add py.typed marker file for type checking in mypy #808

jcreinhold · 2022-01-29T18:00:05Z

Fixes #807.

Description

This PR adds a py.typed marker file so that end users can make use of type annotations in torchio in mypy.

This PR doesn't fix the current state of the type annotations which need to be reworked to work properly with mypy.

I tested this implementation in another project using torchio, and mypy recognizes the py.typed marker file.

Checklist

I have read the CONTRIBUTING docs and have a developer setup (especially important are pre-commitand pytest)
Non-breaking change (would not break existing functionality)
Breaking change (would cause existing functionality to change)
Tests added or modified to cover the changes (Not relevant)
Integration tests passed locally by running pytest
In-line docstrings updated (Not relevant)
Documentation updated, tested running make html inside the docs/ folder (Not relevant)
This pull request is ready to be reviewed
If the PR is ready and there are multiple commits, I have squashed them and force-pushed (Not relevant)

codecov · 2022-01-30T14:24:41Z

Codecov Report

Merging #808 (8263ad4) into main (1c217d8) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main     #808   +/-   ##
=======================================
  Coverage   93.87%   93.87%           
=======================================
  Files          72       72           
  Lines        4524     4524           
=======================================
  Hits         4247     4247           
  Misses        277      277

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fepegar · 2022-01-30T14:29:32Z

Awesome. Many thanks for your contribution, @jcreinhold. May I add you to the list of contributors?

I agree that typing hints in TorchIO are a bit messy. I suppose part of the reason is that I didn't add them since the beginning, and the library was not created to be shared initially. Also, I don't know much about the topic. It would be great to improve typing in the library, and your help would be much appreciated!

fepegar · 2022-01-30T14:37:10Z

For reference, this is currently the output of mypy torchio:

