I'm putting together some pre-commit hooks for a project that I'm working on, and one of the hooks we want to use is MyPy. The pre-commit results are throwing up a lot of non-error notes related to the "annotation-unchecked" flag, which I want to disable to de-clutter the command line output. I have seen from a previous question Suppress Mypy notes that the solution would be to include a disable_error_code = ["annotation-unchecked"] in the pyproject.toml file, however, the notes still appear when running the pre-commit. These are the current references to MyPy in the pyproject.toml file: [tool.mypy] mypy_path = "src" disable_error_code = ["annotation-unchecked"] # Disables non-error messages thrown up by mypy And these are the settings from the pre-commit-config.yaml file: # Type checking - repo: https://github.com/pre-commit/mirrors-mypy #rev: v0.910 rev: v1.9.0 hooks: - id: mypy files: '(src|tests)/.*\.py$' # Single quote critical due to escape character '\' used in RegEx search string (see YAML - 7.3 Flow Scalar Styles) additional_dependencies: [types-requests] These are the MyPy messages printed out in the command line. Note how the "notes" are still being printed despite the settings above. src/pkg/file1.py:14: error: Argument 2 to "from_bytes" of "int" has incompatible type "str"; expected "Literal['little', 'big']" [arg-type] src/pkg/file1.py:21: error: Argument 2 to "from_bytes" of "int" has incompatible type "str"; expected "Literal['little', 'big']" [arg-type] src/pkg/file1.py:23: error: Argument 2 to "from_bytes" of "int" has incompatible type "str"; expected "Literal['little', 'big']" [arg-type] src/pkg/file2.py:60: note: By default the bodies of untyped functions are not checked, consider using --check-untyped-defs [annotation-unchecked] src/pkg/file3.py:143: note: By default the bodies of untyped functions are not checked, consider using --check-untyped-defs [annotation-unchecked] src/pkg/file4.py:125: note: By default the bodies of untyped functions are not checked, consider using --check-untyped-defs [annotation-unchecked] src/pkg/file4.py:126: note: By default the bodies of untyped functions are not checked, consider using --check-untyped-defs [annotation-unchecked] src/pkg/file5.py:20: note: By default the bodies of untyped functions are not checked, consider using --check-untyped-defs [annotation-unchecked] src/pkg/file5.py:21: note: By default the bodies of untyped functions are not checked, consider using --check-untyped-defs [annotation-unchecked] src/pkg/file6.py:75: note: By default the bodies of untyped functions are not checked, consider using --check-untyped-defs [annotation-unchecked] src/pkg/file7.py:164: note: By default the bodies of untyped functions are not checked, consider using --check-untyped-defs [annotation-unchecked] src/pkg/file8.py:709: error: Value of type "Coroutine[Any, Any, None]" must be used [unused-coroutine] src/pkg/file9.py:709: note: Are you missing an await? src/pkg/file10.py:267: note: By default the bodies of untyped functions are not checked, consider using --check-untyped-defs [annotation-unchecked] Found 4 errors in 2 files (checked 72 source files) Advice on what might have gone wrong here would be much appreciated, thanks! It turns out this issue was caused by the presence of a .mypy.ini file in the project folder that I overlooked. Deleting it solved the problem. When multiple configuration files are present in the project folder, MyPy looks for settings in the following order of priority (ref): ./mypy.ini ./.mypy.ini ./pyproject.toml ./setup.cfg $XDG_CONFIG_HOME/mypy/config ~/.config/mypy/config ~/.mypy.ini Where multiple such files exist, @anit3res' answer of adding an argument to the .pre-commit-config.yaml file specifying the config file to look at works beautifully: - repo: https://github.com/pre-commit/mirrors-mypy rev: v1.9.0 hooks: - id: mypy files: '(src|tests)/.*\.py$' # Single quote critical due to escape character '\' used in RegEx search string (see YAML - 7.3 Flow Scalar Styles) additional_dependencies: [types-requests] args: [--config-file=./pyproject.toml] Continue reading...