specs folder creates issue when installing using uv

[frederic-bender]

I don't actually know why, but in the branch v2-migration, the "specs" prevent uv from installing the package correctly. As soon as I delete "specs" it works.

[JR-1991]

@frederic-bender thanks for submitting the issue. Can you share the entire traceback?

The specs directory is not important though and deleting it is fine.

[frederic-bender]

Sure, @JR-1991

$ uv add git+https://github.com/EnzymeML/PyEnzyme.git@v2-migration

Updating https://github.com/EnzymeML/PyEnzyme.git (v2-migration)                                                                                                                                                                           error: Git operation failed
  Caused by: process didn't exit successfully: `/usr/bin/git submodule update --recursive --init` (exit status: 128)
--- stderr
fatal: No url found for submodule path 'specs' in .gitmodules

[JR-1991]

@frederic-bender, thanks a lot! It appears that the uv module isn’t retrieving the .gitmodules file, which results in the submodule being displayed as undefined and causing the error. This seems to be a developer-related issue, and I assume most users won’t be utilizing the git+ functionality. Since it’s working for you, I suggest prioritizing finishing PR #67 and then delving into this problem.