torchio/data/io.py:102: error: Incompatible return value type (got "Tuple[Any, ...]", expected "Tuple[int, int, int, int]")
torchio/data/io.py:396: error: Incompatible types in assignment (expression has type "Tuple[Any, Any, Any, Any, Any, Any, Any, Any, Any]", variable has type "Tuple[Any, Any, Any, Any]")
torchio/utils.py:52: error: Item "PathLike[Any]" of "Union[PathLike[Any], Sequence[Union[str, PathLike[Any]]]]" has no attribute "__iter__" (not iterable)
torchio/utils.py:168: error: Cannot infer type argument 1 of "copyfileobj"
torchio/utils.py:300: error: Missing return statement
torchio/utils.py:307: error: Incompatible return value type (got "str", expected "Optional[Path]")
torchio/utils.py:334: error: Incompatible types in assignment (expression has type "Optional[str]", variable has type "Path")
torchio/data/image.py:291: error: Incompatible return value type (got "Union[Tuple[float, float, float, float], Tuple[float, float, float, float, float, float, float, float, float]]", expected "Tuple[float, float, float, float, float, float, float, float, float]")
torchio/data/image.py:297: error: Incompatible return value type (got "Tuple[Any, ...]", expected "Tuple[float, float, float]")
torchio/data/image.py:302: error: Incompatible return value type (got "Tuple[Any, ...]", expected "Tuple[float, float, float]")
torchio/data/image.py:428: error: Item "PathLike[Any]" of "Union[PathLike[Any], Sequence[Union[str, PathLike[Any]]]]" has no attribute "__iter__" (not iterable)
torchio/data/image.py:430: error: Argument 1 to "_parse_single_path" of "Image" has incompatible type "Union[PathLike[Any], Sequence[Union[str, PathLike[Any]]]]"; expected "Union[str, PathLike[Any]]"
torchio/data/image.py:785: error: Incompatible return value type (got "Union[int, float, bool]", expected "int")
torchio/data/subject.py:54: error: Argument 1 to "_parse_images" of "Subject" has incompatible type "List[Image]"; expected "List[Tuple[str, Image]]"
torchio/data/subject.py:56: error: Need type annotation for "applied_transforms" (hint: "applied_transforms: List[<type>] = ...")
torchio/data/subject.py:201: error: Incompatible return value type (got "Transform", expected "Compose")
torchio/data/subject.py:212: error: Item "Image" of "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]" has no attribute "clear_history"
torchio/data/subject.py:212: error: Item "Tensor" of "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]" has no attribute "clear_history"
torchio/data/subject.py:212: error: Item "ndarray[Any, Any]" of "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]" has no attribute "clear_history"
torchio/data/subject.py:212: error: Item "Dict[Any, Any]" of "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]" has no attribute "clear_history"
torchio/data/subject.py:213: error: Incompatible return value type (got "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]", expected "Subject")
torchio/transforms/data_parser.py:120: error: Argument 1 to "_get_subject_from_tensor" of "DataParser" has incompatible type "Union[Tensor, ndarray[Any, Any]]"; expected "Tensor"
torchio/data/dataset.py:97: error: The erased type of self "torchio.data.dataset.SubjectsDataset" is not a supertype of its class "Type[torchio.data.dataset.SubjectsDataset]"
torchio/data/dataset.py:105: error: "SubjectsDataset" not callable
torchio/data/sampler/sampler.py:40: error: Argument 3 to "crop" of "PatchSampler" has incompatible type "ndarray[Any, Any]"; expected "Tuple[int, int, int]"
torchio/data/sampler/sampler.py:51: error: Incompatible types in assignment (expression has type "ndarray[Any, Any]", variable has type "Tuple[int, int, int]")
torchio/data/sampler/sampler.py:52: error: Incompatible types in assignment (expression has type "ndarray[Any, Any]", variable has type "Tuple[int, int, int]")
torchio/data/sampler/sampler.py:54: error: "Tuple[int, int, int]" has no attribute "tolist"
torchio/data/sampler/sampler.py:54: error: "Tuple[int, int, int, int, int, int]" has no attribute "tolist"
torchio/data/sampler/sampler.py:67: error: Incompatible types in assignment (expression has type "ndarray[Any, Any]", variable has type "Tuple[int, int, int]")
torchio/data/sampler/sampler.py:68: error: Incompatible types in assignment (expression has type "ndarray[Any, Any]", variable has type "Union[int, Tuple[int, int, int]]")
torchio/data/sampler/sampler.py:70: error: Argument 1 to "len" has incompatible type "Union[int, Tuple[int, int, int]]"; expected "Sized"
torchio/data/sampler/sampler.py:71: error: No overload variant of "__add__" of "tuple" matches argument type "int"
torchio/data/sampler/sampler.py:71: note: Possible overload variants:
torchio/data/sampler/sampler.py:71: note:     def __add__(self, Tuple[int, ...]) -> Tuple[int, ...]
torchio/data/sampler/sampler.py:71: note:     def __add__(self, Tuple[Any, ...]) -> Tuple[Any, ...]
torchio/data/sampler/sampler.py:71: note: Right operand is of type "Union[int, Tuple[int, int, int]]"
torchio/data/sampler/sampler.py:72: error: "Tuple[int, int, int]" has no attribute "tolist"
torchio/data/sampler/sampler.py:76: error: Argument 1 to "Crop" has incompatible type "Union[Tuple[Any, Any], Tuple[]]"; expected "Union[int, Tuple[int, int, int], Tuple[int, int, int, int, int, int], None]"
torchio/transforms/transform.py:282: error: "builtins.int" object is not iterable
torchio/transforms/transform.py:282: error: "builtins.float" object is not iterable
torchio/transforms/transform.py:321: error: Incompatible return value type (got "Union[Union[int, float], Tuple[Union[int, float], Union[int, float]]]", expected "Tuple[Union[int, float], Union[int, float]]")
torchio/transforms/transform.py:366: error: Incompatible return value type (got "Tuple[ndarray[Any, Any], ndarray[Any, Any]]", expected "Tuple[Tensor, ndarray[Any, Any]]")
torchio/transforms/transform.py:408: error: Incompatible return value type (got "None", expected "Tuple[int, int, int, int, int, int]")
torchio/transforms/transform.py:410: error: Incompatible types in assignment (expression has type "Tuple[int, ...]", variable has type "Union[int, Tuple[int, int, int], Tuple[int, int, int, int, int, int], None]")
torchio/transforms/transform.py:410: error: Argument 1 to "tuple" has incompatible type "Union[int, Tuple[int, int, int], Tuple[int, int, int, int, int, int]]"; expected "Iterable[int]"
torchio/transforms/transform.py:412: error: Incompatible types in assignment (expression has type "Tuple[Union[int, Tuple[int, int, int], Tuple[int, int, int, int, int, int]]]", variable has type "Union[int, Tuple[int, int, int], Tuple[int, int, int, int, int, int], None]")
