From 219a9a57a96e9698c75b13dbd1ea9e21a7e4ac4d Mon Sep 17 00:00:00 2001 From: KD1880 Date: Fri, 6 Mar 2026 22:36:06 +0530 Subject: [PATCH 1/5] DOC: fix doctest output in transformations.py for newer NumPy --- 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 27e5f01db9f..2c96e6c1291 100644 --- a/package/MDAnalysis/lib/transformations.py +++ b/package/MDAnalysis/lib/transformations.py @@ -795,7 +795,7 @@ def decompose_matrix(matrix): >>> S = scale_matrix(0.123) >>> scale, shear, angles, trans, persp = decompose_matrix(S) >>> scale[0] - 0.123 + np.float64(0.123) >>> R0 = euler_matrix(1, 2, 3) >>> scale, shear, angles, trans, persp = decompose_matrix(R0) >>> R1 = euler_matrix(*angles) From 7493437560448e05bcef2171c45494b587e6b285 Mon Sep 17 00:00:00 2001 From: KD1880 Date: Fri, 6 Mar 2026 23:10:39 +0530 Subject: [PATCH 2/5] DOC: add myself to AUTHORS --- package/AUTHORS | 1 + 1 file changed, 1 insertion(+) diff --git a/package/AUTHORS b/package/AUTHORS index 19b86530505..6c9172602d5 100644 --- a/package/AUTHORS +++ b/package/AUTHORS @@ -273,6 +273,7 @@ Chronological list of authors - Kushagar Garg - Jeremy M. G. Leung - Harshit Gajjela + - Kriti Dogra External code ------------- From d0e2e5423668b52cdfff2169ca2e33e89c602eae Mon Sep 17 00:00:00 2001 From: KD1880 Date: Tue, 10 Mar 2026 15:13:02 +0530 Subject: [PATCH 3/5] DOC: update CHANGELOG for PR #5283 --- package/CHANGELOG | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/package/CHANGELOG b/package/CHANGELOG index eefad7b8a7a..3c06d89e90b 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -22,6 +22,10 @@ The rules for this file: Fixes * Fixes TypeError with np.int64 indexing in GSD Reader (Issue #5224) + * Fix doctest output in transformations.py for newer NumPy + (Issue #3925, PR #5283) + * Fix doctest in util.py for platform-dependent path output + (Issue #3925, PR #5285) * Fixed bug in add_transformations allowing non-callable transformations (Issue #2558, PR #2558) * Drop/Replace lock file test in test_xdr (Issue #5236, PR #5237) From 044c5d5522bb241f8dfc72c3a0a37d7b5e2d13dd Mon Sep 17 00:00:00 2001 From: KD1880 Date: Wed, 11 Mar 2026 23:02:21 +0530 Subject: [PATCH 4/5] DOC: fix CHANGELOG to only include transformations.py entry --- package/CHANGELOG | 3 --- 1 file changed, 3 deletions(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index 3c06d89e90b..184df9e88ef 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -21,11 +21,8 @@ The rules for this file: * 2.11.0 Fixes - * Fixes TypeError with np.int64 indexing in GSD Reader (Issue #5224) * Fix doctest output in transformations.py for newer NumPy (Issue #3925, PR #5283) - * Fix doctest in util.py for platform-dependent path output - (Issue #3925, PR #5285) * Fixed bug in add_transformations allowing non-callable transformations (Issue #2558, PR #2558) * Drop/Replace lock file test in test_xdr (Issue #5236, PR #5237) From 059a83f3789c6b5e6ab6dfacef1ea900e2bc6e3f Mon Sep 17 00:00:00 2001 From: KD1880 Date: Fri, 20 Mar 2026 03:33:26 +0530 Subject: [PATCH 5/5] DOC: fix CHANGELOG and AUTHORS as per review --- package/AUTHORS | 2 +- package/CHANGELOG | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/package/AUTHORS b/package/AUTHORS index 2077fe56bee..1cb83d85c4f 100644 --- a/package/AUTHORS +++ b/package/AUTHORS @@ -273,8 +273,8 @@ Chronological list of authors - Kushagar Garg - Jeremy M. G. Leung - Harshit Gajjela - - Kriti Dogra - Kunj Sinha + - Kriti Dogra External code ------------- diff --git a/package/CHANGELOG b/package/CHANGELOG index 184df9e88ef..b7df09b1403 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -21,8 +21,8 @@ The rules for this file: * 2.11.0 Fixes - * Fix doctest output in transformations.py for newer NumPy - (Issue #3925, PR #5283) + * Fixes TypeError with np.int64 indexing in GSD Reader (Issue #5224) + * Fix doctest output in transformations.py for newer NumPy (Issue #3925, PR #5283) * Fixed bug in add_transformations allowing non-callable transformations (Issue #2558, PR #2558) * Drop/Replace lock file test in test_xdr (Issue #5236, PR #5237)