WIP: Static checking with mypy #621
Draft
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
First run: $ python -m mypy pydra
pydra/utils/messenger.py:185: error: Skipping analyzing "pyld": module is installed, but missing library stubs or py.typed marker [import]
pydra/engine/helpers.py:5: error: Skipping analyzing "cloudpickle": module is installed, but missing library stubs or py.typed marker [import]
pydra/engine/core.py:13: error: Skipping analyzing "cloudpickle": module is installed, but missing library stubs or py.typed marker [import]
pydra/engine/core.py:161: error: Argument 1 to "Path" has incompatible type "Union[str, File]"; expected "Union[str, PathLike[str]]" [arg-type]
pydra/engine/core.py:162: error: Argument 1 to "Path" has incompatible type "Union[str, File]"; expected "Union[str, PathLike[str]]" [arg-type]
pydra/engine/core.py:169: error: Argument after ** must be a mapping, not "Union[str, File, Dict[Any, Any], None]" [arg-type]
pydra/engine/core.py:174: error: Need type annotation for "inp_lf" (hint: "inp_lf: Dict[<type>, <type>] = ...") [var-annotated]
pydra/engine/core.py:179: error: Need type annotation for "_inner_cont_dim" (hint: "_inner_cont_dim: Dict[<type>, <type>] = ...") [var-annotated]
pydra/engine/core.py:180: error: Need type annotation for "_output" (hint: "_output: Dict[<type>, <type>] = ...") [var-annotated]
pydra/engine/core.py:181: error: Need type annotation for "_result" (hint: "_result: Dict[<type>, <type>] = ...") [var-annotated]
pydra/engine/core.py:185: error: Incompatible types in assignment (expression has type "Dict[<nothing>, <nothing>]", variable has type "None") [assignment]
pydra/engine/core.py:903: error: Argument 1 to "_sanitize_input_spec" has incompatible type "Union[List[str], SpecInfo, None]"; expected "Union[SpecInfo, List[str]]" [arg-type]
pydra/engine/core.py:926: error: Need type annotation for "name2obj" (hint: "name2obj: Dict[<type>, <type>] = ...") [var-annotated]
pydra/engine/workers.py:860: error: Cannot find implementation or library stub for module named "dask.distributed" [import]
pydra/engine/task.py:44: error: Skipping analyzing "cloudpickle": module is installed, but missing library stubs or py.typed marker [import]
pydra/engine/task.py:141: error: Argument "fields" to "SpecInfo" has incompatible type "List[Tuple[str, Any]]"; expected "List[Tuple[Any, ...]]" [arg-type]
pydra/engine/task.py:141: note: "List" is invariant -- see https://mypy.readthedocs.io/en/stable/common_issues.html#variance
pydra/engine/task.py:141: note: Consider using "Sequence" instead, which is covariant
pydra/engine/task.py:143: error: Item "BaseSpec" of "Union[SpecInfo, BaseSpec]" has no attribute "fields" [union-attr]
pydra/engine/task.py:184: error: Argument "fields" to "SpecInfo" has incompatible type "List[Tuple[str, Any]]"; expected "List[Tuple[Any, ...]]" [arg-type]
pydra/engine/task.py:184: note: "List" is invariant -- see https://mypy.readthedocs.io/en/stable/common_issues.html#variance
pydra/engine/task.py:184: note: Consider using "Sequence" instead, which is covariant
pydra/engine/task.py:297: error: Argument "bases" to "SpecInfo" has incompatible type "Tuple[Type[ShellOutSpec]]"; expected "Sequence[Type[BaseSpec]]" [arg-type]
pydra/engine/task.py:594: error: Need type annotation for "bindings" (hint: "bindings: Dict[<type>, <type>] = ...") [var-annotated]
pydra/__init__.py:26: error: Skipping analyzing "etelemetry": module is installed, but missing library stubs or py.typed marker [import]
pydra/__init__.py:26: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
pydra/utils/tests/test_messenger.py:52: error: Skipping analyzing "pyld": module is installed, but missing library stubs or py.typed marker [import]
pydra/engine/boutiques.py:95: error: Skipping analyzing "boutiques.searcher": module is installed, but missing library stubs or py.typed marker [import]
pydra/engine/tests/utils.py:16: error: Argument 1 to "__call__" of "_SkipifMarkDecorator" has incompatible type "int"; expected "Union[str, bool]" [arg-type]
pydra/engine/tests/utils.py:164: error: Invalid type comment or annotation [valid-type]
pydra/engine/tests/utils.py:164: note: Suggestion: use ty.NamedTuple[...] instead of ty.NamedTuple(...)
