From 749cdcdd625124e9d8ed58fa844e2c200876efae Mon Sep 17 00:00:00 2001 From: HeetVekariya Date: Sat, 16 Dec 2023 19:33:57 +0530 Subject: [PATCH 1/4] fix: clip_matrix error --- package/MDAnalysis/lib/transformations.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/MDAnalysis/lib/transformations.py b/package/MDAnalysis/lib/transformations.py index bf6cba80018..87698e0375b 100644 --- a/package/MDAnalysis/lib/transformations.py +++ b/package/MDAnalysis/lib/transformations.py @@ -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] From 055415de59c19fa3633d683b430ed13d6656dc6a Mon Sep 17 00:00:00 2001 From: HeetVekariya Date: Sat, 16 Dec 2023 19:35:06 +0530 Subject: [PATCH 2/4] fix: eular_matrix error --- package/MDAnalysis/lib/transformations.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/MDAnalysis/lib/transformations.py b/package/MDAnalysis/lib/transformations.py index 87698e0375b..c17a4a9f230 100644 --- a/package/MDAnalysis/lib/transformations.py +++ b/package/MDAnalysis/lib/transformations.py @@ -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 From 2ee167156bad2c5e8ae32a4730963a43c799eed3 Mon Sep 17 00:00:00 2001 From: HeetVekariya Date: Sat, 16 Dec 2023 19:36:12 +0530 Subject: [PATCH 3/4] fix: quaternion_slerp error --- package/MDAnalysis/lib/transformations.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/MDAnalysis/lib/transformations.py b/package/MDAnalysis/lib/transformations.py index c17a4a9f230..3498f655120 100644 --- a/package/MDAnalysis/lib/transformations.py +++ b/package/MDAnalysis/lib/transformations.py @@ -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 """ From 6a597e1ec2794baf9d5842b667e7e0be6f170cc0 Mon Sep 17 00:00:00 2001 From: HeetVekariya Date: Sat, 16 Dec 2023 19:59:40 +0530 Subject: [PATCH 4/4] change log --- package/CHANGELOG | 1 + 1 file changed, 1 insertion(+) diff --git a/package/CHANGELOG b/package/CHANGELOG index 76270e3089b..576260dd311 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -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)