Document all the algorithm implementations (#1554)

This is the same as #1510 except for all the algorithm implementations.

Depends on #1553

starfish/core/image/Filter/__init__.py

@@ -21,6 +21,6 @@
 all_filters = {
     filter_name: filter_cls
     for filter_name, filter_cls in locals().items()
-    if isinstance(filter_cls, type) and FilterAlgorithm in filter_cls.__mro__
+    if isinstance(filter_cls, type) and issubclass(filter_cls, FilterAlgorithm)
 }
 __all__ = list(all_filters.keys())

starfish/core/image/Segment/__init__.py

@@ -1 +1,10 @@
+from ._base import SegmentAlgorithm
 from .watershed import Watershed
+
+# autodoc's automodule directive only captures the modules explicitly listed in __all__.
+all_filters = {
+    filter_name: filter_cls
+    for filter_name, filter_cls in locals().items()
+    if isinstance(filter_cls, type) and issubclass(filter_cls, SegmentAlgorithm)
+}
+__all__ = list(all_filters.keys())

starfish/core/image/_registration/ApplyTransform/__init__.py

@@ -1 +1,10 @@
+from ._base import ApplyTransformAlgorithm
 from .warp import Warp
+
+# autodoc's automodule directive only captures the modules explicitly listed in __all__.
+all_filters = {
+    filter_name: filter_cls
+    for filter_name, filter_cls in locals().items()
+    if isinstance(filter_cls, type) and issubclass(filter_cls, ApplyTransformAlgorithm)
+}
+__all__ = list(all_filters.keys())

starfish/core/image/_registration/LearnTransform/__init__.py

@@ -1 +1,10 @@
+from ._base import LearnTransformAlgorithm
 from .translation import Translation
+
+# autodoc's automodule directive only captures the modules explicitly listed in __all__.
+all_filters = {
+    filter_name: filter_cls
+    for filter_name, filter_cls in locals().items()
+    if isinstance(filter_cls, type) and issubclass(filter_cls, LearnTransformAlgorithm)
+}
+__all__ = list(all_filters.keys())

starfish/core/spots/AssignTargets/__init__.py

@@ -1 +1,10 @@
+from ._base import AssignTargetsAlgorithm
 from .label import Label
+
+# autodoc's automodule directive only captures the modules explicitly listed in __all__.
+all_filters = {
+    filter_name: filter_cls
+    for filter_name, filter_cls in locals().items()
+    if isinstance(filter_cls, type) and issubclass(filter_cls, AssignTargetsAlgorithm)
+}
+__all__ = list(all_filters.keys())

starfish/core/spots/Decode/__init__.py

@@ -1,2 +1,11 @@
+from ._base import DecodeAlgorithm
 from .metric_decoder import MetricDistance
 from .per_round_max_channel_decoder import PerRoundMaxChannel
+
+# autodoc's automodule directive only captures the modules explicitly listed in __all__.
+all_filters = {
+    filter_name: filter_cls
+    for filter_name, filter_cls in locals().items()
+    if isinstance(filter_cls, type) and issubclass(filter_cls, DecodeAlgorithm)
+}
+__all__ = list(all_filters.keys())

starfish/core/spots/DetectPixels/__init__.py

@@ -1 +1,10 @@
+from ._base import DetectPixelsAlgorithm
 from .pixel_spot_decoder import PixelSpotDecoder
+
+# autodoc's automodule directive only captures the modules explicitly listed in __all__.
+all_filters = {
+    filter_name: filter_cls
+    for filter_name, filter_cls in locals().items()
+    if isinstance(filter_cls, type) and issubclass(filter_cls, DetectPixelsAlgorithm)
+}
+__all__ = list(all_filters.keys())

starfish/core/spots/DetectSpots/__init__.py

@@ -1,8 +1,13 @@
-# from starfish.core.pipeline import import_all_submodules
-# from ._base import DetectSpots
-# import_all_submodules(__file__, __package__)
-
+from ._base import DetectSpotsAlgorithm
 from .blob import BlobDetector
 from .local_max_peak_finder import LocalMaxPeakFinder
 from .local_search_blob_detector import LocalSearchBlobDetector
 from .trackpy_local_max_peak_finder import TrackpyLocalMaxPeakFinder
+
+# autodoc's automodule directive only captures the modules explicitly listed in __all__.
+all_filters = {
+    filter_name: filter_cls
+    for filter_name, filter_cls in locals().items()
+    if isinstance(filter_cls, type) and issubclass(filter_cls, DetectSpotsAlgorithm)
+}
+__all__ = list(all_filters.keys())