Merge branch 'release-recalculate_renormalize_platonic' of https://github.com/glotzerlab/coxeter into release-recalculate_renormalize_platonic

Author: janbridley

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: 'v4.3.0'
+    rev: 'v4.4.0'
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
@@ -19,29 +19,29 @@ repos:
       - id: check-json
       - id: check-yaml
   - repo: https://github.com/asottile/pyupgrade
-    rev: 'v2.34.0'
+    rev: 'v3.3.1'
     hooks:
       - id: pyupgrade
         args:
           - --py38-plus
         exclude: '(?:extern/.*)'
   - repo: https://github.com/PyCQA/isort
-    rev: '5.10.1'
+    rev: '5.12.0'
     hooks:
       - id: isort
         exclude: '(?:extern/.*)'
   - repo: https://github.com/psf/black
-    rev: '22.6.0'
+    rev: '23.1.0'
     hooks:
       - id: black
         exclude: '(?:extern/.*)'
   - repo: https://github.com/PyCQA/pydocstyle
-    rev: '6.1.1'
+    rev: '6.3.0'
     hooks:
       - id: pydocstyle
         exclude: '(?:extern/.*|tests/.*|setup.py|conf.py)'
   - repo: https://github.com/PyCQA/flake8
-    rev: '4.0.1'
+    rev: '6.0.0'
     hooks:
     -   id: flake8
         additional_dependencies: [
@@ -52,7 +52,7 @@ repos:
             'flake8-comprehensions==3.8.0',
         ]
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.3.1
+    rev: 1.6.1
     hooks:
       - id: nbqa-pyupgrade
         args:

paper/figure1/shape_images/Shapes.ipynb

@@ -243,7 +243,6 @@
    "outputs": [],
    "source": [
     "def draw_bun():\n",
-    "\n",
     "    data = np.load(\"data/low_poly_stanford_bunny/data.npz\")\n",
     "    vertices = data[\"vertices\"]\n",
     "    indices = data[\"indices\"]\n",

setup.cfg

@@ -20,8 +20,9 @@ exclude = coxeter/extern/*
 select = E,F,W,B,RST,N
 per-file-ignores = 
     coxeter/__init__.py: F401
+# We prefer line breaks before, not after, binary operators.
 ignore = 
-    W503 # We prefer line breaks before, not after, binary operators.
+    W503
 rst-roles = 
     attr,class,func,meth,mod,obj,ref,term,cite
 

tests/conftest.py

@@ -135,15 +135,12 @@ def points_from_ellipsoid_surface(a, b, c=0, n=10):
     Returns:
         :math:`(N, 3)` or :math:`(N, 2)` :class:`numpy.ndarray`: The points.
     """
-    points = []
-    points = np.zeros((n, 3))
-    points[:, 0] = np.random.normal(0, a, n)
-    points[:, 1] = np.random.normal(0, b, n)
-    if c > 0:
-        points[:, 2] = np.random.normal(0, c, n)
-    ds = np.linalg.norm(points / [a, b, c if c else 1], axis=-1)
+    scale = (a, b, c) if c > 0 else (a, b)
+    size = (n, 3 if c > 0 else 2)
+    points = np.random.normal(0, scale, size)
+    ds = np.linalg.norm(points / ([a, b, c] if c > 0 else [a, b]), axis=-1)
     points /= ds[:, np.newaxis]
-    return points if c else points[:, :2]
+    return points
 
 
 EllipsoidSurfaceStrategy = builds(

tests/test_polyhedron.py

@@ -106,6 +106,7 @@ def test_convex_surface_area(points):
 )
 def test_volume_center_shift(cube):
     """Make sure that moving the center doesn't affect the volume."""
+
     # Use a nested function to avoid warnings from hypothesis. In this case, it
     # is safe to reuse the cube fixture.
     # See https://github.com/HypothesisWorks/hypothesis/issues/377
@@ -417,9 +418,7 @@ def test_inside(convex_cube):
     # Use a nested function to avoid warnings from hypothesis. In this case, it
     # is safe to reuse the convex cube.
     # See https://github.com/HypothesisWorks/hypothesis/issues/377
-    @given(
-        arrays(np.float64, (100, 3), elements=floats(-10, 10, width=64), unique=True)
-    )
+    @given(arrays(np.float64, (100, 3), elements=floats(-10, 10, width=64)))
     def testfun(test_points):
         expected = np.all(np.logical_and(test_points >= 0, test_points <= 1), axis=1)
         actual = convex_cube.is_inside(test_points)
@@ -428,10 +427,10 @@ def testfun(test_points):
     testfun()
 
 
-@settings(deadline=500)
+@settings(max_examples=10)
 @given(
     EllipsoidSurfaceStrategy,
-    arrays(np.float64, (100, 3), elements=floats(0, 1, width=64), unique=True),
+    arrays(np.float64, (100, 3), elements=floats(0, 1, width=64)),
 )
 def test_maximal_centered_bounded_sphere_convex_hulls(points, test_points):
     hull = ConvexHull(points)