From nobody Wed Apr 29 23:15:31 2026 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4g5Y7S1dy6z6c8VZ for ; Wed, 29 Apr 2026 23:15:32 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R13" (not verified)) by mx1.freebsd.org (Postfix) with ESMTPS id 4g5Y7R71zfz445m for ; Wed, 29 Apr 2026 23:15:31 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1777504532; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=1TeuR81PmofgRti3bO5xl3Ei5M+nn2rIvTD76tKMqf0=; b=OqL5cY8Fn78yiuXvvCK7VIB+LOzDMy+UaU1zd5Kqjc3SCBmXAt93kwHLPefl+yzfbXaNTv K0OG6X7Lk3nqoHa8JcCUXp/eA1d0Y8fVYFy5w+ylIQroH2M/hmL6Y5755WEdE2NOHzF/Nc ZEySZQE9vwvJIMq4uNqksLak916eeaL2dMatpLECRm2J+Eu5Vc+Gf10dtE5MzxYd4raTiy u2ZBrCDdM4+mgkYFmV6JubzjiG72Pv3BVH1Vz8V6K6zPHHMiJxJQJKF8c7EP37w5htgrh4 g/13WtgdSGHKpkDVnFSQ8oqdSQzQvE9gdHhaK19sgAOWZjdPE4nmHwYp5BPZ7Q== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1777504532; a=rsa-sha256; cv=none; b=qBe9Ibe6VASzVNCfT2ixknBIGn/lboU8iCRtFA9zlXQcggmXIv+JohSgZWPsl6euMMRRQ0 Wcqw/O2hQz/anFlUhYMYhiuv/Vti6yHm0nSil+yPrPMaqbmCNDTnuC/n25q2pJmSpi85JW erRpZ1pW6yemtQ2uCAn81mLha/F3ZXfxVNig++WbE8/U7JVoxO0TrIR45Hdg1+lO4ixvQt 5lR4PScWg4zyjxyjBeI2g/q8UDU5xL8yRG4Qv4lO01WjYVPpvPbGxAQIHSyexPlEs9ToXg ZmQq8qToz8Obg62cuBO7Fr4UQXYaHLqfUenwAcsJ/fV31qJ2L+dkyekZKjhMAg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1777504532; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=1TeuR81PmofgRti3bO5xl3Ei5M+nn2rIvTD76tKMqf0=; b=GceSB5hVCkdD9l7osQiCPJr5fHDF6C9qzY/t9pfSyJ5IXH65kQ4oDoP1v4K7v3YoLPvfcv lHZl9RWkDqIgCUb7ddUt5+L9uqmcBn5rwxIu1x4wdR5wy+CfGgVJVtwuZqx49dsqVSUhlz OESwL3BXjXjq8w8JLiBPdrjOG+fp0PP0e+KjJdWyqBchdWD2Cia69IdmzlR/GhiVkb01Ke hMtDhUDSaVRBENE8wVynfDCFBOsWUEko4J6liKWpWS2G27Yy5HWcZNKGEAFs9ER12RNOlZ iUUMqbu2SggPcXxQ4zMrIsJwvFP4IvGZV3YU/ZtM6XdIl+QtDGiMsIzwey+pZQ== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4g5Y7R6YyLz11vD for ; Wed, 29 Apr 2026 23:15:31 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from git (uid 1279) (envelope-from git@FreeBSD.org) id 236a5 by gitrepo.freebsd.org (DragonFly Mail Agent v0.13+ on gitrepo.freebsd.org); Wed, 29 Apr 2026 23:15:31 +0000 To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: e25639cf308a - main - science/py-MDAnalysisTests: update 2.7.0=?utf-8?Q? =E2=86=92 2.1?=0.0 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: e25639cf308aaefa9f659673bc77e18afc8f9539 Auto-Submitted: auto-generated Date: Wed, 29 Apr 2026 23:15:31 +0000 Message-Id: <69f29113.236a5.537b10fd@gitrepo.freebsd.org> The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=e25639cf308aaefa9f659673bc77e18afc8f9539 commit e25639cf308aaefa9f659673bc77e18afc8f9539 Author: Yuri Victorovich AuthorDate: 2026-04-29 23:01:11 +0000 Commit: Yuri Victorovich 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 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.