From 70e036f101ff10e50e5b0c7908b0d796c2349dbc Mon Sep 17 00:00:00 2001 From: Sumaira Date: Sat, 3 Feb 2024 10:40:04 +0500 Subject: [PATCH 01/11] tim estamp.pyx fixed --- package/MDAnalysis/coordinates/timestep.pyx | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/package/MDAnalysis/coordinates/timestep.pyx b/package/MDAnalysis/coordinates/timestep.pyx index 09304ec85ee..d660b41289f 100644 --- a/package/MDAnalysis/coordinates/timestep.pyx +++ b/package/MDAnalysis/coordinates/timestep.pyx @@ -493,6 +493,13 @@ cdef class Timestep: vectors lengths followed by their respective angle, or as three triclinic vectors. + .. testsetup:: + + from MDAnalysis.coordinates.timestep import Timestep + ts = Timestep() + + .. doctest:: + >>> ts.dimensions array([ 13., 14., 15., 90., 90., 90.], dtype=float32) >>> ts.triclinic_dimensions From f97dd30414e42dfc0e510ca194e5dfe33015a5c6 Mon Sep 17 00:00:00 2001 From: Sumaira Date: Sat, 17 Feb 2024 10:59:20 +0500 Subject: [PATCH 02/11] timestep not working --- package/MDAnalysis/coordinates/timestep.pyx | 35 ++++++++++++++------- 1 file changed, 24 insertions(+), 11 deletions(-) diff --git a/package/MDAnalysis/coordinates/timestep.pyx b/package/MDAnalysis/coordinates/timestep.pyx index d660b41289f..842acab370f 100644 --- a/package/MDAnalysis/coordinates/timestep.pyx +++ b/package/MDAnalysis/coordinates/timestep.pyx @@ -1,4 +1,4 @@ -# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*- +Fts.dimensions# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- https://www.mdanalysis.org @@ -495,22 +495,35 @@ cdef class Timestep: .. testsetup:: - from MDAnalysis.coordinates.timestep import Timestep - ts = Timestep() + import MDAnalysis as mda + rom MDAnalysis.tests.datafiles import TPR, XTC + import numpy as np .. doctest:: - >>> ts.dimensions - array([ 13., 14., 15., 90., 90., 90.], dtype=float32) - >>> ts.triclinic_dimensions - array([[ 13., 0., 0.], - [ 0., 14., 0.], - [ 0., 0., 15.]], dtype=float32) + >>> u = mda.Universe(TPR, XTC) + >>> ts_1 = u.trajectory[0] + >>> ts_1.dimensions + array([80.13008, 80.13008, 80.13008, 60. , 60. , 90. ], dtype=float32) + >>> ts_1.triclinic_dimensions + array([[80.13008 , 0. , 0. ], + [ 0. , 80.13008 , 0. ], + [40.06504 , 40.06504 , 56.660522]], dtype=float32) Setting the attribute also works:: - >>> ts.triclinic_dimensions = [[15, 0, 0], [5, 15, 0], [5, 5, 15]] - >>> ts.dimensions + .. testsetup:: + + import MDAnalysis as mda + rom MDAnalysis.tests.datafiles import TPR, XTC + import numpy as np + + .. doctest:: + + >>> u = mda.Universe(TPR, XTC) + >>> ts_2 = u.trajectory[0] + >>> ts_2.triclinic_dimensions = [[15, 0, 0], [5, 15, 0], [5, 5, 15]] + >>> ts_2.dimensions array([ 15. , 15.81138802, 16.58312416, 67.58049774, 72.45159912, 71.56504822], dtype=float32) From 1af773c0ee27468218eee9a49de132b8433088f2 Mon Sep 17 00:00:00 2001 From: Sumaira Date: Sat, 17 Feb 2024 11:26:29 +0500 Subject: [PATCH 03/11] timestep errors _v1 --- package/MDAnalysis/coordinates/timestep.pyx | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/package/MDAnalysis/coordinates/timestep.pyx b/package/MDAnalysis/coordinates/timestep.pyx index 842acab370f..80b41a51dc3 100644 --- a/package/MDAnalysis/coordinates/timestep.pyx +++ b/package/MDAnalysis/coordinates/timestep.pyx @@ -1,4 +1,4 @@ -Fts.dimensions# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*- +# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 # # MDAnalysis --- https://www.mdanalysis.org @@ -511,13 +511,7 @@ cdef class Timestep: [40.06504 , 40.06504 , 56.660522]], dtype=float32) Setting the attribute also works:: - - .. testsetup:: - - import MDAnalysis as mda - rom