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Apply mypy in pre-commit/CI #96

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ns-rse opened this issue Jan 7, 2025 · 1 comment · May be fixed by #98
Open
1 task done

Apply mypy in pre-commit/CI #96

ns-rse opened this issue Jan 7, 2025 · 1 comment · May be fixed by #98
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enhancement New feature or request

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@ns-rse
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ns-rse commented Jan 7, 2025 •
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Typehints are already good in this codebase but it would be useful to add in mypy checks
via a pre-commit hook.

  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: v1.14.1
    hooks:
      - id: mypy
        args: [--ignore-missing-imports] # default but useful to be explicit

To help with this we can try running RighTyper against the code base as it
analyses and informs what the typehints should be for a code base. It only works with Python >= 3.12 though (and
currently we can not support Python >= 3.12 with TopoStats due to as yet unresolved issues with the topoly dependency,
see Performance regression of Topoly with Python 3.12 · Issue #927 ·
AFM-SPM/TopoStats). However we should be able to add support for
Python 3.12 in AFMReader.
@ns-rse
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ns-rse commented Jan 7, 2025

First run of mypy against the code base reveals the following errors...

❱ pre-commit run mypy --all-files
mypy.....................................................................Failed
- hook id: mypy
- exit code: 1

tests/test_jpk.py:35: error: Incompatible types in assignment (expression has type "float", variable has type "type[float]")  [assignment]
tests/test_ibw.py:31: error: Incompatible types in assignment (expression has type "float", variable has type "type[float]")  [assignment]
AFMReader/io.py:287: error: Unsupported operand types for + ("bytes" and "str")  [operator]
AFMReader/io.py:318: error: "str" has no attribute "decode"; maybe "encode"?  [attr-defined]
tests/test_io.py:149: error: Value of type "object" is not indexable  [index]
tests/test_io.py:150: error: Value of type "object" is not indexable  [index]
tests/test_io.py:180: error: Value of type "object" is not indexable  [index]
tests/test_io.py:181: error: Value of type "object" is not indexable  [index]
AFMReader/gwy.py:48: error: Item "str" of "Path | str" has no attribute "stem"  [union-attr]
AFMReader/gwy.py:50: error: Need type annotation for "image_data_dict" (hint: "image_data_dict: dict[<type>, <type>] = ...")  [var-annotated]
AFMReader/gwy.py:51: error: Argument 1 to "open" of "Path" has incompatible type "Path | str"; expected "Path"  [arg-type]
AFMReader/gwy.py:56: error: Argument 1 to "gwy_read_object" has incompatible type "IO[Any]"; expected "TextIOWrapper[_WrappedBuffer]"  [arg-type]
AFMReader/gwy.py:66: error: Item "str" of "Path | str" has no attribute "suffix"  [union-attr]
AFMReader/gwy.py:104: error: Argument 1 to "read_uint32" has incompatible type "TextIOWrapper[_WrappedBuffer]"; expected "BinaryIO"  [arg-type]
AFMReader/gwy.py:140: error: Need type annotation for "sub_dict" (hint: "sub_dict: dict[<type>, <type>] = ...")  [var-annotated]
AFMReader/gwy.py:148: error: Incompatible types in assignment (expression has type "int", variable has type "str")  [assignment]
AFMReader/gwy.py:148: error: Argument "open_file" to "read_uint32" has incompatible type "TextIOWrapper[_WrappedBuffer]"; expected "BinaryIO"  [arg-type]
AFMReader/gwy.py:152: error: Incompatible types in assignment (expression has type "float", variable has type "str")  [assignment]
AFMReader/gwy.py:152: error: Argument "open_file" to "read_double" has incompatible type "TextIOWrapper[_WrappedBuffer]"; expected "BinaryIO"  [arg-type]
AFMReader/gwy.py:160: error: Argument "open_file" to "read_uint32" has incompatible type "TextIOWrapper[_WrappedBuffer]"; expected "BinaryIO"  [arg-type]
AFMReader/gwy.py:165: error: Argument "open_file" to "read_double" has incompatible type "TextIOWrapper[_WrappedBuffer]"; expected "BinaryIO"  [arg-type]
AFMReader/gwy.py:239: error: "str" has no attribute "decode"; maybe "encode"?  [attr-defined]
AFMReader/asd.py:324: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:327: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:329: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:330: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:332: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:334: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:335: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:337: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:338: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:340: error: Incompatible types in assignment (expression has type "float", target has type "str")  [assignment]
AFMReader/asd.py:342: error: Incompatible types in assignment (expression has type "float", target has type "str")  [assignment]
AFMReader/asd.py:344: error: Incompatible types in assignment (expression has type "float", target has type "str")  [assignment]
AFMReader/asd.py:349: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:350: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:350: error: Unsupported operand types for ^ ("int" and "str")  [operator]
AFMReader/asd.py:352: error: Incompatible types in assignment (expression has type "bool", target has type "str")  [assignment]
