Relative paths in `per-file-ignores` not respected when running `ruff` outside working directory using `--config` with `pyproject.toml`

[mihirsamdarshi]

Description

I noticed this (potential) issue while debugging koxudaxi/ruff-pycharm-plugin#359 for PyCharm. It's may be expected behavior, so please close this issue if so.

When running ruff from a directory that is not the same as the one containing the pyproject.toml file and specifying the --config option, the relative paths specified in the pyproject.toml's per-file-ignores configuration are not respected.

This normally isn't a problem, since the pyproject.toml lives in the root of project files, but I have a full-stack application where the python source code does not live in the source code (see the issue above). I open this root folder in PyCharm. Unfortunately, the ruff-pycharm-plugin runs ruff from the project's root directory, and therefore needs to pass the --config parameter.

Steps to Reproduce

1. Create a new project, and install ruff

   ❯ rye init example-project
   ❯ cd example-project
   ❯ uv venv && source .venv/bin/activate # or `rye sync`
   ❯ uv pip install ruff
   ❯ example-project/.venv/bin/ruff --version
   ruff 0.4.10
   

2. In example-project/pyproject.toml, configure per-file-ignores with relative paths:

   [tool.ruff.lint]
   # The default `rye` project will error on `D103` and `D104` when select = ["ALL"] is used
   select = ["ALL"]
   
   [tool.ruff.lint.per-file-ignores]
   "./src/example_project/__init__.py" = ["D104"]
   

3. Deactivate the venv, verify that the ruff check command's output is correct from the project's working directory.

   ❯ deactivate
   ❯ .venv/bin/ruff check --config pyproject.toml src/
   warning: `one-blank-line-before-class` (D203) and `no-blank-line-before-class` (D211) are incompatible. Ignoring `one-blank-line-before-class`.
   warning: `multi-line-summary-first-line` (D212) and `multi-line-summary-second-line` (D213) are incompatible. Ignoring `multi-line-summary-second-line`.
   example-project/src/example_project/__init__.py:1:5: D103 Missing docstring in public function
   Found 1 error.
   

4. Navigate up a directory, then run ruff check again

   ❯ cd ..
   ❯ example-project/.venv/bin/ruff check example-project/src/ --config example-project/pyproject.toml
   warning: `one-blank-line-before-class` (D203) and `no-blank-line-before-class` (D211) are incompatible. Ignoring `one-blank-line-before-class`.
   warning: `multi-line-summary-first-line` (D212) and `multi-line-summary-second-line` (D213) are incompatible. Ignoring `multi-line-summary-second-line`.
   example-project/src/example_project/__init__.py:1:1: D104 Missing docstring in public package
   example-project/src/example_project/__init__.py:1:5: D103 Missing docstring in public function
   Found 2 errors.
   

Environment

• Ruff version: 0.4.10
• OS: macOS 14.5
• Shell: fish

Possible Solution

Consider adjusting how ruff resolves relative paths in the per-file-ignores configuration. It may need to use the directory of the pyproject.toml file as the base for resolving these paths, rather than the current working directory.