Summary

Summary

When switching extras with uv sync (or uv tool install), packages that provide conflicting files (like typer and typer-slim) can corrupt the venv. Installing typer-slim overwrites typer's files, and uninstalling typer-slim deletes them—leaving uv's metadata incorrectly showing typer as installed while the actual files are gone.

Reproduction

I created a repo with the repro example: https://github.com/pimlock/uv-bug-repro

When this happened in my workflow, the dependency tree was more complex, the base package depended on typer and one of deps defined in extra had typer-slim as a dep few levels deep.

Here's the verbose output when running all the commands with the spot where the "issue" happens being highlighted

• https://github.com/pimlock/uv-bug-repro/blob/main/repro-output.txt#L180-L192

Commands:

git clone https://github.com/pimlock/uv-bug-repro
cd uv-bug-repro

uv sync                     # ✓ works
uv sync --extra extra1      # ✓ works
uv sync --extra extra2      # ✗ ModuleNotFoundError: No module named 'typer'

The package has:

• Base dependency: typer>=0.20.0
• extra1: typer-slim>=0.20.0
• extra2: rich>=13.0.0 (note: what deps extra2 has is irrelevant for this issue)

What happens

1. uv sync installs typer (which doesn't depend on typer-slim)
2. uv sync --extra extra1 adds typer-slim
3. uv sync --extra extra2 removes typer-slim, but because they "contribute" the same module in venv, the typer's files get removed as well.

This issue is likely caused by how typer and typer-slim are set up (i.e. typer doesn't depend on typer-slim), but it may be potentially causing similar issues with other packages (AFAIK pydantic uses the -slim pattern, but in a different way).

• typer requires: click, typing-extensions, shellingham, rich
• typer-slim requires: click, typing-extensions

They conflict because they both install files to the same typer/ directory. So here's what's happening:

1. Step 1: typer installed → typer/ directory created
2. Step 2: typer-slim installed → overwrites typer/ directory
3. Step 3: typer-slim uninstalled → deletes typer/ directory

Expected

Base dependency typer>=0.20.0 should always be installed regardless of which extras are selected.

Workaround

uv sync --extra extra2 --reinstall works correctly.

Platform

Darwin 25.2.0 arm64

Version

uv 0.9.26 (ee4f003 2026-01-15)

Python version

CPython 3.14.0