torchio/transforms/transform.py:415: error: Item "int" of "Union[int, Tuple[int, int, int], Tuple[int, int, int, int, int, int]]" has no attribute "__iter__" (not iterable)
torchio/transforms/transform.py:422: error: Incompatible types in assignment (expression has type "Tuple[int, ...]", variable has type "Union[int, Tuple[int, int, int], Tuple[int, int, int, int, int, int], None]")
torchio/transforms/transform.py:422: error: Item "int" of "Union[int, Tuple[int, int, int], Tuple[int, int, int, int, int, int]]" has no attribute "__iter__" (not iterable)
torchio/transforms/transform.py:423: error: Argument 1 to "len" has incompatible type "Union[int, Tuple[int, int, int], Tuple[int, int, int, int, int, int]]"; expected "Sized"
torchio/transforms/transform.py:425: error: Incompatible return value type (got "Union[int, Tuple[int, int, int], Tuple[int, int, int, int, int, int]]", expected "Tuple[int, int, int, int, int, int]")
torchio/transforms/transform.py:427: error: Incompatible return value type (got "Union[int, Tuple[int, ...]]", expected "Tuple[int, int, int, int, int, int]")
torchio/transforms/transform.py:429: error: Incompatible return value type (got "Tuple[Any, ...]", expected "Tuple[int, int, int, int, int, int]")
torchio/transforms/transform.py:470: error: Argument 1 to "get_mask_from_bounds" of "Transform" has incompatible type "Union[str, int, Tuple[int, int, int], Tuple[int, int, int, int, int, int]]"; expected "Union[int, Tuple[int, int, int], Tuple[int, int, int, int, int, int], None]"
torchio/data/sampler/weighted.py:66: error: Incompatible types in assignment (expression has type "ndarray[Any, Any]", variable has type "Tensor")
torchio/data/sampler/weighted.py:68: error: Argument 1 to "get_cumulative_distribution_function" of "WeightedSampler" has incompatible type "Tensor"; expected "ndarray[Any, Any]"
torchio/data/sampler/weighted.py:72: error: Argument 2 to "extract_patch" of "WeightedSampler" has incompatible type "Tensor"; expected "ndarray[Any, Any]"
torchio/data/sampler/weighted.py:72: error: Argument 3 to "extract_patch" of "WeightedSampler" has incompatible type "Tuple[ndarray[Any, Any], ndarray[Any, Any]]"; expected "ndarray[Any, Any]"
torchio/data/sampler/weighted.py:104: error: Argument 2 to "clear_probability_borders" of "WeightedSampler" has incompatible type "ndarray[Any, Any]"; expected "Union[int, Tuple[int, int, int]]"
torchio/data/sampler/weighted.py:147: error: Unsupported operand types for // ("Tuple[int, int, int]" and "int")
torchio/data/sampler/weighted.py:147: note: Left operand is of type "Union[int, Tuple[int, int, int]]"
torchio/data/sampler/weighted.py:148: error: Unsupported operand types for - ("Tuple[int, int, int]" and "int")
torchio/data/sampler/weighted.py:148: note: Left operand is of type "Union[int, Tuple[int, int, int]]"
torchio/data/sampler/weighted.py:149: error: "builtins.int" object is not iterable
torchio/data/sampler/weighted.py:172: error: Incompatible return value type (got "ndarray[Any, Any]", expected "Tuple[ndarray[Any, Any], ndarray[Any, Any]]")
torchio/data/sampler/weighted.py:174: error: Signature of "extract_patch" incompatible with supertype "PatchSampler"
torchio/data/sampler/weighted.py:181: error: Argument 2 to "crop" of "PatchSampler" has incompatible type "ndarray[Any, Any]"; expected "Tuple[int, int, int]"
torchio/data/sampler/weighted.py:181: error: Argument 3 to "crop" of "PatchSampler" has incompatible type "ndarray[Any, Any]"; expected "Tuple[int, int, int]"
torchio/data/sampler/uniform.py:31: error: Argument 2 to "extract_patch" of "PatchSampler" has incompatible type "ndarray[Any, Any]"; expected "Tuple[int, int, int]"
torchio/data/sampler/grid.py:76: error: Argument 1 to "_pad" of "GridSampler" has incompatible type "Optional[Subject]"; expected "Subject"
torchio/data/sampler/grid.py:94: error: Argument 1 to "Pad" has incompatible type "ndarray[Any, dtype[signedinteger[Any]]]"; expected "Union[int, Tuple[int, int, int], Tuple[int, int, int, int, int, int], None]"
torchio/data/sampler/grid.py:95: error: Incompatible types in assignment (expression has type "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]", variable has type "Subject")
torchio/data/sampler/grid.py:102: error: Argument 1 to "_parse_sizes" of "GridSampler" has incompatible type "*Tuple[Any, ndarray[Any, Any], ndarray[Any, Any]]"; expected "Tuple[int, int, int]"
torchio/data/sampler/grid.py:103: error: Argument 1 to "_get_patches_locations" of "GridSampler" has incompatible type "*Tuple[Any, ndarray[Any, Any], ndarray[Any, Any]]"; expected "Tuple[int, int, int]"
torchio/data/sampler/grid.py:105: error: Signature of "_generate_patches" incompatible with supertype "PatchSampler"
torchio/data/sampler/grid.py:111: error: Argument 1 to "_parse_sizes" of "GridSampler" has incompatible type "*Tuple[Any, ndarray[Any, Any], ndarray[Any, Any]]"; expected "Tuple[int, int, int]"
torchio/data/sampler/grid.py:112: error: Argument 1 to "_get_patches_locations" of "GridSampler" has incompatible type "*Tuple[Any, ndarray[Any, Any], ndarray[Any, Any]]"; expected "Tuple[int, int, int]"
torchio/data/sampler/grid.py:123: error: Incompatible types in assignment (expression has type "ndarray[Any, Any]", variable has type "Tuple[int, int, int]")
torchio/data/sampler/grid.py:124: error: Incompatible types in assignment (expression has type "ndarray[Any, Any]", variable has type "Tuple[int, int, int]")
torchio/data/sampler/grid.py:125: error: Incompatible types in assignment (expression has type "ndarray[Any, Any]", variable has type "Tuple[int, int, int]")
torchio/data/sampler/grid.py:138: error: Unsupported operand types for % ("Tuple[int, int, int]" and "int")
torchio/transforms/lambda_transform.py:39: error: Incompatible types in assignment (expression has type "Tuple[str, str]", variable has type "Tuple[]")
torchio/transforms/intensity_transform.py:32: error: Need type annotation for "name"
torchio/data/sampler/label.py:66: error: Argument "probability_map" to "__init__" of "WeightedSampler" has incompatible type "Optional[str]"; expected "str"
torchio/transforms/preprocessing/label/remap_labels.py:61: error: Incompatible types in assignment (expression has type "Tuple[str, str]", variable has type "Tuple[]")
torchio/transforms/preprocessing/label/one_hot.py:18: error: Incompatible types in assignment (expression has type "Tuple[str]", variable has type "Tuple[]")
torchio/transforms/preprocessing/intensity/clamp.py:46: error: Incompatible types in assignment (expression has type "Tuple[str, str]", variable has type "Tuple[]")
torchio/transforms/preprocessing/intensity/clamp.py:50: error: Argument 1 to "apply_clamp" of "Clamp" has incompatible type "Image"; expected "ScalarImage"