AFMReader/asd.py:354: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:358: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:359: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:360: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:361: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:362: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:363: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:365: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:367: error: Incompatible types in assignment (expression has type "float", target has type "str")  [assignment]
AFMReader/asd.py:368: error: Incompatible types in assignment (expression has type "float", target has type "str")  [assignment]
AFMReader/asd.py:374: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:376: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:378: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:380: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:382: error: Argument "length_bytes" to "read_null_separated_utf8" has incompatible type "str"; expected "int"  [arg-type]
AFMReader/asd.py:384: error: Incompatible types in assignment (expression has type "float", target has type "str")  [assignment]
AFMReader/asd.py:386: error: Incompatible types in assignment (expression has type "float", target has type "str")  [assignment]
AFMReader/asd.py:388: error: Incompatible types in assignment (expression has type "int", target has type "str")  [assignment]
AFMReader/asd.py:390: error: Argument 2 to "skip_bytes" has incompatible type "str"; expected "int"  [arg-type]
AFMReader/asd.py:393: error: No overload variant of "range" matches argument type "str"  [call-overload]
AFMReader/asd.py:393: note: Possible overload variants:
AFMReader/asd.py:393: note:     def range(SupportsIndex, /) -> range
AFMReader/asd.py:393: note:     def range(SupportsIndex, SupportsIndex, SupportsIndex = ..., /) -> range
AFMReader/asd.py:433: error: Incompatible types in assignment (expression has type "str", target has type "int")  [assignment]
AFMReader/asd.py:434: error: Incompatible types in assignment (expression has type "str", target has type "int")  [assignment]
AFMReader/asd.py:464: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:466: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:468: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:476: error: Incompatible types in assignment (expression has type "str", target has type "int")  [assignment]
AFMReader/asd.py:482: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:483: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:485: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:486: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:487: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:489: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:495: error: Incompatible types in assignment (expression has type "str", target has type "int")  [assignment]
AFMReader/asd.py:501: error: Incompatible types in assignment (expression has type "str", target has type "int")  [assignment]
AFMReader/asd.py:539: error: Incompatible types in assignment (expression has type "str", target has type "int")  [assignment]
AFMReader/asd.py:540: error: Incompatible types in assignment (expression has type "str", target has type "int")  [assignment]
AFMReader/asd.py:570: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:572: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:574: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:582: error: Incompatible types in assignment (expression has type "str", target has type "int")  [assignment]
AFMReader/asd.py:588: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:589: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:591: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:592: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:593: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:595: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:601: error: Incompatible types in assignment (expression has type "str", target has type "int")  [assignment]
AFMReader/asd.py:607: error: Incompatible types in assignment (expression has type "str", target has type "int")  [assignment]
AFMReader/asd.py:614: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:686: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:687: error: Incompatible types in assignment (expression has type "float", target has type "int")  [assignment]
AFMReader/asd.py:702: error: "VoltageLevelConverter" has no attribute "level_to_voltage"  [attr-defined]
AFMReader/asd.py:704: error: "bytes" has no attribute "reshape"  [attr-defined]
tests/test_topostats.py:47: error: Missing positional argument "self" in call to "keys" of "dict"  [call-arg]
tests/test_gwy.py:31: error: Need type annotation for "test_dict" (hint: "test_dict: dict[<type>, <type>] = ...")  [var-annotated]
tests/test_gwy.py:32: error: Argument "open_file" to "gwy_read_object" has incompatible type "BufferedReader"; expected "TextIOWrapper[_WrappedBuffer]"  [arg-type]
tests/test_gwy.py:42: error: Need type annotation for "test_dict" (hint: "test_dict: dict[<type>, <type>] = ...")  [var-annotated]
tests/test_gwy.py:43: error: Argument "open_file" to "gwy_read_component" has incompatible type "BufferedReader"; expected "TextIOWrapper[_WrappedBuffer]"  [arg-type]
tests/test_gwy.py:111: error: Argument 1 to "read_gwy_component_dtype" has incompatible type "BufferedReader"; expected "TextIOWrapper[_WrappedBuffer]"  [arg-type]
tests/test_asd.py:28: error: Argument 1 to "len" has incompatible type "type[list[Any]]"; expected "Sized"  [arg-type]
Found 98 errors in 9 files (checked 17 source files)

@ns-rse ns-rse linked a pull request Jan 7, 2025 that will close this issue
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@ns-rse ns-rse added the enhancement New feature or request label Jan 7, 2025
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Add mypy to pre-commit and improve typehints AFM-SPM/AFMReader
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