refactor(api): redefine well geometry structure (#16392)

## Overview
After discovering some new shapes and generally interacting with the new
well geometry data structures, I think it would be better to reshape the
geometry data a little bit. Rather than having each section of a well be
represented by its top cross-section and top height, let's just
represent a section in its entirety, with bottom and top cross-sections
and bottom and top heights being present in every shape that is not a
`SphericalSegment`.

## Changelog

- add `RoundedRectangle` class
- add `TruncatedCircle` class
- add `CircularFrustum` and `RectangularFrustum` classes
- adjust `frustum_helpers` and tests to use the new data structure

## TODO
- We should [write some more
tests](https://opentrons.atlassian.net/browse/EXEC-743?atlOrigin=eyJpIjoiYzg5OThhMjQ2NTViNDRmNGI2OTkwMWEwYTExMmFjNjIiLCJwIjoiaiJ9)
to make sure invalid wells don't get passed in without an error being
raised.
- Implement the math for [truncated
circle](https://opentrons.atlassian.net/browse/EXEC-712) calculations
- Implement the math for [rounded
rectangle](https://opentrons.atlassian.net/browse/EXEC-744) calculations

---------

Co-authored-by: Ryan howard <[email protected]>

api/tests/opentrons/protocol_engine/state/test_geometry_view.py

@@ -83,10 +83,10 @@
 )
 from opentrons.protocol_engine.state.geometry import GeometryView, _GripperMoveType
 from opentrons.protocol_engine.state.frustum_helpers import (
-    height_from_volume_circular,
-    height_from_volume_rectangular,
-    volume_from_height_circular,
-    volume_from_height_rectangular,
+    _height_from_volume_circular,
+    _height_from_volume_rectangular,
+    _volume_from_height_circular,
+    _volume_from_height_rectangular,
 )
 from ..pipette_fixtures import get_default_nozzle_map
 from ..mock_circular_frusta import TEST_EXAMPLES as CIRCULAR_TEST_EXAMPLES
@@ -2776,7 +2776,7 @@ def _find_volume_from_height_(index: int) -> None:
         top_width = frustum["width"][index]
         target_height = frustum["height"][index]
 
-        found_volume = volume_from_height_rectangular(
+        found_volume = _volume_from_height_rectangular(
             target_height=target_height,
             total_frustum_height=total_frustum_height,
             top_length=top_length,
@@ -2785,7 +2785,7 @@ def _find_volume_from_height_(index: int) -> None:
             bottom_width=bottom_width,
         )
 
-        found_height = height_from_volume_rectangular(
+        found_height = _height_from_volume_rectangular(
             volume=found_volume,
             total_frustum_height=total_frustum_height,
             top_length=top_length,
@@ -2815,14 +2815,14 @@ def _find_volume_from_height_(index: int) -> None:
         top_radius = frustum["radius"][index]
         target_height = frustum["height"][index]
 
-        found_volume = volume_from_height_circular(
+        found_volume = _volume_from_height_circular(
             target_height=target_height,
             total_frustum_height=total_frustum_height,
             top_radius=top_radius,
             bottom_radius=bottom_radius,
         )
 
-        found_height = height_from_volume_circular(
+        found_height = _height_from_volume_circular(
             volume=found_volume,
             total_frustum_height=total_frustum_height,
             top_radius=top_radius,

api/tests/opentrons/protocol_runner/test_json_translator.py

@@ -13,7 +13,7 @@
     Group,
     Metadata1,
     WellDefinition,
-    RectangularBoundedSection,
+    CuboidalFrustum,
     InnerWellGeometry,
     SphericalSegment,
 )
@@ -685,32 +685,39 @@ def _load_labware_definition_data() -> LabwareDefinition:
                 y=75.43,
                 z=75,
                 totalLiquidVolume=1100000,
-                shape="rectangular",
+                shape="circular",
             )
         },
         dimensions=Dimensions(yDimension=85.5, zDimension=100, xDimension=127.75),
         cornerOffsetFromSlot=CornerOffsetFromSlot(x=0, y=0, z=0),
         innerLabwareGeometry={
             "welldefinition1111": InnerWellGeometry(
-                frusta=[
-                    RectangularBoundedSection(
-                        shape="rectangular",
-                        xDimension=7.6,
-                        yDimension=8.5,
+                sections=[
+                    CuboidalFrustum(
+                        shape="cuboidal",
+                        topXDimension=7.6,
+                        topYDimension=8.5,
+                        bottomXDimension=5.6,
+                        bottomYDimension=6.5,
                         topHeight=45,
+                        bottomHeight=20,
                     ),
-                    RectangularBoundedSection(
-                        shape="rectangular",
-                        xDimension=5.6,
-                        yDimension=6.5,
+                    CuboidalFrustum(
+                        shape="cuboidal",
+                        topXDimension=5.6,
+                        topYDimension=6.5,
+                        bottomXDimension=4.5,
+                        bottomYDimension=4.0,
                         topHeight=20,
+                        bottomHeight=10,
+                    ),
+                    SphericalSegment(
+                        shape="spherical",
+                        radiusOfCurvature=6,
+                        topHeight=10,
+                        bottomHeight=0.0,
                     ),
                 ],
-                bottomShape=SphericalSegment(
-                    shape="spherical",
-                    radiusOfCurvature=6,
-                    depth=10,
-                ),
             )
         },
         brand=BrandData(brand="foo"),