torchio/transforms/preprocessing/label/remove_labels.py:58: error: Incompatible types in assignment (expression has type "Tuple[str, str, str]", variable has type "Tuple[]")
torchio/data/inference/aggregator.py:88: error: Incompatible return value type (got "Tuple[List[Any], ndarray[Any, Any]]", expected "Tuple[Union[Tensor, ndarray[Any, Any]], ndarray[Any, Any]]")
torchio/data/inference/aggregator.py:94: error: Incompatible types in assignment (expression has type "Tensor", variable has type "None")
torchio/data/inference/aggregator.py:104: error: Incompatible types in assignment (expression has type "Tensor", variable has type "None")
torchio/data/inference/aggregator.py:130: error: Argument 2 to "crop_batch" of "GridAggregator" has incompatible type "Tensor"; expected "ndarray[Any, Any]"
torchio/data/inference/aggregator.py:135: error: Unsupported target for indexed assignment ("None")
torchio/data/inference/aggregator.py:144: error: Value of type "None" is not indexable
torchio/data/inference/aggregator.py:144: error: Unsupported target for indexed assignment ("None")
torchio/data/inference/aggregator.py:149: error: Value of type "None" is not indexable
torchio/data/inference/aggregator.py:149: error: Unsupported target for indexed assignment ("None")
torchio/data/inference/aggregator.py:157: error: "None" has no attribute "dtype"
torchio/data/inference/aggregator.py:163: error: "None" has no attribute "type"
torchio/data/inference/aggregator.py:169: error: Argument 1 to "true_divide" has incompatible type "None"; expected "Union[Tensor, Union[int, float, bool]]"
torchio/data/inference/aggregator.py:169: error: Argument 2 to "true_divide" has incompatible type "None"; expected "Union[Tensor, Union[int, float, bool]]"
torchio/data/inference/aggregator.py:171: error: Incompatible types in assignment (expression has type "None", variable has type "Tensor")
torchio/data/inference/aggregator.py:176: error: Argument 1 to "Crop" has incompatible type "ndarray[Any, dtype[signedinteger[Any]]]"; expected "Union[int, Tuple[int, int, int], Tuple[int, int, int, int, int, int], None]"
torchio/data/inference/aggregator.py:177: error: Incompatible return value type (got "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]", expected "Tensor")
torchio/transforms/preprocessing/spatial/resize.py:44: error: Incompatible types in assignment (expression has type "Tuple[str, str, str]", variable has type "Tuple[]")
torchio/transforms/preprocessing/spatial/resize.py:65: error: Item "Tensor" of "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]" has no attribute "spatial_shape"
torchio/transforms/preprocessing/spatial/resize.py:65: error: Item "ndarray[Any, Any]" of "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]" has no attribute "spatial_shape"
torchio/transforms/preprocessing/spatial/resize.py:65: error: Item "Dict[Any, Any]" of "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]" has no attribute "spatial_shape"
torchio/transforms/preprocessing/spatial/resize.py:67: error: Item "Tensor" of "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]" has no attribute "spatial_shape"
torchio/transforms/preprocessing/spatial/resize.py:67: error: Item "ndarray[Any, Any]" of "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]" has no attribute "spatial_shape"
torchio/transforms/preprocessing/spatial/resize.py:67: error: Item "Dict[Any, Any]" of "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]" has no attribute "spatial_shape"
torchio/transforms/preprocessing/spatial/resize.py:71: error: Argument 1 to "CropOrPad" has incompatible type "ndarray[Any, Any]"; expected "Union[int, Tuple[int, int, int], None]"
torchio/transforms/preprocessing/spatial/resize.py:73: error: Incompatible return value type (got "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]", expected "Subject")
torchio/transforms/preprocessing/spatial/resample.py:92: error: Incompatible types in assignment (expression has type "Tuple[str, str, str, str, str]", variable has type "Tuple[]")
torchio/transforms/preprocessing/spatial/resample.py:103: error: Need type annotation for "result"
torchio/transforms/preprocessing/spatial/resample.py:154: error: Argument 1 to "check_affine_key_presence" of "Resample" has incompatible type "Optional[str]"; expected "str"
torchio/transforms/preprocessing/spatial/resample.py:178: error: Argument 1 to "check_affine" of "Resample" has incompatible type "Optional[str]"; expected "str"
torchio/transforms/preprocessing/spatial/resample.py:190: error: Argument 2 to "_set_resampler_reference" of "Resample" has incompatible type "Union[Union[float, Tuple[float, float, float]], str, Path, Image, None]"; expected "Union[Union[float, Tuple[float, float, float]], Union[str, PathLike[Any]], Image]"
torchio/transforms/preprocessing/spatial/resample.py:242: error: Unpacking a string is disallowed
torchio/transforms/preprocessing/spatial/resample.py:243: error: Argument 1 to "len" has incompatible type "Iterable[Any]"; expected "Sized"
torchio/transforms/preprocessing/spatial/pad.py:65: error: Incompatible types in assignment (expression has type "Tuple[str, str]", variable has type "Tuple[]")
torchio/transforms/preprocessing/spatial/ensure_shape_multiple.py:129: error: "object" not callable
torchio/transforms/preprocessing/spatial/ensure_shape_multiple.py:132: error: Incompatible return value type (got "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]", expected "Subject")
torchio/transforms/preprocessing/spatial/crop_or_pad.py:155: error: Incompatible return value type (got "Tuple[int, ...]", expected "Tuple[int, int, int, int, int, int]")
torchio/transforms/preprocessing/spatial/crop_or_pad.py:167: error: Incompatible types in assignment (expression has type "None", variable has type "Tuple[int, int, int, int, int, int]")
torchio/transforms/preprocessing/spatial/crop_or_pad.py:173: error: Incompatible types in assignment (expression has type "None", variable has type "Tuple[int, int, int, int, int, int]")
torchio/transforms/preprocessing/spatial/crop_or_pad.py:203: error: Argument 4 to "get_mask_from_masking_method" of "Transform" has incompatible type "Optional[Sequence[int]]"; expected "Optional[List[Any]]"
torchio/transforms/preprocessing/spatial/crop_or_pad.py:260: error: Incompatible types in assignment (expression has type "ndarray[Any, Any]", variable has type "List[int]")
torchio/transforms/preprocessing/spatial/crop_or_pad.py:261: error: Incompatible types in assignment (expression has type "ndarray[Any, Any]", variable has type "List[Any]")
torchio/transforms/preprocessing/spatial/crop_or_pad.py:262: error: "List[int]" has no attribute "tolist"
