How to Fix Common pytest Errors with uv

Pytest failures that have nothing to do with your actual tests are some of the most frustrating errors in Python development. This guide covers the problems people hit most often when running pytest in uv-managed projects and how to fix them.

ModuleNotFoundError

The most common pytest error in uv projects. There are several causes.

Missing uv sync

If you see ModuleNotFoundError for your own package, the project likely has not been installed into the virtual environment:

ModuleNotFoundError: No module named 'my_package'

Fix it by syncing your project:

uv sync

This installs your project and its dependencies into the virtual environment. After syncing, uv run pytest should find your package.

Flat Layout Import Issues

Projects that use a flat layout (source code at the repository root, not inside a src/ directory) can fail because pytest does not add the project root to sys.path by default:

tests/test_app.py:1: in <module>
    from app import create_app
ModuleNotFoundError: No module named 'app'

Add pythonpath to your pytest configuration in pyproject.toml:

[tool.pytest.ini_options]
pythonpath = ["."]

This tells pytest to add the project root to sys.path before collecting tests, making top-level modules importable.

Missing __init__.py

If your tests can import some modules but not others, check for a missing __init__.py:

my_package/
├── __init__.py
├── core.py
└── utils/          # <-- missing __init__.py
    └── helpers.py

Python will not treat utils as a package without __init__.py (unless you are using namespace packages intentionally). Add the file:

touch my_package/utils/__init__.py

Choosing Between uv run pytest, uvx pytest, and uv run --with pytest pytest

These three commands look similar but behave differently:

uv run pytest is the right choice for most projects. It runs pytest from the project’s virtual environment, with your package installed and all dependencies available.

uvx pytest runs pytest in an isolated, temporary environment with no access to your project’s dependencies. Use it for running pytest on standalone scripts that have no imports from your project.

uv run --with pytest pytest is useful when pytest is not listed in your project’s dependencies but you still want to test against the project’s installed packages.

conftest.py Not Found

If fixtures or hooks defined in conftest.py are not being picked up, the file is likely in the wrong directory. Pytest looks for conftest.py in the test directory and every parent directory up to the root:

my_project/
├── conftest.py          # Available to all tests
├── tests/
│   ├── conftest.py      # Available to tests in tests/
│   ├── test_api.py
│   └── integration/
│       ├── conftest.py  # Available to tests in integration/
│       └── test_e2e.py

A conftest.py inside src/ or a subdirectory that pytest does not traverse will be ignored.

Fixture Not Found Across Files

fixture 'db_connection' not found

Fixtures defined in one test file are not visible to other test files. If multiple test files need the same fixture, move it to a conftest.py file in a shared parent directory:

# tests/conftest.py
import pytest

@pytest.fixture
def db_connection():
    conn = create_test_database()
    yield conn
    conn.close()

Any test file under tests/ will now have access to db_connection without importing it.

See Also

• Setting up testing with pytest and uv for a complete project setup walkthrough
• How to run tests using uv for basic test execution
• pytest reference for an overview of pytest features