No module named kmerdb in the bin script from pyproject.toml's entry_point.

[MatthewRalston]

Traceback (most recent call last):
  File "path/to/python-version/bin/kmerdb", line 5, in <module>
    from kmerdb import cli
ModuleNotFoundError: No module named 'kmerdb'

[MatthewRalston]

Looks related to this StackOverflow post.

https://stackoverflow.com/questions/73958714/python-error-when-creating-cli-entry-point-configuration-for-my-project-what-am

[MatthewRalston]

What is my environment?

Python 3.10.1
pip 22.3.1

What have I tried?

cd kmerdb
python -m build
pip install -I dist/kmerdb-0.7.2-py3-none-any.whl

Install completes successfully.

pyproject.toml

[build-system]
requires = ["setuptools", "wheel", "numpy>=1.19.0", "Cython>=0.29.21"]
build-backend = "setuptools.build_meta"

[project]
name = "kmerdb"
version = "0.7.2"
description = "Yet another kmer library for Python"

#...


[project.entry-points]
console_scripts = {kmerdb = "kmerdb:cli"}

Expected

I expect the installed bin script to not produce the following.

(kdb) [matt@argo] git:pyprojecttoml_build_twine+ </ffast2/kdb>>kmerdb -h
Traceback (most recent call last):
  File "/home/matt/.pyenv/versions/kdb/bin/kmerdb", line 5, in <module>
    from kmerdb import cli
ModuleNotFoundError: No module named 'kmerdb'
(kdb) [matt@argo] git:pyprojecttoml_build_twine+ </ffast2/kdb>>python
Python 3.10.1 (main, Jan  1 2022, 21:28:19) [GCC 11.1.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import kmerdb
>>> # Imports successfully
(kdb) [matt@argo] git:pyprojecttoml_build_twine+ </ffast2/kdb>>cat ~/.pyenv/versions/kdb/bin/kmerdb 
#!/home/matt/.pyenv/versions/3.10.1/envs/kdb/bin/python3.10
# -*- coding: utf-8 -*-
import re
import sys
from kmerdb import cli
if __name__ == '__main__':
    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
    sys.exit(cli())

[MatthewRalston]

Issue borking the debug process on my end: pyenv/pyenv#2572

[MatthewRalston]

It seems that this is a generic issue regardless of the virtualenv strategy I'm using. For PyPI folks who may come here, know that I've ruled out a middleware-specific issue by using both classical virtualenv and pyenv virtualenv scenarios to instantiate my Python virtual environment.

The issue is that regardless of whether my python package kmerdb command is invoked from a pyenv shim, or classically with the bin script produced by setup on installation of my wheel, built with python -m build, it has an invalid pythonpath somehow in the shell script.

Virtualenv, pip, setuptools, and python versions can all be found in the relevant issues in your repository.
But again,
pip 22.3.1
virtualenv 20.17.1
python 3.10.1
setuptools 61.0 (specified in pyproject.toml)

The legacy setup.py which did produce the correct bin script can be found here

[MatthewRalston]

What's interesting is that the virtualenv seems to be setting my pythonpath correctly, so i can still import and invoke the module independently, just can use the kmerdb bin script. For example, the one found at .venv/bin/kmerdb, with the contents as described previously:

#!path/to/.venv/bin/python
# -*- coding: utf-8 -*-
import re
import sys
from kmerdb import cli
if __name__ == '__main__':
    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
    sys.exit(cli())

Which again produces the output as above, regarding the kmerdb module not being available to the bin script.

Thanks again for your help!