          """ Add a call to add model input size to the re-aligner """
          self._re_align.set_input_size_and_centering(self.input_size, self.realign_centering)
          super().initialize(*args, **kwargs)
  
      def _handle_realigns(self, queue: "Queue") -> Optional[Tuple[bool, AlignerBatch]]:
          """ Handle any items waiting for a second pass through the aligner.
  
          If EOF has been recieved and items are still being processed through the first pass
          then wait for a short time and try again to collect them.
  
 
</s> remove         self._normalize_method = cast(Optional[Literal["clahe", "hist", "mean"]], method)
 </s> add         self._normalize_method = T.cast(T.Literal["clahe", "hist", "mean"] | None, method) </s> remove     def set_input_size_and_centering(self, input_size: int, centering: "CenteringType") -> None:
 </s> add     def set_input_size_and_centering(self, input_size: int, centering: CenteringType) -> None: </s> remove     def _process_batch(self, filenames: List[str]) -> BatchType:
 </s> add     def _process_batch(self, filenames: list[str]) -> BatchType: </s> remove     def get_batch(self, queue: "Queue") -> Tuple[bool, DetectorBatch]:
 </s> add     def get_batch(self, queue: Queue) -> tuple[bool, DetectorBatch]: </s> remove     def add_skip_list(self, skip_list: List[int]) -> None:
 </s> add     def add_skip_list(self, skip_list: list[int]) -> None:
    def _handle_realigns(self, queue: Queue) -> tuple[bool, AlignerBatch] | None:
          """ Add a call to add model input size to the re-aligner """
          self._re_align.set_input_size_and_centering(self.input_size, self.realign_centering)
          super().initialize(*args, **kwargs)
  
    def _handle_realigns(self, queue: Queue) -> tuple[bool, AlignerBatch] | None:
          """ Handle any items waiting for a second pass through the aligner.
  
          If EOF has been recieved and items are still being processed through the first pass
          then wait for a short time and try again to collect them.
  
keep keep keep keep replace keep keep keep keep keep
 Rebase code (#1326)

* Remove tensorflow_probability requirement

* setup.py - fix progress bars

* requirements.txt: Remove pre python 3.9 packages

* update apple requirements.txt

* update INSTALL.md

* Remove python<3.9 code

* setup.py - fix Windows Installer

* typing: python3.9 compliant

* Update pytest and readthedocs python versions

* typing fixes

* Python Version updates
  - Reduce max version to 3.10
  - Default to 3.10 in installers
  - Remove incompatible 3.11 tests

* Update dependencies

* Downgrade imageio dep for Windows

* typing: merge optional unions and fixes

* Updates
  - min python version 3.10
  - typing to python 3.10 spec
  - remove pre-tf2.10 code
  - Add conda tests

* train: re-enable optimizer saving

* Update dockerfiles

* Update setup.py
  - Apple Conda deps to setup.py
  - Better Cuda + dependency handling

* bugfix: Patch logging to prevent Autograph errors

* Update dockerfiles

* Setup.py - Setup.py - stdout to utf-8

* Add more OSes to github Actions

* suppress mac-os end to end test 
plugins/extract/align/_base/aligner.py