Code of Conduct

• I agree to follow the PSF Code of Conduct.

[uranusjr]

This looks like an issue in Red Hat’s Python (or maybe they don’t support this use case). You will need to report this to Red Hat.

[uranusjr]

Duplicate of #7953