torchio/transforms/preprocessing/spatial/crop_or_pad.py:262: error: "List[int]" has no attribute "any"
torchio/transforms/preprocessing/spatial/crop_or_pad.py:263: error: "List[Any]" has no attribute "tolist"
torchio/transforms/preprocessing/spatial/crop_or_pad.py:263: error: "List[Any]" has no attribute "any"
torchio/transforms/preprocessing/spatial/crop_or_pad.py:264: error: Incompatible return value type (got "Tuple[Optional[Tuple[Any, ...]], Optional[Tuple[Any, ...]]]", expected "Tuple[Optional[Tuple[int, int, int, int, int, int]], Optional[Tuple[int, int, int, int, int, int]]]")
torchio/transforms/preprocessing/spatial/crop_or_pad.py:271: error: Incompatible types in assignment (expression has type "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]", variable has type "Subject")
torchio/transforms/preprocessing/spatial/crop_or_pad.py:273: error: Incompatible types in assignment (expression has type "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]", variable has type "Subject")
torchio/transforms/preprocessing/spatial/crop.py:39: error: Incompatible types in assignment (expression has type "Tuple[str]", variable has type "Tuple[]")
torchio/transforms/preprocessing/spatial/copy_affine.py:71: error: Incompatible types in assignment (expression has type "Tuple[str]", variable has type "Tuple[]")
torchio/transforms/preprocessing/intensity/z_normalization.py:21: error: Incompatible types in assignment (expression has type "Tuple[str]", variable has type "Tuple[]")
torchio/transforms/preprocessing/intensity/z_normalization.py:48: error: Incompatible return value type (got "None", expected "Tensor")
torchio/transforms/preprocessing/intensity/rescale.py:59: error: Incompatible types in assignment (expression has type "Tuple[str, str, str]", variable has type "Tuple[]")
torchio/transforms/preprocessing/intensity/rescale.py:88: error: No overload variant of "clip" matches argument types "Any", "Any", "Any"
torchio/transforms/preprocessing/intensity/rescale.py:88: note: Possible overload variants:
torchio/transforms/preprocessing/intensity/rescale.py:88: note:     def clip(a: Union[Sequence[Sequence[Sequence[Sequence[Sequence[Any]]]]], Union[Union[_SupportsArray[dtype[Any]], Sequence[_SupportsArray[dtype[Any]]], Sequence[Sequence[_SupportsArray[dtype[Any]]]], Sequence[Sequence[Sequence[_SupportsArray[dtype[Any]]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype[Any]]]]]]], Union[bool, int, float, complex, str, bytes, Sequence[Union[bool, int, float, complex, str, bytes]], Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]], Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]], Sequence[Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]]]]]], a_min: Union[Sequence[Sequence[Sequence[Sequence[Sequence[Any]]]]], Union[Union[_SupportsArray[dtype[Any]], Sequence[_SupportsArray[dtype[Any]]], Sequence[Sequence[_SupportsArray[dtype[Any]]]], Sequence[Sequence[Sequence[_SupportsArray[dtype[Any]]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype[Any]]]]]]], Union[bool, int, float, complex, str, bytes, Sequence[Union[bool, int, float, complex, str, bytes]], Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]], Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]], Sequence[Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]]]]]], a_max: Union[Sequence[Sequence[Sequence[Sequence[Sequence[Any]]]]], _SupportsArray[dtype[Any]], Sequence[_SupportsArray[dtype[Any]]], Sequence[Sequence[_SupportsArray[dtype[Any]]]], Sequence[Sequence[Sequence[_SupportsArray[dtype[Any]]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype[Any]]]]]], bool, int, float, complex, str, bytes, Sequence[Union[bool, int, float, complex, str, bytes]], Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]], Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]], Sequence[Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]]], None], out: Optional[ndarray[Any, Any]] = ..., **kwargs: Any) -> Any
torchio/transforms/preprocessing/intensity/rescale.py:88: note:     def clip(a: Union[Sequence[Sequence[Sequence[Sequence[Sequence[Any]]]]], Union[Union[_SupportsArray[dtype[Any]], Sequence[_SupportsArray[dtype[Any]]], Sequence[Sequence[_SupportsArray[dtype[Any]]]], Sequence[Sequence[Sequence[_SupportsArray[dtype[Any]]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype[Any]]]]]]], Union[bool, int, float, complex, str, bytes, Sequence[Union[bool, int, float, complex, str, bytes]], Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]], Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]], Sequence[Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]]]]]], a_min: None, a_max: Union[Sequence[Sequence[Sequence[Sequence[Sequence[Any]]]]], Union[Union[_SupportsArray[dtype[Any]], Sequence[_SupportsArray[dtype[Any]]], Sequence[Sequence[_SupportsArray[dtype[Any]]]], Sequence[Sequence[Sequence[_SupportsArray[dtype[Any]]]]], Sequence[Sequence[Sequence[Sequence[_SupportsArray[dtype[Any]]]]]]], Union[bool, int, float, complex, str, bytes, Sequence[Union[bool, int, float, complex, str, bytes]], Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]], Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]], Sequence[Sequence[Sequence[Sequence[Union[bool, int, float, complex, str, bytes]]]]]]]], out: Optional[ndarray[Any, Any]] = ..., **kwargs: Any) -> Any
torchio/transforms/preprocessing/intensity/mask.py:60: error: Argument 4 to "get_mask_from_masking_method" of "Transform" has incompatible type "Optional[Sequence[int]]"; expected "Optional[List[Any]]"
torchio/transforms/preprocessing/intensity/mask.py:62: error: Argument 1 to "apply_masking" of "Mask" has incompatible type "Image"; expected "LabelMap"
torchio/transforms/preprocessing/intensity/histogram_standardization.py:57: error: Incompatible types in assignment (expression has type "Tuple[str, str]", variable has type "Tuple[]")
torchio/transforms/preprocessing/intensity/histogram_standardization.py:92: error: Argument "mask" to "normalize" has incompatible type "Tensor"; expected "Optional[ndarray[Any, Any]]"
torchio/transforms/preprocessing/intensity/histogram_standardization.py:156: error: Argument 1 to "len" has incompatible type "Union[Sequence[Union[str, PathLike[Any]]], str, PathLike[Any], None]"; expected "Sized"
torchio/transforms/preprocessing/intensity/histogram_standardization.py:158: error: Argument 1 to "len" has incompatible type "Union[Sequence[Union[str, PathLike[Any]]], str, PathLike[Any], None]"; expected "Sized"
torchio/transforms/preprocessing/intensity/histogram_standardization.py:165: error: Argument 1 to "_get_percentiles" has incompatible type "ndarray[Any, dtype[signedinteger[Any]]]"; expected "Tuple[float, float]"
