Plugin name already registered & ImportPathMismatchError

[Sheila-nk]

On running the command pytest --doctest-modules scipy/constants -v on the Scipy shell, you get the following error:

ValueError: Plugin name already registered: /Users/sheilakahwai/Documents/Work/scipy/build-install/lib/python3.11/site-packages/scipy/conftest.py=<module 'scipy.conftest' from '/Users/sheilakahwai/Documents/Work/scipy/build-install/lib/python3.11/site-packages/scipy/conftest.py'>

The problem seems to be with pytest's import mode: prepend which basically prepends the directory containing test files to the python path leading to conflicts with modules that have the same name but exist in different locations. You can find more information here: choosing an import mode

The issue occurs in Scipy because the build system copies the python source files to build-install.

Currently, to overcome this issue, you can either:

1. Run doctests on the files present in build-install

   pytest --doctest-modules build-install/lib/python3.11/site-packages/scipy/constants -v 

2. Change the import mode to importlib

   pytest --doctest-modules scipy/constants --import-mode=importlib -v

You might also come across the following error:

ImportError while loading conftest '/Users/sheilakahwai/Documents/Work/scipy/scipy/conftest.py'.
_pytest.pathlib.ImportPathMismatchError: ('scipy.conftest', '/Users/sheilakahwai/Documents/Work/scipy/build-install/lib/python3.11/site-packages/scipy/conftest.py', PosixPath('/Users/sheilakahwai/Documents/Work/scipy/scipy/conftest.py'))

This seems to be a pytest issue: https://github.com/pytest-dev/pytest/issues/9567#issuecomment-1117538794

A temporary fix is setting the environment variable: PY_IGNORE_IMPORTMISMATCH=1

[ev-br]

For completeness, here's the one way to run doctests and suppress these collection errors:

$ python dev.py shell
<... new shell opens>
$ PY_IGNORE_IMPORTMISMATCH=1 pytest --doctest-modules --pyargs scipy -x --ignore=/home/br/repos/scipy/scipy/build-install/lib/python3.10/site-packages/scipy/_lib --ignore=/home/br/repos/scipy/scipy/build-install/lib/python3.10/site-packages/scipy/interpolate/_interpnd_info.py

(this ignores the whole of scipy/_lib for simplicity)

[ev-br]

This seems to have been a combination of several things:

• duplication between the scipy root and build-install. Solution: only run on build-install.
• duplication between the public and _impl modules (scipy.signal.__init__ imports names from scipy.signal._signaltools etc). Solution: skip anything with a leading underscore in the full qualified name (https://github.com/ev-br/scpdt/commit/de5e3f1d184a4d4c7c526bef37f3e6711f4035c2)
• a glitch in SciPy itself where it did have two modules with the same name. Fixed in https://github.com/scipy/scipy/pull/20112

So this issue seems to have been fixed, let's close as completed. Thanks Sheila!