pixi not installing explicit dependencies after irrelevant changes to pyproject/pixi.lock

[tfriedel]

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• I have checked that this issue has not already been reported.

• I have confirmed this bug exists on the latest version of pixi, using pixi --version.

Reproducible example

Sometimes, when a colleague changes the pyproject.toml / pixi.lock drastically just running "pixi install" is not creating the same pixi environment. I have observed that some packages are missing. E.g. just today pydantic was missing, even though it was an explicit dependency. In these situations I just delete .pixi and run "pixi install" again. This solves the problem. But I think there's a bug, because these packages shouldn't be missing.

I have exported two states of our pyproject.toml and pixi.lock here:
pixi_issue.tar.gz

How to reproduce the problem:

cp step1/* .
pixi install
pixi shell
python3 -c 'import pydantic' 

output: nothing

Then:

cp step2/* .
pixi install
pixi shell
python3 -c 'import pydantic' 

The output shouldn't show anything here either, but instead we see:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'pydantic'

Note that in both pyproject.toml files we have pydantic = ">=2.4.2" as a pypi dependency.

This is with pixi 0.32.1

Issue description

Expected behavior