To reproduce the issue reported by @xavgit in #295 (comment)

Here's an example with conflicting versions of packaging and setuptools:

setuptools = 75.6.0
packaging = 21.3

If changing the versions in the environment is not a desirable option, here's a quick solution, that controls the versions in the isolated build environment. Vina was using the same trick (?), although this is not a fully tomlized setup.

First, place pyproject.toml in the downloaded repository directory Meeko and let the content be:

[build-system]
requires = ["setuptools>=66.0", "wheel", "packaging>=22.0"]
build-backend = "setuptools.build_meta"

Then, run pip install . or pip install -e . as needed.