torchio/transforms/preprocessing/intensity/histogram_standardization.py:175: error: Value of type "Union[Sequence[Union[str, PathLike[Any]]], PathLike[Any]]" is not indexable
torchio/transforms/preprocessing/intensity/histogram_standardization.py:183: error: Incompatible types in assignment (expression has type "ndarray[Any, Any]", variable has type "List[Any]")
torchio/transforms/preprocessing/intensity/histogram_standardization.py:184: error: Argument 1 to "_get_average_mapping" has incompatible type "List[Any]"; expected "ndarray[Any, Any]"
torchio/transforms/preprocessing/intensity/histogram_standardization.py:260: error: Argument 1 to "_standardize_cutoff" has incompatible type "Tuple[float, float]"; expected "ndarray[Any, Any]"
torchio/transforms/preprocessing/intensity/histogram_standardization.py:262: error: Argument 1 to "_get_percentiles" has incompatible type "ndarray[Any, dtype[signedinteger[Any]]]"; expected "Tuple[float, float]"
torchio/transforms/augmentation/composition.py:47: error: Incompatible types in assignment (expression has type "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]", variable has type "Subject")
torchio/transforms/augmentation/composition.py:110: error: Incompatible return value type (got "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]", expected "Subject")
torchio/transforms/augmentation/spatial/random_flip.py:61: error: Incompatible return value type (got "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]", expected "Subject")
torchio/transforms/augmentation/spatial/random_elastic_deformation.py:132: error: Argument 1 to "_parse_num_control_points" has incompatible type "Tuple[Union[int, float], ...]"; expected "Tuple[int, int, int]"
torchio/transforms/augmentation/spatial/random_elastic_deformation.py:134: error: Argument 1 to "_parse_max_displacement" has incompatible type "Tuple[Union[int, float], ...]"; expected "Tuple[float, float, float]"
torchio/transforms/augmentation/spatial/random_elastic_deformation.py:177: error: Argument 1 to "get_params" of "RandomElasticDeformation" has incompatible type "Tuple[Union[int, float], ...]"; expected "Tuple[int, int, int]"
torchio/transforms/augmentation/spatial/random_elastic_deformation.py:178: error: Argument 2 to "get_params" of "RandomElasticDeformation" has incompatible type "Tuple[Union[int, float], ...]"; expected "Tuple[float, float, float]"
torchio/transforms/augmentation/spatial/random_elastic_deformation.py:191: error: Incompatible return value type (got "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]", expected "Subject")
torchio/transforms/augmentation/spatial/random_elastic_deformation.py:222: error: Incompatible types in assignment (expression has type "Tuple[str, str, str, str]", variable has type "Tuple[]")
torchio/transforms/augmentation/spatial/random_elastic_deformation.py:297: error: Argument 2 to "parse_free_form_transform" of "ElasticDeformation" has incompatible type "Tuple[float, float, float]"; expected "Sequence[Tuple[int, int, int]]"
torchio/transforms/augmentation/spatial/random_anisotropy.py:69: error: No overload variant of "__getitem__" of "tuple" matches argument type "Tensor"
torchio/transforms/augmentation/spatial/random_anisotropy.py:69: note: Possible overload variants:
torchio/transforms/augmentation/spatial/random_anisotropy.py:69: note:     def __getitem__(self, int) -> int
torchio/transforms/augmentation/spatial/random_anisotropy.py:69: note:     def __getitem__(self, slice) -> Tuple[int, ...]
torchio/transforms/augmentation/spatial/random_anisotropy.py:71: error: Incompatible return value type (got "Tuple[Any, Any]", expected "List[bool]")
torchio/transforms/augmentation/spatial/random_anisotropy.py:104: error: Argument "target" to "Resample" has incompatible type "Tuple[Any, ...]"; expected "Union[Union[float, Tuple[float, float, float]], str, Path, Image, None]"
torchio/transforms/augmentation/spatial/random_anisotropy.py:111: error: Argument "target" to "Resample" has incompatible type "Tuple[Tuple[int, int, int], ndarray[Any, Any]]"; expected "Union[Union[float, Tuple[float, float, float]], str, Path, Image, None]"
torchio/transforms/augmentation/spatial/random_anisotropy.py:116: error: Incompatible return value type (got "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]", expected "Subject")
torchio/transforms/augmentation/spatial/random_affine.py:172: error: Incompatible return value type (got "Union[Subject, Image, Tensor, ndarray[Any, Any], Any, Dict[Any, Any], Any]", expected "Subject")
torchio/transforms/augmentation/spatial/random_affine.py:251: error: Incompatible types in assignment (expression has type "Tuple[str, str, str, str, str, str, str, str]", variable has type "Tuple[]")
torchio/transforms/augmentation/spatial/random_affine.py:269: error: Incompatible types in assignment (expression has type "ndarray[Any, Any]", variable has type "Sequence[float]")
torchio/transforms/augmentation/spatial/random_affine.py:290: error: Argument 1 to "ras_to_lps" has incompatible type "Sequence[float]"; expected "ndarray[Any, Any]"
torchio/transforms/augmentation/spatial/random_affine.py:369: error: Incompatible types in assignment (expression has type "Union[str, float]", variable has type "int")
torchio/transforms/augmentation/intensity/random_swap.py:61: error: Argument 1 to "get_random_indices_from_shape" has incompatible type "Size"; expected "Tuple[int, int, int]"
torchio/transforms/augmentation/intensity/random_swap.py:62: error: Argument 2 to "get_random_indices_from_shape" has incompatible type "ndarray[Any, Any]"; expected "Tuple[int, int, int]"
torchio/transforms/augmentation/intensity/random_swap.py:62: note: (Skipping most remaining errors due to unresolved imports or missing stubs; fix these first)
torchio/transforms/augmentation/intensity/random_labels_to_image.py:123: error: Syntax error in type annotation
torchio/transforms/augmentation/intensity/random_labels_to_image.py:123: note: Suggestion: Use Tuple[T1, ..., Tn] instead of (T1, ..., Tn)
torchio/transforms/augmentation/intensity/random_blur.py:6: error: Skipping analyzing "scipy.ndimage": found module but no type hints or library stubs
torchio/transforms/augmentation/intensity/random_blur.py:6: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
torchio/transforms/augmentation/intensity/random_blur.py:6: error: Skipping analyzing "scipy": found module but no type hints or library stubs
torchio/visualization.py:15: error: Skipping analyzing "matplotlib": found module but no type hints or library stubs
torchio/visualization.py:16: error: Skipping analyzing "matplotlib.pyplot": found module but no type hints or library stubs
Found 177 errors in 39 files (checked 95 source files)

