We've observed an odd behavior where the extend-select = ["I"] is not honored for code in tests/ when a very specific set of circumstances occur. I'm not even sure I have the minimum reproduction steps completely down, but I can very consistently reproduce the situation.

1. The tests import items from specific module mod1
2. The python code structure starts at src instead of the repo root
3. A directory mod1 exists at the repo root. This directory can be empty
4. This is the most bizarre part: This depends on the contents of the test files tests/test_mod1.py. Modifying the file contents can in some cases cause extend-select from pyproject.toml to be respected. Some of these are very insignificant changes, like insertion of a comment between imports, removal of a blank line between imports, etc.
5. Run ruff check --no-cache and observe that tests/test_mod1.py is not checked for I001 as requested in pyproject.toml. Be sure to use --no-cache during tests because some actions will not invalidate the cache that otherwise would, like creating/removing the top-level mod1 directory.

The minimum reproduction is below, but is also available as a git repository https://github.com/jamesharr/ruff-issue-12453

This bug was initially spotted due to a dirty working directory, and we eventually narrowed it down to an empty to-level folder that matches one of the modules a test imports. Of course git ignores empty directories, so we were chasing our tails on this one for a few days.

Ruff version: ruff 0.5.4 on macOS 14.5, though we've also seen it with 0.5.2 and 0.5.3

Command: ruff check --no-cache .

Directory structure:

% tree .
.
├── README.md
├── mod1                   # Empty directory required for bug reproduction
├── pyproject.toml         # Sets "extend-select" to "I"
├── src
│   └── mod1
│       └── __init__.py
└── tests
    └── test_mod1.py       # File is not always check

5 directories, 4 files

Contents of pyproject.toml

[tool.poetry]
name = "ruff-bug"
version = "0.0.0"
description = "Ruff bug demo project"
authors = []
readme = "README.md"
packages = [
    { include = "mod1", from = "src" },
]

[tool.ruff.lint]
extend-select = ["I"]

Contents of tests/test_mod1.py

def test_bug1():
    # For the bug to occur:
    # - [repo-root]/mod1 must exist as a directory; contents of directory do not seem to matter
    # - There must be an empty line after the first import import
    # - It cannot be two blank lines
    # - It cannot be line with a comment
    # - It can be a line consisting of only tabs/whitespaces
    # - All 3 imports must exist and in this order
    # - All 3 imports must exist within the function
    #
    # When the above conditions are met, then tests/* are NOT checked for I001 (unsorted imports)
    # as requested in pyproject.toml.
    #
    # Files in src/* are checked for I001 as requested in pyproject.toml, regardless of the contents
    # of this file.

    from external_lib import qux

    from mod1 import foo
    from mod1.bar import baz

    # I think the code below is only important because it uses the above imports
    print(qux)
    print(foo)
    print(baz)

% cat src/mod1/__init__.py
# The contents of this file seem to have no bearing bug reproduction
# - I001 seems to always be checked for this file, as specified in pyproject.toml
#
# You can illustrate this by re-ordering these imports
import os
import sys

# The following code only exists to use the imports and avoid F401 (imported but unused)
print(os)
print(sys)