Date: Wed, 29 Apr 2026 23:15:31 +0000 From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: e25639cf308a - main - science/py-MDAnalysisTests: update 2.7.0=?utf-8?Q? =E2=86=92 2.1?=0.0 Message-ID: <69f29113.236a5.537b10fd@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=e25639cf308aaefa9f659673bc77e18afc8f9539 commit e25639cf308aaefa9f659673bc77e18afc8f9539 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2026-04-29 23:01:11 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2026-04-29 23:01:11 +0000 science/py-MDAnalysisTests: update 2.7.0 → 2.10.0 --- science/py-MDAnalysisTests/Makefile | 8 +++-- science/py-MDAnalysisTests/distinfo | 6 ++-- ...h-MDAnalysisTests_transformations_test__base.py | 37 +++++----------------- science/py-MDAnalysisTests/pkg-descr | 5 ++- 4 files changed, 21 insertions(+), 35 deletions(-) diff --git a/science/py-MDAnalysisTests/Makefile b/science/py-MDAnalysisTests/Makefile index d29cf5c94e6e..df63e224953b 100644 --- a/science/py-MDAnalysisTests/Makefile +++ b/science/py-MDAnalysisTests/Makefile @@ -1,6 +1,5 @@ PORTNAME= MDAnalysisTests -DISTVERSION= 2.7.0 -PORTREVISION= 3 +DISTVERSION= 2.10.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -15,9 +14,14 @@ LICENSE_FILE= ${WRKSRC}/LICENSE RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy1>=1.16:math/py-numpy1@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}MDAnalysis>0:science/py-MDAnalysis@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}hypothesis>0:devel/py-hypothesis@${PY_FLAVOR} +TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}hypothesis>0:devel/py-hypothesis@${PY_FLAVOR} USES= python USE_PYTHON= distutils autoplist pytest NO_ARCH= yes +WRKSRC= ${WRKDIR}/mdanalysistests-${DISTVERSION} + +# tests as of 2.10.0 + .include <bsd.port.mk> diff --git a/science/py-MDAnalysisTests/distinfo b/science/py-MDAnalysisTests/distinfo index f39c637c7f98..fbbb381eca33 100644 --- a/science/py-MDAnalysisTests/distinfo +++ b/science/py-MDAnalysisTests/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1715029181 -SHA256 (MDAnalysisTests-2.7.0.tar.gz) = 326d65d7f14da8d1b047aab87ca312a68459a5fd18ddf6d8cb9ac9c3ca51d9e5 -SIZE (MDAnalysisTests-2.7.0.tar.gz) = 55704756 +TIMESTAMP = 1777493576 +SHA256 (MDAnalysisTests-2.10.0.tar.gz) = 286b8678e19195093a19b57b26d76b8274415d33ac23fc872355639fcb49beef +SIZE (MDAnalysisTests-2.10.0.tar.gz) = 57933275 diff --git a/science/py-MDAnalysisTests/files/patch-MDAnalysisTests_transformations_test__base.py b/science/py-MDAnalysisTests/files/patch-MDAnalysisTests_transformations_test__base.py index 02b82d1edb7e..4dfaa1f28897 100644 --- a/science/py-MDAnalysisTests/files/patch-MDAnalysisTests_transformations_test__base.py +++ b/science/py-MDAnalysisTests/files/patch-MDAnalysisTests_transformations_test__base.py @@ -1,6 +1,10 @@ ---- MDAnalysisTests/transformations/test_base.py.orig 2022-06-02 18:49:13 UTC +-- threadpoolctl is not available/functional on FreeBSD. +-- This patch comments out threadpoolctl import and usage to allow the package +-- to build and run on FreeBSD. +--- +--- MDAnalysisTests/transformations/test_base.py.orig 2026-04-29 20:16:20 UTC +++ MDAnalysisTests/transformations/test_base.py -@@ -23,7 +23,8 @@ from numpy.testing import assert_equal +@@ -22,7 +22,8 @@ from numpy.testing import assert_equal import numpy as np import pytest from numpy.testing import assert_equal @@ -19,36 +23,11 @@ ts.positions = ts.positions + 1 return ts -@@ -54,7 +55,7 @@ class CustomTransformation(TransformationBase): - parallelizable=parallelizable) +@@ -57,7 +58,7 @@ class CustomTransformation(TransformationBase): + ) def _transform(self, ts): - self.runtime_info = threadpool_info() + """self.runtime_info = threadpool_info()""" ts.positions = ts.positions + 1 return ts - -@@ -88,17 +89,17 @@ def test_thread_limit_apply(u): - - - def test_thread_limit_apply(u): -- default_thread_info = threadpool_info() -+ """default_thread_info = threadpool_info() - default_num_thread_limit_list = [thread_info['num_threads'] - for thread_info in default_thread_info] - - new_trans = CustomTransformation(max_threads=2) - _ = new_trans(u.trajectory.ts) -- for thread_info in new_trans.runtime_info: -- assert thread_info['num_threads'] == 2 -+ for thread_info in new_trans.runtime_info:""" -+ assert thread_info['num_threads'] == 2 - - # test the thread limit is only applied locally. -- new_thread_info = threadpool_info() -+ """new_thread_info = threadpool_info() - new_num_thread_limit_list = [thread_info['num_threads'] -- for thread_info in new_thread_info] -- assert_equal(default_num_thread_limit_list, new_num_thread_limit_list) -+ for thread_info in new_thread_info]""" -+ assert_equal(default_num_thread_limit_list, 2) diff --git a/science/py-MDAnalysisTests/pkg-descr b/science/py-MDAnalysisTests/pkg-descr index ade8e8a2faf0..4242bfbbab4c 100644 --- a/science/py-MDAnalysisTests/pkg-descr +++ b/science/py-MDAnalysisTests/pkg-descr @@ -1 +1,4 @@ -Test code and data for science/py-MDAnalysis. +Test code and trajectory data for the test cases of MDAnalysis. + +This package provides the test suite and test data files required to run the +full test suite of MDAnalysis.home | help
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