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Option `per-file-ignores` was introduced in flake8 version 3.7.0. It allows to ignore specific errors in specific files using glob syntax. For example `per-file-ignores = src/generated/*.py:F401` will ignore `F401` error in all python files in `src/generated`. Thus ale has to run flake8 from project root where .flake8 config is placed otherwise glob won't match linted file.