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Fix: Transformations.py doctest errors #4370

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merged 4 commits into from
Dec 16, 2023
Merged

Fix: Transformations.py doctest errors #4370

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749cdcd
fix: clip_matrix error
HeetVekariya Dec 16, 2023
055415d
fix: eular_matrix error
HeetVekariya Dec 16, 2023
2ee1671
fix: quaternion_slerp error
HeetVekariya Dec 16, 2023
6a597e1
change log
HeetVekariya Dec 16, 2023
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1 change: 1 addition & 0 deletions package/CHANGELOG
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ The rules for this file:
* 2.7.0

Fixes
* Fix doctest errors of lib/transformations.py (Issue #3925, PR #4370)
* Fix documentation building errors due to `html_static_path` and unindented
block of code (Issue #4362, PR #4365)
* Updated cimport for numpy to maintain cimport consistency (Issue #3908)
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6 changes: 3 additions & 3 deletions package/MDAnalysis/lib/transformations.py
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Expand Up @@ -628,7 +628,7 @@ def clip_matrix(left, right, bottom, top, near, far, perspective=False):
>>> np.dot(M, [frustrum[0], frustrum[2], frustrum[4], 1.0])
array([-1., -1., -1., 1.])
>>> np.dot(M, [frustrum[1], frustrum[3], frustrum[5], 1.0])
array([ 1., 1., 1., 1.])
array([1., 1., 1., 1.])
>>> M = clip_matrix(perspective=True, *frustrum)
>>> v = np.dot(M, [frustrum[0], frustrum[2], frustrum[4], 1.0])
>>> v / v[3]
Expand Down Expand Up @@ -1031,7 +1031,7 @@ def euler_matrix(ai, aj, ak, axes='sxyz'):
ai, aj, ak : Euler's roll, pitch and yaw angles
axes : One of 24 axis sequences as string or encoded tuple

>>> from MDAnalysis.lib.transformations import (euler_matrix
>>> from MDAnalysis.lib.transformations import (euler_matrix,
... _AXES2TUPLE, _TUPLE2AXES)
>>> import math
>>> import numpy as np
Expand Down Expand Up @@ -1454,7 +1454,7 @@ def quaternion_slerp(quat0, quat1, fraction, spin=0, shortestpath=True):
>>> q = quaternion_slerp(q0, q1, 0.5)
>>> angle = math.acos(np.dot(q0, q))
>>> np.allclose(2.0, math.acos(np.dot(q0, q1)) / angle) or \
np.allclose(2.0, math.acos(-np.dot(q0, q1)) / angle)
... np.allclose(2.0, math.acos(-np.dot(q0, q1)) / angle)
True

"""
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