From 8eb0d624dd4776875063b60ee1936ff618b88a6e Mon Sep 17 00:00:00 2001 From: eeshsaxena Date: Mon, 29 Jun 2026 23:15:43 +0530 Subject: [PATCH 1/3] Fix incorrect parameter names in docstrings Several docstrings documented parameter names that don't match their signatures: - util.which documented 'programe' (typo) instead of 'program'. - TransformationsBase.add_transformations (FrameIteratorBase and MemoryReader) documented 'transform_list' instead of 'transformations'. - GuesserBase.is_guessable documented 'guess' instead of 'attr_to_guess'. --- package/MDAnalysis/coordinates/base.py | 4 ++-- package/MDAnalysis/coordinates/memory.py | 2 +- package/MDAnalysis/guesser/base.py | 2 +- package/MDAnalysis/lib/util.py | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/package/MDAnalysis/coordinates/base.py b/package/MDAnalysis/coordinates/base.py index a9a13598efc..553a4dadd55 100644 --- a/package/MDAnalysis/coordinates/base.py +++ b/package/MDAnalysis/coordinates/base.py @@ -1416,7 +1416,7 @@ def add_transformations(self, *transformations): Parameters ---------- - transform_list : list + transformations : list list of all the transformations that will be applied to the coordinates in the order given in the list @@ -1779,7 +1779,7 @@ def add_transformations(self, *transformations): Parameters ---------- - transform_list : list + transformations : list list of all the transformations that will be applied to the coordinates See Also diff --git a/package/MDAnalysis/coordinates/memory.py b/package/MDAnalysis/coordinates/memory.py index 07c31fa2258..12bf38ec2ee 100644 --- a/package/MDAnalysis/coordinates/memory.py +++ b/package/MDAnalysis/coordinates/memory.py @@ -675,7 +675,7 @@ def add_transformations(self, *transformations): Parameters ---------- - transform_list : list + transformations : list list of all the transformations that will be applied to the coordinates See Also diff --git a/package/MDAnalysis/guesser/base.py b/package/MDAnalysis/guesser/base.py index c7bcc21e823..712f3d6e211 100644 --- a/package/MDAnalysis/guesser/base.py +++ b/package/MDAnalysis/guesser/base.py @@ -110,7 +110,7 @@ def is_guessable(self, attr_to_guess): Parameters ---------- - guess: str + attr_to_guess: str Attribute to be guessed then added to the Universe Returns diff --git a/package/MDAnalysis/lib/util.py b/package/MDAnalysis/lib/util.py index 0f497892f13..b3af22a9e2d 100644 --- a/package/MDAnalysis/lib/util.py +++ b/package/MDAnalysis/lib/util.py @@ -577,7 +577,7 @@ def which(program): Parameters ---------- - programe : str + program : str name of the executable Returns From fdefbbb182d514c2455c1e596208208f5f2b6dcf Mon Sep 17 00:00:00 2001 From: eeshsaxena Date: Mon, 29 Jun 2026 23:17:57 +0530 Subject: [PATCH 2/3] Add CHANGELOG and AUTHORS entries for docstring fixes --- package/AUTHORS | 1 + package/CHANGELOG | 6 +++++- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/package/AUTHORS b/package/AUTHORS index ed82321a9e8..61f368800d9 100644 --- a/package/AUTHORS +++ b/package/AUTHORS @@ -284,6 +284,7 @@ Chronological list of authors - Sai Udayagiri - Apoorva Verma - Aryaman Chaudhri + - Eesh Saxena External code ------------- diff --git a/package/CHANGELOG b/package/CHANGELOG index 71411414874..4479fe25848 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -18,7 +18,7 @@ The rules for this file: spyke7, talagayev, tanii1125, BradyAJohnston, hejamu, jeremyleung521, harshitgajjela-droid, kunjsinha, aygarwal, jauy123, Dreamstick9, ollyfutur, Amarendra22, charity-g, ParthUppal523, apoorva-01, RMeli, - raulloiscuns, Aryaman-Chaudhri + raulloiscuns, Aryaman-Chaudhri, eeshsaxena * 2.11.0 @@ -28,6 +28,10 @@ Fixes * `Merge()` no longer raises a TypeError on Universes that have a `cmaps` attribute; cmaps are now combined like the other connection attributes (bonds, angles, dihedrals, impropers) (Issue #3672). + * Fixed several docstrings that documented parameter names not matching + their signatures: ``util.which`` (``programe`` -> ``program``), + ``add_transformations`` (``transform_list`` -> ``transformations``) and + ``GuesserBase.is_guessable`` (``guess`` -> ``attr_to_guess``) (PR #5412). * The `principal_axes` method in :class:`Masses` now uses `np.linalg.eigh` instead of `np.linalg.eig`, improving numerical stability. This may lead to slightly different results from previous From c36a27b352067e9f3ecb079a3ae12f1e008dd166 Mon Sep 17 00:00:00 2001 From: eeshsaxena Date: Mon, 29 Jun 2026 23:23:37 +0530 Subject: [PATCH 3/3] Drop coordinates/base.py change (file not yet black-formatted) The same add_transformations docstring fix remains in coordinates/memory.py; base.py is left untouched to avoid a large unrelated reformatting diff. --- package/MDAnalysis/coordinates/base.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/package/MDAnalysis/coordinates/base.py b/package/MDAnalysis/coordinates/base.py index 553a4dadd55..a9a13598efc 100644 --- a/package/MDAnalysis/coordinates/base.py +++ b/package/MDAnalysis/coordinates/base.py @@ -1416,7 +1416,7 @@ def add_transformations(self, *transformations): Parameters ---------- - transformations : list + transform_list : list list of all the transformations that will be applied to the coordinates in the order given in the list @@ -1779,7 +1779,7 @@ def add_transformations(self, *transformations): Parameters ---------- - transformations : list + transform_list : list list of all the transformations that will be applied to the coordinates See Also