MDAnalysis.tests.datafiles import TPR, XTC - import numpy as np - + .. doctest:: >>> u = mda.Universe(TPR, XTC) From 2df693b9d2aa7ac5aa0f23a151780b8b15c538ef Mon Sep 17 00:00:00 2001 From: Sumaira Date: Sun, 18 Feb 2024 01:13:56 +0500 Subject: [PATCH 04/11] minor mistakes --- package/MDAnalysis/coordinates/timestep.pyx | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package/MDAnalysis/coordinates/timestep.pyx b/package/MDAnalysis/coordinates/timestep.pyx index 80b41a51dc3..8f5f07efe87 100644 --- a/package/MDAnalysis/coordinates/timestep.pyx +++ b/package/MDAnalysis/coordinates/timestep.pyx @@ -495,9 +495,9 @@ cdef class Timestep: .. testsetup:: - import MDAnalysis as mda - rom MDAnalysis.tests.datafiles import TPR, XTC - import numpy as np + >>> import MDAnalysis as mda + >>> from MDAnalysis.tests.datafiles import TPR, XTC + >>> import numpy as np .. doctest:: From 18696b57d2ac56e69d4efcd4ba1ff281a41d67cc Mon Sep 17 00:00:00 2001 From: Sumaira Date: Tue, 20 Feb 2024 09:30:27 +0500 Subject: [PATCH 05/11] rounding the values as requested --- package/MDAnalysis/coordinates/timestep.pyx | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/package/MDAnalysis/coordinates/timestep.pyx b/package/MDAnalysis/coordinates/timestep.pyx index 8f5f07efe87..84cfd8a59ba 100644 --- a/package/MDAnalysis/coordinates/timestep.pyx +++ b/package/MDAnalysis/coordinates/timestep.pyx @@ -503,12 +503,12 @@ cdef class Timestep: >>> u = mda.Universe(TPR, XTC) >>> ts_1 = u.trajectory[0] - >>> ts_1.dimensions - array([80.13008, 80.13008, 80.13008, 60. , 60. , 90. ], dtype=float32) - >>> ts_1.triclinic_dimensions - array([[80.13008 , 0. , 0. ], - [ 0. , 80.13008 , 0. ], - [40.06504 , 40.06504 , 56.660522]], dtype=float32) + >>> print(np.round(ts_1.dimensions)) + [80. 80. 80. 60. 60. 90.] + >>> print(np.round(ts_1.triclinic_dimensions)) + [[80. 0. 0.] + [ 0. 80. 0.] + [40. 40. 57.]] Setting the attribute also works:: @@ -517,10 +517,9 @@ cdef class Timestep: >>> u = mda.Universe(TPR, XTC) >>> ts_2 = u.trajectory[0] >>> ts_2.triclinic_dimensions = [[15, 0, 0], [5, 15, 0], [5, 5, 15]] - >>> ts_2.dimensions - array([ 15. , 15.81138802, 16.58312416, 67.58049774, - 72.45159912, 71.56504822], dtype=float32) - + >>> print(np.round(ts_2.dimensions)) + [15. 16. 17. 68. 72. 72.] + See Also -------- :func:`MDAnalysis.lib.mdamath.triclinic_vectors` From 198eaf3119a0021d004515b1df50c3ab7966a2e3 Mon Sep 17 00:00:00 2001 From: Sumaira Date: Wed, 21 Feb 2024 09:42:07 +0500 Subject: [PATCH 06/11] some checks --- package/MDAnalysis/coordinates/timestep.pyx | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/package/MDAnalysis/coordinates/timestep.pyx b/package/MDAnalysis/coordinates/timestep.pyx index 84cfd8a59ba..121c2e3ee6a 100644 --- a/package/MDAnalysis/coordinates/timestep.pyx +++ b/package/MDAnalysis/coordinates/timestep.pyx @@ -498,11 +498,11 @@ cdef class Timestep: >>> import MDAnalysis as mda >>> from MDAnalysis.tests.datafiles import TPR, XTC >>> import numpy as np + >>> u = mda.Universe(TPR, XTC) + >>> ts = u.trajectory[0] .. doctest:: - - >>> u = mda.Universe(TPR, XTC) - >>> ts_1 = u.trajectory[0] + >>> print(np.round(ts_1.dimensions)) [80. 80. 80. 60. 60. 90.] >>> print(np.round(ts_1.triclinic_dimensions)) @@ -513,10 +513,8 @@ cdef class Timestep: Setting the attribute also works:: .. doctest:: - - >>> u = mda.Universe(TPR, XTC) - >>> ts_2 = u.trajectory[0] - >>> ts_2.triclinic_dimensions = [[15, 0, 0], [5, 15, 0], [5, 5, 15]] + + >>> ts.triclinic_dimensions = [[15, 0, 0], [5, 15, 0], [5, 5, 15]] >>> print(np.round(ts_2.dimensions)) [15. 16. 17. 68. 72. 