jcreinhold · 2022-01-30T16:33:08Z

Awesome. Many thanks for your contribution, @jcreinhold. May I add you to the list of contributors?

Sure! That'd be great

I agree that typing hints in TorchIO are a bit messy. I suppose part of the reason is that I didn't add them since the beginning, and the library was not created to be shared initially. Also, I don't know much about the topic. It would be great to improve typing in the library, and your help would be much appreciated!

Sometimes adding them from the beginning makes it more difficult to update them later to reflect what the project actually requires. I've grafted type annotations on to many of my research and work projects now, and I can start going through torchio function by function and updating them to pass mypy inspection. mypy has caught a good number of errors in my code, and proper type annotations make development much easier in a modern IDE (IMO), so I think it'd be worth the effort.

Since this would change a good number of files (39 it looks like, although some of the errors might be fixed by fixing the type issue elsewhere), I could do the following:

Make a mypy feature branch
Define the least strict base types the project requires
Fix the mypy issues in one function
Commit the changes
Repeat 3-4 until no more mypy errors
Submit a PR

Alternatively, I could make a mypy-modulename feature branch and submit a PR for each module (e.g., at the level of torchio/data/image.py or torchio/data). It might get a bit tedious, but it'd avoid a giant PR; however, type annotations are very entangled, so I'm not sure how effective that workflow would be at eliminating errors from the project, but I could try and see how it goes and update you if it's untenable.

I'd avoid changing any actual functionality, although there are likely to be be some bugs caught while going through the process. If I find a potential error, I'd just raise an issue instead of correcting it.

Would some workflow like the above make sense?

fepegar · 2022-01-30T16:37:37Z

That sounds great! If a single PR makes your life easier than the individual ones, I suggest following that route. Thanks a lot for working on this!

