Remove deprecated code (#1621)

1. MaxProject filter.  Deprecated since 0.1.2 (june 19)
2. remove `enable_inplace_mode`.  Deprecated since 0.1.4 (july 17)
3. remove `FieldOfView.show_aligned_image_groups` and `FieldOfView.iterate_image_type`.  Deprecated since 0.1.4 (july 17)

starfish/core/experiment/builder/inplace.py

@@ -6,7 +6,6 @@
 
 
 import abc
-import warnings
 from pathlib import Path
 from typing import Mapping, Optional
 
@@ -32,15 +31,6 @@ def write_tile(
         return tile.provider.sha256
 
 
-def enable_inplace_mode():
-    """
-    .. deprecated:: 0.1.4
-        This method is no longer necessary.  Call `write_experiment_json` with
-        `writer_contract=InplaceWriterContract()`.
-    """
-    warnings.warn("`enable_inplace_mode()` is no longer necessary.", DeprecationWarning)
-
-
 class InplaceFetchedTile(FetchedTile):
     """Data formatters that operate in-place should return tiles that extend this class."""
     @property

starfish/core/experiment/experiment.py

@@ -52,8 +52,8 @@ class FieldOfView:
     The decoding of :py:class:`~slicedimage.TileSet` to
     :py:class:`~starfish.imagestack.imagestack.ImageStack`
     does not happen until the image is accessed. ImageStacks can only be initialized with
-    aligned tilesets, so if thereare multiple you may need to iterate through the groups
-    using :py:func:`~starfish.experiment.experiment.FieldOfView.iterate_image_type`
+    aligned tilesets, so if there are multiple you may need to iterate through the groups
+    using :py:func:`~starfish.experiment.experiment.FieldOfView.get_images`
     and process each one individually.
 
     Be prepared to handle errors when images are accessed.
@@ -100,23 +100,6 @@ def name(self) -> str:
     def image_types(self) -> Set[str]:
         return set(self._images.keys())
 
-    def show_aligned_image_groups(self) -> None:
-        """
-        .. deprecated:: 0.1.4
-            Use `FieldOfView.get_images()` to retrieve all the aligned image groups.
-        """
-        raise DeprecationWarning("This method has been deprecated. Aligned groups are now parsed "
-                                 "as a part of, FieldOfView.get_images() and are determined by the "
-                                 "selected axes provided to the method.")
-
-    def iterate_image_type(self, image_type: str) -> Iterator[ImageStack]:
-        """
-        .. deprecated:: 0.1.4
-            Use `FieldOfView.get_images()` to retrieve all the aligned image groups.
-        """
-        raise DeprecationWarning("This method has been deprecated. Instead use "
-                                 "FieldOfView.get_images(image_type)")
-
     def get_image(self, item: str,
                   aligned_group: Any = _SINGLETON,
                   rounds: Optional[Collection[int]] = None,

starfish/core/image/Filter/__init__.py

@@ -10,7 +10,6 @@
 from .linear_unmixing import LinearUnmixing
 from .map import Map
 from .match_histograms import MatchHistograms
-from .max_proj import MaxProject
 from .mean_high_pass import MeanHighPass
 from .reduce import Reduce
 from .richardson_lucy_deconvolution import DeconvolvePSF

starfish/core/image/Filter/test/test_api_contract.py

@@ -22,7 +22,6 @@
 
 from starfish import ImageStack
 from starfish.core.image import Filter
-from starfish.core.image.Filter.max_proj import MaxProject
 from starfish.core.image.Filter.reduce import Reduce
 
 
@@ -35,7 +34,6 @@
     'guassian_high_pass': Filter.GaussianHighPass,
     'guassian_low_pass': Filter.GaussianLowPass,
     'laplace': Filter.Laplace,
-    'max_proj': Filter.MaxProject,
     'mean_high_pass': Filter.MeanHighPass,
     'reduce': Filter.Reduce,
     'deconvolve': Filter.DeconvolvePSF,
@@ -72,7 +70,7 @@ def test_all_methods_adhere_to_contract(filter_class):
 
     # Max Proj and Reduce don't have an in_place, n_processes, verbose option,
     # so we need to skip these tests
-    if filter_class not in [MaxProject, Reduce]:
+    if filter_class not in [Reduce]:
         # return None if in_place = True
         try:
             filtered = instance.run(data, in_place=True)

starfish/core/imagestack/imagestack.py

@@ -1146,7 +1146,8 @@ def max_proj(self, *dims: Axes) -> "ImageStack":
         This method is deprecated.  Please ``ImageStack.reduce(axes, func="max")`` to do max
         projection operations.
         """
-        raise DeprecatedAPIError("Please Filter.MaxProject to do max projection operations.")
+        raise DeprecatedAPIError(
+            """Please ImageStack.reduce(axes, func="max") to do max projection operations.""")
 
     def _squeezed_numpy(self, *dims: Axes):
         """return this ImageStack's data as a squeezed numpy array"""