72.] From a545ba2bc94eb6daa3551c1c76af4c30f3b90a19 Mon Sep 17 00:00:00 2001 From: Sumaira Date: Wed, 21 Feb 2024 09:43:24 +0500 Subject: [PATCH 07/11] some_changes_v2 --- package/MDAnalysis/coordinates/timestep.pyx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/package/MDAnalysis/coordinates/timestep.pyx b/package/MDAnalysis/coordinates/timestep.pyx index 121c2e3ee6a..f98353e9766 100644 --- a/package/MDAnalysis/coordinates/timestep.pyx +++ b/package/MDAnalysis/coordinates/timestep.pyx @@ -503,9 +503,9 @@ cdef class Timestep: .. doctest:: - >>> print(np.round(ts_1.dimensions)) + >>> print(np.round(ts.dimensions)) [80. 80. 80. 60. 60. 90.] - >>> print(np.round(ts_1.triclinic_dimensions)) + >>> print(np.round(ts.triclinic_dimensions)) [[80. 0. 0.] [ 0. 80. 0.] [40. 40. 57.]] From ac4519bca76b4d9e403662dc707ca657bcda1549 Mon Sep 17 00:00:00 2001 From: Sumaira Date: Thu, 22 Feb 2024 21:18:09 +0500 Subject: [PATCH 08/11] recompiled timestep.py --- package/MDAnalysis/coordinates/timestep.pyx | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package/MDAnalysis/coordinates/timestep.pyx b/package/MDAnalysis/coordinates/timestep.pyx index f98353e9766..f170059cddc 100644 --- a/package/MDAnalysis/coordinates/timestep.pyx +++ b/package/MDAnalysis/coordinates/timestep.pyx @@ -507,15 +507,15 @@ cdef class Timestep: [80. 80. 80. 60. 60. 90.] >>> print(np.round(ts.triclinic_dimensions)) [[80. 0. 0.] - [ 0. 80. 0.] - [40. 40. 57.]] + [ 0. 80. 0.] + [40. 40. 57.]] Setting the attribute also works:: .. doctest:: >>> ts.triclinic_dimensions = [[15, 0, 0], [5, 15, 0], [5, 5, 15]] - >>> print(np.round(ts_2.dimensions)) + >>> print(np.round(ts.dimensions)) [15. 16. 17. 68. 72. 72.] See Also From a5bb78ef86f4b8ff47ad0bdd4226883defff4f4e Mon Sep 17 00:00:00 2001 From: nataliyah123 Date: Mon, 11 Mar 2024 11:24:03 +0500 Subject: [PATCH 09/11] Update AUTHORS --- package/AUTHORS | 2 ++ 1 file changed, 2 insertions(+) diff --git a/package/AUTHORS b/package/AUTHORS index 0e1b5d77b83..dd5762d9698 100644 --- a/package/AUTHORS +++ b/package/AUTHORS @@ -233,6 +233,8 @@ Chronological list of authors - Lawson Woods - Johannes Stöckelmaier - Jenna M. Swarthout Goddard +2024 + - Sumaira Ahmad External code ------------- From 578218f1e3edde6f1e86985698b31b148d1660cf Mon Sep 17 00:00:00 2001 From: Sumaira Date: Mon, 11 Mar 2024 12:07:16 +0500 Subject: [PATCH 10/11] added to authors --- package/AUTHORS | 1 + 1 file changed, 1 insertion(+) diff --git a/package/AUTHORS b/package/AUTHORS index 35e4029f776..f8483204402 100644 --- a/package/AUTHORS +++ b/package/AUTHORS @@ -236,6 +236,7 @@ Chronological list of authors 2024 - Aditya Keshari - Philipp Stärk + - Sumaira Ahmad External code ------------- From 1e5ae0d6b9a04b439c751643b915b8afaab71a86 Mon Sep 17 00:00:00 2001 From: Sumaira Date: Tue, 12 Mar 2024 22:41:03 +0500 Subject: [PATCH 11/11] added to changelog --- package/AUTHORS | 5 ++--- package/CHANGELOG | 2 +- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/package/AUTHORS b/package/AUTHORS index a970e70d1da..2cac431048e 100644 --- a/package/AUTHORS +++ b/package/AUTHORS @@ -233,11 +233,10 @@ Chronological list of authors - Lawson Woods - Johannes Stöckelmaier - Jenna M. Swarthout Goddard - -2024 + 2024 - Aditya Keshari - Philipp Stärk - - Sumaira Ahmad + - SumairaAhmad External code ------------- diff --git a/package/CHANGELOG b/package/CHANGELOG index b51a00014a9..9882e6f8a0a 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -62,7 +62,7 @@ Deprecations 12/26/23 IAlibay, ianmkenney, PicoCentauri, pgbarletta, p-j-smith, richardjgowers, lilyminium, ALescoulie, hmacdope, HeetVekariya, - JoStoe, jennaswa, ljwoods2 + JoStoe, jennaswa, ljwoods2, SumairaAhmad * 2.7.0