Update with nnunet master

[silvandeleemput]

This PR pulls and merges the latest changes from the original nnUNet master branch (https://github.com/MIC-DKFZ/nnUNet).

[nlessmann]

Awesome!

[silvandeleemput]

The training tests are failing now, I'll start investigating...

[silvandeleemput]

Strange typing error in batchgenerators, I'll try reproducing it locally, it might have been introduced going from 0.23 -> 0.24.

tests/test_training.py:55: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
nnunet/run/default_configuration.py:59: in get_default_configuration
    trainer_class = recursive_find_python_class([join(*search_in)], network_trainer,
nnunet/training/model_restore.py:37: in recursive_find_python_class
    tr = recursive_find_python_class([join(folder[0], modname)], trainer_name, current_module=next_current_module)
nnunet/training/model_restore.py:37: in recursive_find_python_class
    tr = recursive_find_python_class([join(folder[0], modname)], trainer_name, current_module=next_current_module)
nnunet/training/model_restore.py:28: in recursive_find_python_class
    m = importlib.import_module(current_module + "." + modname)
/usr/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1014: in _gcd_import
    ???
<frozen importlib._bootstrap>:991: in _find_and_load
    ???
<frozen importlib._bootstrap>:975: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:671: in _load_unlocked
    ???
<frozen importlib._bootstrap_external>:848: in exec_module
    ???
<frozen importlib._bootstrap>:[219](https://github.com/DIAGNijmegen/nnUNet/runs/6504419310?check_suite_focus=true#step:3:220): in _call_with_frames_removed
    ???
nnunet/training/network_training/nnUNet_variants/data_augmentation/nnUNetTrainerV2_DA5.py:22: in <module>
    from batchgenerators.transforms.local_transforms import BrightnessGradientAdditiveTransform, LocalGammaTransform
/usr/local/lib/python3.8/dist-packages/batchgenerators/transforms/local_transforms.py:21: in <module>
    from batchgenerators.utilities.custom_types import ScalarType, sample_scalar
/usr/local/lib/python3.8/dist-packages/batchgenerators/utilities/custom_types.py:19: in <module>
    ScalarType = Union[Union[int, float], Tuple[float, float], Callable[[Any, ...], Union[float, int]]]
/usr/lib/python3.8/typing.py:816: in __getitem__
    return self.__getitem_inner__(params)
/usr/lib/python3.8/typing.py:261: in inner
    return func(*args, **kwds)
/usr/lib/python3.8/typing.py:839: in __getitem_inner__
    args = tuple(_type_check(arg, msg) for arg in args)
/usr/lib/python3.8/typing.py:839: in <genexpr>
    args = tuple(_type_check(arg, msg) for arg in args)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

arg = Ellipsis, msg = 'Callable[[arg, ...], result]: each arg must be a type.'
is_argument = True

    def _type_check(arg, msg, is_argument=True):
        """Check that the argument is a type, and return it (internal helper).

        As a special case, accept None and return type(None) instead. Also wrap strings
        into ForwardRef instances. Consider several corner cases, for example plain
        special forms like Union are not valid, while Union[int, str] is OK, etc.
        The msg argument is a human-readable error message, e.g::

            "Union[arg, ...]: arg should be a type."

        We append the repr() of the actual value (truncated to 100 chars).
        """
        invalid_generic_forms = (Generic, Protocol)
        if is_argument:
            invalid_generic_forms = invalid_generic_forms + (ClassVar, Final)

        if arg is None:
            return type(None)
        if isinstance(arg, str):
            return ForwardRef(arg)
        if (isinstance(arg, _GenericAlias) and
                arg.__origin__ in invalid_generic_forms):
            raise TypeError(f"{arg} is not valid as type argument")
        if (isinstance(arg, _SpecialForm) and arg not in (Any, NoReturn) or
                arg in (Generic, Protocol)):
            raise TypeError(f"Plain {arg} is not valid as type argument")
        if isinstance(arg, (type, TypeVar, ForwardRef)):
            return arg
        if not callable(arg):
>           raise TypeError(f"{msg} Got {arg!r:.100}.")
E           TypeError: Callable[[arg, ...], result]: each arg must be a type. Got Ellipsis.

[silvandeleemput]

Ok, nevermind, all seems good now. I just needed to remove the old docker containers from the private runners and use freshly build ones. This PR should be good to go.