Fix shapely imports; fix test_filter_non_polygons

codecov.yml

@@ -6,6 +6,12 @@ coverage:
   round: down
   range: "70...100"
   status:
+    project:
+      default:
+        # basic
+        target: auto
+        threshold: 5%
+        base: auto
     patch: off
 
 parsers:
@@ -16,4 +22,4 @@ parsers:
       method: no
       macro: no
 
-comment: false
+comment: false

docs/source/requirements_docs.txt

@@ -1,6 +1,6 @@
 scipy
 numpy
-shapely
+shapely>=2.0
 matplotlib>=3.4
 more_itertools
 triangle

examples/01-advanced/05_trapz_approximation.py

@@ -25,7 +25,7 @@
 # Shapely `Polygon` object.
 import numpy as np
 import matplotlib.pyplot as plt
-from shapely.geometry import Polygon
+from shapely import Polygon
 import sectionproperties.pre.geometry as geometry
 import sectionproperties.pre.pre as pre
 import sectionproperties.pre.library.primitive_sections as sections

sectionproperties/analysis/section.py

@@ -27,9 +27,8 @@
 import sectionproperties.analysis.solver as solver
 import sectionproperties.post.post as post
 
-from shapely.geometry import Polygon
+from shapely import Polygon, Point
 from shapely.strtree import STRtree
-from shapely.geometry import Point
 
 
 class Section:
@@ -194,7 +193,6 @@ def __init__(
             Polygon(self.geometry.mesh["vertices"][tri][0:3])
             for tri in self.geometry.mesh["triangles"]
         ]
-        self.poly_mesh_idx = dict((id(poly), i) for i, poly in enumerate(p_mesh))
         self.mesh_search_tree = STRtree(p_mesh)
 
         # initialise class storing section properties
@@ -2260,11 +2258,7 @@ def get_stress_at_points(
 
         for pt in pts:
             query_geom = Point(pt)
-            tri_ids = [
-                self.poly_mesh_idx[id(poly)]
-                for poly in self.mesh_search_tree.query(query_geom)
-                if poly.intersects(query_geom)
-            ]
+            tri_ids = self.mesh_search_tree.query(query_geom, predicate="intersects")
             if len(tri_ids) == 0:
                 sig = None
             elif len(tri_ids) == 1:

sectionproperties/pre/bisect_section.py

@@ -1,7 +1,7 @@
 from typing import Tuple, Union, List, Optional
 
 import numpy as np
-import shapely
+from shapely import LineString, GeometryCollection, Polygon
 
 
 def create_line_segment(
@@ -23,19 +23,19 @@ def create_line_segment(
 
         scale_factor_1 = (b_1 - p_x) / vector[0]
         y_1 = scale_factor_1 * vector[1] + p_y
-        return shapely.geometry.LineString([(b_1, y_1), (b_2, y_2)])
+        return LineString([(b_1, y_1), (b_2, y_2)])
     else:  # Vertical line
         scale_factor_2 = (b_2 - p_y) / vector[1]
         x_2 = scale_factor_2 * vector[0] + p_x
 
         scale_factor_1 = (b_1 - p_y) / vector[1]
         x_1 = scale_factor_1 * vector[0] + p_x
-        return shapely.geometry.LineString([(x_1, b_1), (x_2, b_2)])
+        return LineString([(x_1, b_1), (x_2, b_2)])
 
 
 def group_top_and_bottom_polys(
-    polys: shapely.geometry.GeometryCollection,
-    line: shapely.geometry.LineString,
+    polys: GeometryCollection,
+    line: LineString,
 ) -> Tuple[list, list]:
     """
     Returns tuple of two lists representing the list of Polygons in 'polys' on the "top" side of 'line' and the
@@ -67,7 +67,7 @@ def group_top_and_bottom_polys(
 
 
 def line_mx_plus_b(
-    line: shapely.geometry.LineString,
+    line: LineString,
 ) -> Tuple[float, float]:
     """
     Returns a tuple representing the values of "m" and "b" from the definition of 'line' as "y = mx + b".
@@ -120,7 +120,7 @@ def line_intersection(
 
 
 def sum_poly_areas(
-    lop: List[shapely.geometry.Polygon],
+    lop: List[Polygon],
 ) -> float:
     """
     Returns a float representing the total area of all polygons

sectionproperties/pre/geometry.py

@@ -7,17 +7,17 @@
 import pathlib
 import more_itertools
 import numpy as np
-from shapely.geometry import (
+from shapely import (
     Polygon,
     MultiPolygon,
     LineString,
     LinearRing,
     Point,
-    box,
     GeometryCollection,
+    box,
+    affinity,
 )
 from shapely.ops import split, unary_union
-import shapely
 import matplotlib
 import matplotlib.pyplot as plt
 import sectionproperties.pre.pre as pre
@@ -51,7 +51,7 @@ class Geometry:
 