@all-contributors please add @jcreinhold for code

allcontributors · 2022-01-30T16:37:45Z

@fepegar

I've put up a pull request to add @jcreinhold! 🎉

@asottile

Use type of current instance instead of hardcoded subject type fix copy behavior Stop running some unstable tests on CI (fepegar#796) * Print output messages during testing * Skip MedMNIST tests on GitHub Actions * Fix AttributeError * Add reason for skipping test Add support to specify the interpolation type for label images (fepegar#791) * Add label_interpolation option in spatial transforms and augmentations * Add label_interpolation option in spatial transforms and augmentations * Adds missing backtick * update docs 782 * Minor docs edits Co-authored-by: Fernando Pérez-García <[email protected]> docs: add snavalm as a contributor for code (fepegar#802) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Bump version: 0.18.71 → 0.18.72 Add py.typed marker file for type checking (fepegar#808) docs: add jcreinhold as a contributor for code (fepegar#809) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Bump version: 0.18.72 → 0.18.73 Fix overlapping in patches aggregator (fepegar#832) Bump version: 0.18.73 → 0.18.74 Update announcement docs: add Hsuxu as a contributor for bug (fepegar#833) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Add check for shapes of input batch and output location Add support for torch >= 1.11 (fepegar#838) * added support for pytorch>=1.11.0 * Replace type with isinstance Co-authored-by: Fernando Pérez-García <[email protected]> Bump version: 0.18.74 → 0.18.75 docs: add snipdome as a contributor for bug (fepegar#839) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Remove redundant tests in GitHub actions (fepegar#850) Fix new SimpleITK release breaking tests (fepegar#852) Bump version: 0.18.75 → 0.18.76 Disable fail-fast in CI matrix strategy Fix wrong mapping in SequentialLabels transform (fepegar#841) docs: add iamSmallY as a contributor for bug (fepegar#855) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Fix SimpleITK version in docs requirements Fix examples format in docstrings Improve documentation and tests for label transforms (fepegar#857) * Improve documentation and tests for label transforms * Add parametrization with duplicated values in dict Add example of RandomLabelsToImage Add example of RandomGamma Use sphinx-opengraph for documentation Improve quality of figures from plot directive [pre-commit.ci] pre-commit autoupdate (fepegar#859) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pre-commit/pre-commit-hooks: v4.0.1 → v4.2.0](pre-commit/pre-commit-hooks@v4.0.1...v4.2.0) - [github.com/pycqa/flake8: 3.9.2 → 4.0.1](PyCQA/flake8@3.9.2...4.0.1) - [github.com/asottile/pyupgrade: v2.29.0 → v2.32.0](asottile/pyupgrade@v2.29.0...v2.32.0) * Fix pre-commit not installing flake8 This commit address the comments by @asottile in pre-commit-ci/issues#118. Thanks, @asottile! Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Fernando Pérez-García <[email protected]> Validate arguments of add/remove_image Return figure in plot_volume function (fepegar#872) Co-authored-by: Derk <[email protected]> docs: add guigautier as a contributor for ideas (fepegar#875) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Update flake8 error codes [pre-commit.ci] pre-commit autoupdate (fepegar#874) updates: - [github.com/asottile/pyupgrade: v2.32.0 → v2.32.1](asottile/pyupgrade@v2.32.0...v2.32.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Fernando Pérez-García <[email protected]> Stop upgrading pip in CI (fepegar#877) Update bug report template docs: add AyedSamy as a contributor for bug (fepegar#878) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Add tests for Python 3.10 (fepegar#880) * Add tests for Python 3.10 * Fix Python version in YAML Use PyTorch to compute Fourier transforms (fepegar#389) * Use PyTorch for FFT if available * Make sure tensor in on CPU before calling numpy() Remove support for Python 3.6 (fepegar#881) * Remove support for Python 3.6 * Fix Python version Add support to use different numbers of samples in the queue (fepegar#795) docs: add jmlipman as a contributor for ideas, code (fepegar#882) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Juan Miguel <[email protected]> Fix computation of kernels in `Blur` transform (fepegar#861) * Fix size of Gaussian kernel for blurring * Fix typo in docstring Add support to pass label keys for dict input (fepegar#879) * Add support to pass label keys for dict input * Add reference to @josegcpa's code Co-authored-by: josegcpa <[email protected]> docs: add josegcpa as a contributor for ideas (fepegar#883) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Bump version: 0.18.76 → 0.18.77 Fix support for NiBabel inputs Remove unnecessary check Remove error for multichannel NiBabel input Cover method to print queue memory Add gallery example for custom resampling transform docs: add saikhu as a contributor for bug (fepegar#887) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Move package code to `src` directory (fepegar#896) * Move package to src directory * Update setup.py * Update setup.py * Move requirements * Include requirements file in MANIFEST.in * Stop using requirements file * Fix warning in docs Remove setup.py script and add pyproject.toml config file (fepegar#898) * Remove setup.py and add pyproject.toml * Add version to setup config * Remove bumpversion config for setup.py * Fix path to __init__ * Stop removing trailing whitespaces from setup.cfg See peritus/bumpversion#78 * Update version replacing in bumpversion config * Fix tox configuration for pyproject.toml * Add keywords * Remove requirements file * Update authors config Bump version: 0.18.77 → 0.18.78 Enable verbose mode for publishing GHA Fix version Fix version not being updated As it seems that bump2version is not able to modify its own config file. Add citation file [pre-commit.ci] pre-commit autoupdate (fepegar#902) updates: - [github.com/pre-commit/pre-commit-hooks: v4.2.0 → v4.3.0](pre-commit/pre-commit-hooks@v4.2.0...v4.3.0) - [github.com/asottile/pyupgrade: v2.32.1 → v2.34.0](asottile/pyupgrade@v2.32.1...v2.34.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Fix warning in RTD documentation build (fepegar#903) Add hook for trailing commas (fepegar#904) * Add hook for trailing commas * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix flake8 issues Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Disable Binder buttons in Sphinx gallery (fepegar#905) * Disable Binder buttons in Sphinx gallery * Update RTD config to use pip installation * Fix extra requirements string * Add missing doc requirement Add checks for TOML and YAML files Add support to mask 4D images with 3D masks (fepegar#908) * Add failing test * Add support to mask 4D images with 3D masks * Improve docstring Co-authored-by: cbri92 <[email protected]> Co-authored-by: valabregue <[email protected]> docs: add cbri92 as a contributor for bug (fepegar#909) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Bump version: 0.18.78 → 0.18.79 Add fftshift to fourier_transform with torch.fft (fepegar#912) This makes the behavior of fourier_transform and inv_fourier_transform consistent with earlier versions of torchio. It is also independent of whether torch or numpy is used to perform the transform. Solves fepegar#911 docs: add iimog as a contributor for bug (fepegar#913) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Bump version: 0.18.79 → 0.18.80 Remove incorrect Contributors badge Stop ignoring some missing imports for mypy Fix tox running on Python 3.7 only (fepegar#915) Create dependabot.yml (fepegar#917) Test all Python versions in Ubuntu only (fepegar#918) * Test all Python versions in Ubuntu only * Fix exclusions Bump actions/setup-python from 2 to 4 (fepegar#919) Bumps [actions/setup-python](https:/actions/setup-python) from 2 to 4. - [Release notes](https:/actions/setup-python/releases) - [Commits](actions/setup-python@v2...v4) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Ignore some files in MANIFEST (fepegar#916) * Ignore some files in MANIFEST * Always publish to TestPyPI * Skip existing TestPyPI versions Bump actions/checkout from 2 to 3 (fepegar#920) Bumps [actions/checkout](https:/actions/checkout) from 2 to 3. - [Release notes](https:/actions/checkout/releases) - [Changelog](https:/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v2...v3) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Update fpg.py Proper copy of subclass copies [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci fix parenthesis imports Fix proper subject subclass copy old-style type annotations linting [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Fix proper subject subclass copy

add py.typed marker file for type checking

8263ad4

fepegar merged commit 989ae03 into fepegar:main Jan 30, 2022

jcreinhold deleted the 807-py-typed branch January 30, 2022 15:57

allcontributors bot mentioned this pull request Jan 30, 2022

docs: add jcreinhold as a contributor for code #809

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jcreinhold mentioned this pull request Jan 30, 2022

Add and fix type annotations for type checking with mypy #810

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add py.typed marker file for type checking in mypy #808

add py.typed marker file for type checking in mypy #808

jcreinhold commented Jan 29, 2022

codecov bot commented Jan 30, 2022 •

edited

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fepegar commented Jan 30, 2022

fepegar commented Jan 30, 2022

jcreinhold commented Jan 30, 2022

fepegar commented Jan 30, 2022

allcontributors bot commented Jan 30, 2022

add py.typed marker file for type checking in mypy #808

add py.typed marker file for type checking in mypy #808

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fepegar commented Jan 30, 2022

allcontributors bot commented Jan 30, 2022

codecov bot commented Jan 30, 2022 •

edited

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