pydra/engine/tests/utils.py:197: error: Argument 1 to "open" has incompatible type "Union[str, File, Path]"; expected "Union[int, Union[str, bytes, PathLike[str], PathLike[bytes]]]" [arg-type]
pydra/engine/tests/utils.py:199: error: Incompatible return value type (got "Path", expected "File") [return-value]
pydra/engine/tests/utils.py:199: error: Argument 1 to "Path" has incompatible type "Union[str, File, Path]"; expected "Union[str, PathLike[str]]" [arg-type]
pydra/engine/tests/utils.py:205: error: Argument 1 to "open" has incompatible type "Union[str, File, Path]"; expected "Union[int, Union[str, bytes, PathLike[str], PathLike[bytes]]]" [arg-type]
pydra/engine/tests/utils.py:207: error: Argument 1 to "Path" has incompatible type "Union[str, File, Path]"; expected "Union[str, PathLike[str]]" [arg-type]
pydra/engine/tests/utils.py:217: error: Argument 1 to "open" has incompatible type "Union[str, File, Path]"; expected "Union[int, Union[str, bytes, PathLike[str], PathLike[bytes]]]" [arg-type]
pydra/engine/tests/utils.py:219: error: Argument 1 to "Path" has incompatible type "Union[str, File, Path]"; expected "Union[str, PathLike[str]]" [arg-type]
pydra/engine/tests/utils.py:221: error: Incompatible types in assignment (expression has type "int", target has type "Path") [assignment]
pydra/engine/tests/utils.py:227: error: No overload variant of "open" matches argument type "File" [call-overload]
pydra/engine/tests/utils.py:227: note: Possible overload variants:
pydra/engine/tests/utils.py:227: note: def open(file: Union[int, Union[str, bytes, PathLike[str], PathLike[bytes]]], mode: Union[Literal['r+', '+r', 'rt+', 'r+t', '+rt', 'tr+', 't+r', '+tr', 'w+', '+w', 'wt+', 'w+t', '+wt', 'tw+', 't+w', '+tw', 'a+', '+a', 'at+', 'a+t', '+at', 'ta+', 't+a', '+ta', 'x+', '+x', 'xt+', 'x+t', '+xt', 'tx+', 't+x', '+tx'], Literal['w', 'wt', 'tw', 'a', 'at', 'ta', 'x', 'xt', 'tx'], Literal['r', 'rt', 'tr', 'U', 'rU', 'Ur', 'rtU', 'rUt', 'Urt', 'trU', 'tUr', 'Utr']] = ..., buffering: int = ..., encoding: Optional[str] = ..., errors: Optional[str] = ..., newline: Optional[str] = ..., closefd: bool = ..., opener: Optional[Any] = ...) -> TextIOWrapper
pydra/engine/tests/utils.py:227: note: def open(file: Union[int, Union[str, bytes, PathLike[str], PathLike[bytes]]], mode: Union[Literal['rb+', 'r+b', '+rb', 'br+', 'b+r', '+br', 'wb+', 'w+b', '+wb', 'bw+', 'b+w', '+bw', 'ab+', 'a+b', '+ab', 'ba+', 'b+a', '+ba', 'xb+', 'x+b', '+xb', 'bx+', 'b+x', '+bx'], Literal['rb', 'br', 'rbU', 'rUb', 'Urb', 'brU', 'bUr', 'Ubr'], Literal['wb', 'bw', 'ab', 'ba', 'xb', 'bx']], buffering: Literal[0], encoding: None = ..., errors: None = ..., newline: None = ..., closefd: bool = ..., opener: Optional[Any] = ...) -> FileIO
pydra/engine/tests/utils.py:227: note: def open(file: Union[int, Union[str, bytes, PathLike[str], PathLike[bytes]]], mode: Literal['rb+', 'r+b', '+rb', 'br+', 'b+r', '+br', 'wb+', 'w+b', '+wb', 'bw+', 'b+w', '+bw', 'ab+', 'a+b', '+ab', 'ba+', 'b+a', '+ba', 'xb+', 'x+b', '+xb', 'bx+', 'b+x', '+bx'], buffering: Literal[-1, 1] = ..., encoding: None = ..., errors: None = ..., newline: None = ..., closefd: bool = ..., opener: Optional[Any] = ...) -> BufferedRandom