     def __init__(
         self,
-        geom: shapely.geometry.Polygon,
+        geom: Polygon,
         material: pre.Material = pre.DEFAULT_MATERIAL,
         control_points: Optional[Union[Point, List[float, float]]] = None,
         tol=12,
@@ -544,11 +544,11 @@ def shift_section(
         # Move assigned control point
         new_ctrl_point = None
         if self.assigned_control_point:
-            new_ctrl_point = shapely.affinity.translate(
+            new_ctrl_point = affinity.translate(
                 self.assigned_control_point, x_offset, y_offset
             ).coords[0]
         new_geom = Geometry(
-            shapely.affinity.translate(self.geom, x_offset, y_offset),
+            affinity.translate(self.geom, x_offset, y_offset),
             self.material,
             new_ctrl_point,
         )
@@ -585,11 +585,11 @@ def rotate_section(
             rotate_point = rot_point
             if rot_point == "center":
                 rotate_point = box(*self.geom.bounds).centroid
-            new_ctrl_point = shapely.affinity.rotate(
+            new_ctrl_point = affinity.rotate(
                 self.assigned_control_point, angle, rotate_point, use_radians
             ).coords[0]
         new_geom = Geometry(
-            shapely.affinity.rotate(self.geom, angle, rot_point, use_radians),
+            affinity.rotate(self.geom, angle, rot_point, use_radians),
             self.material,
             new_ctrl_point,
         )
@@ -625,13 +625,13 @@ def mirror_section(
             x_mirror = -x_mirror
         elif axis == "y":
             y_mirror = -y_mirror
-        mirrored_geom = shapely.affinity.scale(
+        mirrored_geom = affinity.scale(
             self.geom, xfact=y_mirror, yfact=x_mirror, zfact=1.0, origin=mirror_point
         )
 
         new_ctrl_point = None
         if self.assigned_control_point:
-            new_ctrl_point = shapely.affinity.scale(
+            new_ctrl_point = affinity.scale(
                 self.assigned_control_point,
                 xfact=y_mirror,
                 yfact=x_mirror,
@@ -677,7 +677,7 @@ def split_section(
         The following example splits a 200PFC section about the y-axis::
 
             import sectionproperties.pre.library.steel_sections as steel_sections
-            from shapely.geometry import LineString
+            from shapely import LineString
 
             geometry = steel_sections.channel_section(d=200, b=75, t_f=12, t_w=6, r=12, n_r=8)
             right_geom, left_geom = geometry.split_section((0, 0), (0, 1))
@@ -1672,7 +1672,7 @@ def split_section(
         The following example splits a 200PFC section about the y-axis::
 
             import sectionproperties.pre.library.steel_sections as steel_sections
-            from shapely.geometry import LineString
+            from shapely import LineString
 
             geometry = steel_sections.channel_section(d=200, b=75, t_f=12, t_w=6, r=12, n_r=8)
             right_geom, left_geom = geometry.split_section((0, 0), (0, 1))

sectionproperties/pre/library/bridge_sections.py

@@ -1,5 +1,5 @@
 import numpy as np
-from shapely.geometry import Polygon
+from shapely import Polygon
 import sectionproperties.pre.geometry as geometry
 import sectionproperties.pre.pre as pre
 

sectionproperties/pre/library/nastran_sections.py

@@ -1,5 +1,5 @@
 import numpy as np
-from shapely.geometry import Polygon
+from shapely import Polygon
 import sectionproperties.pre.geometry as geometry
 import sectionproperties.pre.pre as pre
 from sectionproperties.pre.library.utils import draw_radius

sectionproperties/pre/library/primitive_sections.py

@@ -1,5 +1,5 @@
 import numpy as np
-from shapely.geometry import Polygon
+from shapely import Polygon
 import sectionproperties.pre.geometry as geometry
 import sectionproperties.pre.pre as pre
 from sectionproperties.pre.library.utils import draw_radius

sectionproperties/pre/library/steel_sections.py

@@ -1,5 +1,5 @@
 import numpy as np
-from shapely.geometry import Polygon
+from shapely import Polygon
 import sectionproperties.pre.geometry as geometry
 import sectionproperties.pre.pre as pre
 from sectionproperties.pre.library.utils import draw_radius, rotate

sectionproperties/pre/rhino.py

@@ -1,6 +1,6 @@
 import pathlib
 from typing import List, Union
-from shapely.geometry.polygon import Polygon
+from shapely import Polygon
 from rhino_shapely_interop.importers import RhImporter
 
