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At least one function/test is incompatible with NumPy updated to 2.4 (released 2025-12-20).
NumPy 2.4:
====================================================== FAILURES =======================================================
____________________________________________ VectorTests.test_coord_space _____________________________________________
TypeError: only 0-dimensional arrays can be converted to Python scalars
The above exception was the direct cause of the following exception:
self = <test_PDB_vectors.VectorTests testMethod=test_coord_space>
def test_coord_space(self):
"""Confirm can generate coordinate space transform for 3 points."""
# start with 3 points already aligned to axes
point_set = (
np.array([[2.0], [0.0], [2.0], [1.0]]),
np.array([[0.0], [0.0], [0.0], [1.0]]),
np.array([[0.0], [0.0], [2.0], [1.0]]),
)
# confirm get id matrix to transform to/from coord space
homog_id = np.array([[1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 1, 0], [0, 0, 0, 1]])
> mtxs = coord_space(point_set[0], point_set[1], point_set[2], True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Tests\test_PDB_vectors.py:208:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
Bio\PDB\vectors.py:559: in coord_space
set_homog_trans_mtx(-a1[0], -a1[1], -a1[2], tm)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
x = array([-0.]), y = array([-0.]), z = array([-0.])
mtx = array([[1., 0., 0., 0.],
[0., 1., 0., 0.],
[0., 0., 1., 0.],
[0., 0., 0., 1.]])
def set_homog_trans_mtx(x: float, y: float, z: float, mtx: np.ndarray):
"""Update existing translation matrix to new values."""
> mtx[0][3] = x
^^^^^^^^^
E ValueError: setting an array element with a sequence.
Bio\PDB\vectors.py:475: ValueError
=============================================== short test summary info ===============================================
FAILED Tests/test_PDB_vectors.py::VectorTests::test_coord_space - ValueError: setting an array element with a sequence.
================================================== 1 failed in 1.86s ==================================================
Numpy 1.26.4 (also works in 2.3.5):
=========================================== 1 passed, 126 warnings in 3.41s ===========================================
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