pydra/engine/tests/utils.py:227: note: def open(file: Union[int, Union[str, bytes, PathLike[str], PathLike[bytes]]], mode: Literal['wb', 'bw', 'ab', 'ba', 'xb', 'bx'], buffering: Literal[-1, 1] = ..., encoding: None = ..., errors: None = ..., newline: None = ..., closefd: bool = ..., opener: Optional[Any] = ...) -> BufferedWriter
pydra/engine/tests/utils.py:227: note: def open(file: Union[int, Union[str, bytes, PathLike[str], PathLike[bytes]]], mode: Literal['rb', 'br', 'rbU', 'rUb', 'Urb', 'brU', 'bUr', 'Ubr'], buffering: Literal[-1, 1] = ..., encoding: None = ..., errors: None = ..., newline: None = ..., closefd: bool = ..., opener: Optional[Any] = ...) -> BufferedReader
pydra/engine/tests/utils.py:227: note: def open(file: Union[int, Union[str, bytes, PathLike[str], PathLike[bytes]]], mode: Union[Literal['rb+', 'r+b', '+rb', 'br+', 'b+r', '+br', 'wb+', 'w+b', '+wb', 'bw+', 'b+w', '+bw', 'ab+', 'a+b', '+ab', 'ba+', 'b+a', '+ba', 'xb+', 'x+b', '+xb', 'bx+', 'b+x', '+bx'], Literal['rb', 'br', 'rbU', 'rUb', 'Urb', 'brU', 'bUr', 'Ubr'], Literal['wb', 'bw', 'ab', 'ba', 'xb', 'bx']], buffering: int = ..., encoding: None = ..., errors: None = ..., newline: None = ..., closefd: bool = ..., opener: Optional[Any] = ...) -> BinaryIO
pydra/engine/tests/utils.py:227: note: def open(file: Union[int, Union[str, bytes, PathLike[str], PathLike[bytes]]], mode: str, buffering: int = ..., encoding: Optional[str] = ..., errors: Optional[str] = ..., newline: Optional[str] = ..., closefd: bool = ..., opener: Optional[Any] = ...) -> IO[Any]
pydra/engine/tests/utils.py:236: error: No overload variant of "open" matches argument type "File" [call-overload]
pydra/engine/tests/utils.py:236: note: Possible overload variants:
pydra/engine/tests/utils.py:236: note: def open(file: Union[int, Union[str, bytes, PathLike[str], PathLike[bytes]]], mode: Union[Literal['r+', '+r', 'rt+', 'r+t', '+rt', 'tr+', 't+r', '+tr', 'w+', '+w', 'wt+', 'w+t', '+wt', 'tw+', 't+w', '+tw', 'a+', '+a', 'at+', 'a+t', '+at', 'ta+', 't+a', '+ta', 'x+', '+x', 'xt+', 'x+t', '+xt', 'tx+', 't+x', '+tx'], Literal['w', 'wt', 'tw', 'a', 'at', 'ta', 'x', 'xt', 'tx'], Literal['r', 'rt', 'tr', 'U', 'rU', 'Ur', 'rtU', 'rUt', 'Urt', 'trU', 'tUr', 'Utr']] = ..., buffering: int = ..., encoding: Optional[str] = ..., errors: Optional[str] = ..., newline: Optional[str] = ..., closefd: bool = ..., opener: Optional[Any] = ...) -> TextIOWrapper
pydra/engine/tests/utils.py:236: note: def open(file: Union[int, Union[str, bytes, PathLike[str], PathLike[bytes]]], mode: Union[Literal['rb+', 'r+b', '+rb', 'br+', 'b+r', '+br', 'wb+', 'w+b', '+wb', 'bw+', 'b+w', '+bw', 'ab+', 'a+b', '+ab', 'ba+', 'b+a', '+ba', 'xb+', 'x+b', '+xb', 'bx+', 'b+x', '+bx'], Literal['rb', 'br', 'rbU', 'rUb', 'Urb', 'brU', 'bUr', 'Ubr'], Literal['wb', 'bw', 'ab', 'ba', 'xb', 'bx']], buffering: Literal[0], encoding: None = ..., errors: None = ..., newline: None = ..., closefd: bool = ..., opener: Optional[Any] = ...) -> FileIO
