The shapely.ops.substring() function fails if not all vertices of the LineString have a Z coordinate

[vadimcn]

The shapely.ops.substring() function fails if not all vertices of the LineString have a Z coordinate (which stems from some operations like segmentize() losing Z, but I guess that's a GEOS issue).

Steps to reproduce the problem.

import math
from shapely import LineString
from shapely.ops import substring
l = LineString([[0, 0, 0], [1, 2, math.nan], [10, 10, 0]])
substring(l, 0.1, 0.9, normalized=True)

Error

Traceback (most recent call last)
File repro.py:6
      [4](repro.py:4) from shapely.ops import substring
      [5](repro.py:5) l = LineString([[0, 0, 0], [1, 2, math.nan], [10, 10, 0]])
----> [6](repro.py:6) substring(l, 0.1, 0.9, normalized=True)

File ~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/ops.py:674, in substring(geom, start_dist, end_dist, normalized)
    [671](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/ops.py:671) else:
    [672](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/ops.py:672)     vertex_list.append(tuple(*end_point.coords))
--> [674](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/ops.py:674) return LineString(vertex_list)

File ~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/geometry/linestring.py:73, in LineString.__new__(self, coordinates)
     [68](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/geometry/linestring.py:68) if len(coordinates) == 0:
     [69](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/geometry/linestring.py:69)     # empty geometry
     [70](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/geometry/linestring.py:70)     # TODO better constructor + should shapely.linestrings handle this?
     [71](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/geometry/linestring.py:71)     return shapely.from_wkt("LINESTRING EMPTY")
---> [73](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/geometry/linestring.py:73) geom = shapely.linestrings(coordinates)
     [74](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/geometry/linestring.py:74) if not isinstance(geom, LineString):
     [75](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/geometry/linestring.py:75)     raise ValueError("Invalid values passed to LineString constructor")

File ~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/decorators.py:77, in multithreading_enabled.<locals>.wrapped(*args, **kwargs)
     [75](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/decorators.py:75)     for arr in array_args:
     [76](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/decorators.py:76)         arr.flags.writeable = False
---> [77](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/decorators.py:77)     return func(*args, **kwargs)
     [78](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/decorators.py:78) finally:
     [79](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/decorators.py:79)     for arr, old_flag in zip(array_args, old_flags):

File ~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/creation.py:119, in linestrings(coords, y, z, indices, out, **kwargs)
    [117](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/creation.py:117) coords = _xyz_to_coords(coords, y, z)
    [118](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/creation.py:118) if indices is None:
--> [119](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/creation.py:119)     return lib.linestrings(coords, out=out, **kwargs)
    [120](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/creation.py:120) else:
    [121](~/bin/miniconda/envs/mapgpt/lib/python3.11/site-packages/shapely/creation.py:121)     return simple_geometries_1d(coords, indices, GeometryType.LINESTRING, out=out)

ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (3,) + inhomogeneous part.

Operating system

Ubuntu 22.04

Shapely version and provenance

shapely 2.0.3 installed from PyPI using pip