 

sectionproperties/tests/test_offset.py

@@ -3,7 +3,7 @@
 import sectionproperties.pre.library.primitive_sections as sections
 import sectionproperties.pre.library.steel_sections as steel_sections
 from sectionproperties.analysis.section import Section
-from shapely.geometry import Polygon
+from shapely import Polygon
 from sectionproperties.pre.geometry import Geometry
 
 

sectionproperties/tests/test_sections.py

@@ -8,15 +8,15 @@
 from sectionproperties.analysis.section import Section
 from sectionproperties.pre.pre import DEFAULT_MATERIAL, Material
 from sectionproperties.pre.rhino import load_3dm, load_brep_encoding
-from shapely.geometry import (
+from shapely import (
     Polygon,
     MultiPolygon,
     LineString,
     Point,
     GeometryCollection,
     box,
+    wkt,
 )
-from shapely import wkt
 import json
 
 big_sq = rectangular_section(d=300, b=250)
@@ -133,7 +133,7 @@ def test_geometry_from_points():
         holes=holes,
         material=material,
     )
-    wkt_test_geom = shapely.wkt.loads(
+    wkt_test_geom = wkt.loads(
         "POLYGON ((6 10, 6 -10, -6 -10, -6 10, 6 10), (-4 4, 4 4, 4 8, -4 8, -4 4), (4 -8, 4 -4, -4 -4, -4 -8, 4 -8))"
     )
     assert (new_geom.geom - wkt_test_geom) == Polygon()
@@ -195,7 +195,7 @@ def test_compound_geometry_from_points():
     new_geom = CompoundGeometry.from_points(
         points, facets, control_points, materials=materials
     )
-    wkt_test_geom = shapely.wkt.loads(
+    wkt_test_geom = wkt.loads(
         "MULTIPOLYGON (((-0.05 -2, 0.05 -2, 0.05 -0.05, 1 -0.05, 1 0.05, -0.05 0.05, -0.05 -2)), ((-1 -2, 1 -2, 1 -2.1, -1 -2.1, -1 -2)))"
     )
     assert (new_geom.geom - wkt_test_geom) == Polygon()
@@ -283,7 +283,7 @@ def test_multi_nested_compound_geometry_from_points():
         holes=holes,
         materials=materials,
     )
-    wkt_test_geom = shapely.wkt.loads(
+    wkt_test_geom = wkt.loads(
         "MULTIPOLYGON (((50 50, 50 -50, -50 -50, -50 50, 50 50), (12.5 12.5, -12.5 12.5, -12.5 -12.5, 12.5 -12.5, 12.5 12.5)), ((-37.5 -37.5, -37.5 37.5, 37.5 37.5, 37.5 -37.5, -37.5 -37.5), (12.5 12.5, -12.5 12.5, -12.5 -12.5, 12.5 -12.5, 12.5 12.5)), ((-25 -25, -25 25, 25 25, 25 -25, -25 -25), (12.5 12.5, -12.5 12.5, -12.5 -12.5, 12.5 -12.5, 12.5 12.5)))"
     )
     assert (nested_compound.geom - wkt_test_geom) == Polygon()
@@ -447,17 +447,17 @@ def test_mirror_section():
 
 
 def test_filter_non_polygons():
-    point1 = Point([0, 0])
-    point2 = Point([1, 1])
-    point3 = Point([1, 0])
+    point1 = (0, 0)
+    point2 = (1, 1)
+    point3 = (1, 0)
     line = LineString([point1, point2])
     poly = Polygon([point1, point2, point3])
     multi_poly = MultiPolygon([poly, poly])
-    collection = GeometryCollection([poly, point1, line])
+    collection = GeometryCollection([poly, Point(point1), line])
     out = filter_non_polygons(collection)
     assert filter_non_polygons(poly) == poly
     assert filter_non_polygons(multi_poly) == multi_poly
-    assert filter_non_polygons(point1) == Polygon()
+    assert filter_non_polygons(Point(point1)) == Polygon()
     assert filter_non_polygons(line) == Polygon()
     assert filter_non_polygons(collection) == poly
 

sectionproperties/tests/test_validation.py

@@ -1,5 +1,5 @@
 import pytest_check as check
-from shapely.geometry import Polygon
+from shapely import Polygon
 from sectionproperties.pre.geometry import Geometry
 import sectionproperties.pre.library.primitive_sections as sections
 import sectionproperties.pre.library.steel_sections as steel_sections

setup.cfg

@@ -40,7 +40,7 @@ install_requires =
     scipy
     more_itertools
     matplotlib>=3.4
-    shapely
+    shapely>=2.0
     triangle
     cad_to_shapely>=0.3
     rich