pydra/engine/tests/utils.py:236: note: def open(file: Union[int, Union[str, bytes, PathLike[str], PathLike[bytes]]], mode: Literal['rb+', 'r+b', '+rb', 'br+', 'b+r', '+br', 'wb+', 'w+b', '+wb', 'bw+', 'b+w', '+bw', 'ab+', 'a+b', '+ab', 'ba+', 'b+a', '+ba', 'xb+', 'x+b', '+xb', 'bx+', 'b+x', '+bx'], buffering: Literal[-1, 1] = ..., encoding: None = ..., errors: None = ..., newline: None = ..., closefd: bool = ..., opener: Optional[Any] = ...) -> BufferedRandom
pydra/engine/tests/utils.py:236: note: def open(file: Union[int, Union[str, bytes, PathLike[str], PathLike[bytes]]], mode: Literal['wb', 'bw', 'ab', 'ba', 'xb', 'bx'], buffering: Literal[-1, 1] = ..., encoding: None = ..., errors: None = ..., newline: None = ..., closefd: bool = ..., opener: Optional[Any] = ...) -> BufferedWriter
pydra/engine/tests/utils.py:236: note: def open(file: Union[int, Union[str, bytes, PathLike[str], PathLike[bytes]]], mode: Literal['rb', 'br', 'rbU', 'rUb', 'Urb', 'brU', 'bUr', 'Ubr'], buffering: Literal[-1, 1] = ..., encoding: None = ..., errors: None = ..., newline: None = ..., closefd: bool = ..., opener: Optional[Any] = ...) -> BufferedReader
pydra/engine/tests/utils.py:236: note: def open(file: Union[int, Union[str, bytes, PathLike[str], PathLike[bytes]]], mode: Union[Literal['rb+', 'r+b', '+rb', 'br+', 'b+r', '+br', 'wb+', 'w+b', '+wb', 'bw+', 'b+w', '+bw', 'ab+', 'a+b', '+ab', 'ba+', 'b+a', '+ba', 'xb+', 'x+b', '+xb', 'bx+', 'b+x', '+bx'], Literal['rb', 'br', 'rbU', 'rUb', 'Urb', 'brU', 'bUr', 'Ubr'], Literal['wb', 'bw', 'ab', 'ba', 'xb', 'bx']], buffering: int = ..., encoding: None = ..., errors: None = ..., newline: None = ..., closefd: bool = ..., opener: Optional[Any] = ...) -> BinaryIO
pydra/engine/tests/utils.py:236: note: def open(file: Union[int, Union[str, bytes, PathLike[str], PathLike[bytes]]], mode: str, buffering: int = ..., encoding: Optional[str] = ..., errors: Optional[str] = ..., newline: Optional[str] = ..., closefd: bool = ..., opener: Optional[Any] = ...) -> IO[Any]
pydra/engine/tests/test_tasks_files.py:20: error: No overload variant of "listdir" matches argument type "Directory" [call-overload]
pydra/engine/tests/test_tasks_files.py:20: note: Possible overload variants:
pydra/engine/tests/test_tasks_files.py:20: note: def listdir(path: Optional[Union[str, PathLike[str]]] = ...) -> List[str]
pydra/engine/tests/test_tasks_files.py:20: note: def listdir(path: Union[bytes, PathLike[bytes]]) -> List[bytes]
pydra/engine/tests/test_tasks_files.py:20: note: def listdir(path: int) -> List[str]
pydra/engine/tests/test_tasks_files.py:45: error: Invalid type comment or annotation [valid-type]
pydra/engine/tests/test_tasks_files.py:45: note: Suggestion: use ty.NamedTuple[...] instead of ty.NamedTuple(...)
pydra/engine/tests/test_tasks_files.py:46: error: Argument 1 to "load" has incompatible type "File"; expected "Union[str, bytes, PathLike[Any], _SupportsReadSeek[bytes]]" [arg-type]
pydra/engine/tests/test_tasks_files.py:56: error: Invalid type comment or annotation [valid-type]
pydra/engine/tests/test_tasks_files.py:56: note: Suggestion: use ty.NamedTuple[...] instead of ty.NamedTuple(...)
pydra/engine/tests/test_tasks_files.py:57: error: Argument 1 to "load" has incompatible type "File"; expected "Union[str, bytes, PathLike[Any], _SupportsReadSeek[bytes]]" [arg-type]
pydra/engine/tests/test_singularity.py:13: error: Argument 1 to "__call__" of "_SkipifMarkDecorator" has incompatible type "int"; expected "Union[str, bool]" [arg-type]
pydra/engine/tests/test_profiles.py:6: error: Skipping analyzing "pympler": module is installed, but missing library stubs or py.typed marker [import]
pydra/engine/tests/test_helpers_file.py:258: error: Need type annotation for "MOUNT_OUTPUTS" [var-annotated]
pydra/engine/tests/test_task.py:5: error: Skipping analyzing "cloudpickle": module is installed, but missing library stubs or py.typed marker [import]
pydra/engine/tests/test_task.py:326: error: No overload variant of "sum" matches argument type "Union[float, int]" [call-overload]
pydra/engine/tests/test_task.py:326: note: Possible overload variants:
pydra/engine/tests/test_task.py:326: note: def sum(Iterable[bool], /, start: int = ...) -> int
pydra/engine/tests/test_task.py:326: note: def [_SupportsSumNoDefaultT <: _SupportsSumWithNoDefaultGiven] sum(Iterable[_SupportsSumNoDefaultT], /) -> Union[_SupportsSumNoDefaultT, Literal[0]]
pydra/engine/tests/test_task.py:326: note: def [_AddableT1 <: SupportsAdd[Any, Any], _AddableT2 <: SupportsAdd[Any, Any]] sum(Iterable[_AddableT1], /, start: _AddableT2) -> Union[_AddableT1, _AddableT2]
pydra/engine/tests/test_task.py:339: error: Argument 1 to "sum" has incompatible type "Union[str, int]"; expected "Iterable[bool]" [arg-type]
pydra/engine/tests/test_task.py:379: error: Argument 1 to "len" has incompatible type "MultiInputObj"; expected "Sized" [arg-type]
pydra/engine/tests/test_task.py:394: error: Argument 1 to "len" has incompatible type "MultiInputObj"; expected "Sized" [arg-type]
pydra/engine/tests/test_task.py:410: error: Argument 1 to "len" has incompatible type "MultiInputObj"; expected "Sized" [arg-type]
pydra/engine/tests/test_shelltask_inputspec.py:2172: error: Argument "fields" to "SpecInfo" has incompatible type "List[Tuple[str, type, Dict[str, object]]]"; expected "List[Tuple[Any, ...]]" [arg-type]
pydra/engine/tests/test_shelltask_inputspec.py:2172: note: "List" is invariant -- see https://mypy.readthedocs.io/en/stable/common_issues.html#variance
pydra/engine/tests/test_shelltask_inputspec.py:2172: note: Consider using "Sequence" instead, which is covariant
pydra/engine/tests/test_shelltask_inputspec.py:2173: error: Need type annotation for "task_output_fields" (hint: "task_output_fields: List[<type>] = ...") [var-annotated]
pydra/engine/tests/test_shelltask_inputspec.py:2175: error: Argument "bases" to "SpecInfo" has incompatible type "Tuple[Type[ShellOutSpec]]"; expected "Sequence[Type[BaseSpec]]" [arg-type]
pydra/engine/tests/test_nipype1_convert.py:18: error: Argument "bases" to "SpecInfo" has incompatible type "Tuple[Type[ShellOutSpec]]"; expected "Sequence[Type[BaseSpec]]" [arg-type]
pydra/engine/tests/test_helpers.py:8: error: Skipping analyzing "cloudpickle": module is installed, but missing library stubs or py.typed marker [import]
pydra/engine/tests/test_boutiques.py:15: error: Argument 1 to "__call__" of "_SkipifMarkDecorator" has incompatible type "int"; expected "Union[str, bool]" [arg-type] |
Codecov ReportBase: 81.17% // Head: 80.49% // Decreases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## master #621 +/- ##
==========================================
- Coverage 81.17% 80.49% -0.69%
==========================================
Files 20 20
Lines 4393 4393
Branches 1264 0 -1264
==========================================
- Hits 3566 3536 -30
- Misses 823 857 +34
+ Partials 4 0 -4
Flags with carried forward coverage won't be shown. Click here to find out more.
Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here. ☔ View full report at Codecov. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Work in progress
See methodology here.