From nobody Tue Jun 21 17:26:26 2022 X-Original-To: dev-commits-ports-all@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 1899785DCB4; Tue, 21 Jun 2022 17:26:27 +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 "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4LSD2W09jTz3myK; Tue, 21 Jun 2022 17:26:27 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1655832387; 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=x5IHTCyD4M9tf/WF3t+kvuMfQ9yyO3bP4sAdPNRNUSY=; b=pzcQBFflsrwzK8dHHbrw7ePrUPxFjia21SIdMwqdTSihYDQwzWbsKiEM8lAeMCnrE7ppcG cyvNgpTnuKpsLTNh4OPytlna40TspMkezTQ3omtcn9D5AA/bb91GYkqSDk97Fs/Ww77ivz YcTyhujNcYHOcdxvdvCBpXtCP2Xb51Hc/1XqtsmViwBPD2GiXn8uhCqu6oZP5CcFpHkHyo d7T5/CJHXc1LZWnSOgUB+XApdc0h/tBo9/rV+MazPnftl2CK/2YQX0TEAwTli6gFGtP0T+ N/axlAjINT6U9Mj2hZ2DQGe5mokCBcFndurtfwAwslZQsX28jrOOL9s7IT5UGg== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (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 did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id D608C16020; Tue, 21 Jun 2022 17:26:26 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 25LHQQjb028665; Tue, 21 Jun 2022 17:26:26 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 25LHQQDh028664; Tue, 21 Jun 2022 17:26:26 GMT (envelope-from git) Date: Tue, 21 Jun 2022 17:26:26 GMT Message-Id: <202206211726.25LHQQDh028664@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Thierry Thomas Subject: git: 40568cac8e3e - main - science/py-MDAnalysis*: upgrade to 2.2.0 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: thierry X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 40568cac8e3e1931ca48becdfd18e2bf0aab1061 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1655832387; 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=x5IHTCyD4M9tf/WF3t+kvuMfQ9yyO3bP4sAdPNRNUSY=; b=lWBrCuSoZuqESxhBB4kbR4iFIDtAazZFD2UQz1IW6BXW0w1z4h1+g5N/RDy5FfVe/ldWgc Y4iKhpx/5Ojd0N0hUrXWDjJPizr2nmATdnIK0IiPjGB4mg5RsNmCViXiiD5JrDbMzSP/Al Q8mHJfNZ5xlJn4OXfVFl5QpexaM8kuHA4yUmj4ULwbWdTau0Tj/JUDIbggIcEDnABBWhKu 0/2wg7mSEbkpfrVMNASYaD+vA4wSmdWY7xiJC57ncEWKSSZDsT9TmRpIEsFntL2bBWuF+b seXVbIu+f/qItcb0V2r0wA/OjEord0rAkFA37Lv0EW5VHSXHEphF7tDuhSv5DA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1655832387; a=rsa-sha256; cv=none; b=yGlxGTBa/lSUGeeD0IeJvAVbPtc5lpt+LPprIXJkKSw/50wQgmmhF2Ygt6lBdhw0dC+PfL kYq9aKlyIyvuu9T8c47iLLMgOew1NeZzNvRyLJS43tQyvf2mnOnyOOo8+Md7IE03Fzz8ah WwlhcINE3xxUiPebt48bLilIvHiOydoMV3kKnm1Z//UNlBAjxXQXTsmo2H4Wcc0aFNx0dL cShiAdic6llaWm+tyQDS7Kxl0SHmRMDbUsCMdhZYCRc7TZtUjaY8nyvH6kpmhnOCfzWEJi x+gseIHzvnn+myyJqJ8KOYDqRJz4q1/WJnaHXkv88XJrPN2tB5Un2vXtgF82cQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by thierry: URL: https://cgit.FreeBSD.org/ports/commit/?id=40568cac8e3e1931ca48becdfd18e2bf0aab1061 commit 40568cac8e3e1931ca48becdfd18e2bf0aab1061 Author: Thierry Thomas AuthorDate: 2022-06-16 16:10:38 +0000 Commit: Thierry Thomas CommitDate: 2022-06-21 17:26:21 +0000 science/py-MDAnalysis*: upgrade to 2.2.0 Version 0.19.2 is too old and does not support Python-3.9. Remark: threadpoolctl is disabled in this port. See for the impacts on performance. Releases notes at . PR: 264716 Approved by: yuri (maintainer) --- science/py-MDAnalysis/Makefile | 27 +++++++---- science/py-MDAnalysis/distinfo | 6 +-- .../files/patch-MDAnalysis.egg-info_requires.txt | 10 ++++ .../files/patch-MDAnalysis_transformations_base.py | 23 +++++++++ science/py-MDAnalysis/files/patch-setup.py | 20 +++++--- science/py-MDAnalysisTests/Makefile | 7 ++- science/py-MDAnalysisTests/distinfo | 6 +-- ...h-MDAnalysisTests_transformations_test__base.py | 54 ++++++++++++++++++++++ 8 files changed, 129 insertions(+), 24 deletions(-) diff --git a/science/py-MDAnalysis/Makefile b/science/py-MDAnalysis/Makefile index f3d5d837c8a0..8f3478c38c4b 100644 --- a/science/py-MDAnalysis/Makefile +++ b/science/py-MDAnalysis/Makefile @@ -1,6 +1,5 @@ PORTNAME= MDAnalysis -DISTVERSION= 0.19.2 -PORTREVISION= 2 +DISTVERSION= 2.2.0 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -11,21 +10,33 @@ COMMENT= Python library to analyze molecular dynamics trajectories LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE -BUILD_DEPENDS= ${PYNUMPY} +BUILD_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}packaging>=2.0:devel/py-packaging@${PY_FLAVOR} RUN_DEPENDS= ${PYNUMPY} \ + clustalw2:biology/clustalw \ + rdkit>0:science/rdkit \ ${PYTHON_PKGNAMEPREFIX}biopython>=1.71:biology/py-biopython@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}duecredit>0:textproc/py-duecredit@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}GridDataFormats>=0.4.0:math/py-GridDataFormats@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}gsd>=1.4.0:science/py-gsd@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}gsd>=1.9.3:science/py-gsd@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}joblib>0:devel/py-joblib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=1.5.1:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}mmtf-python>=1.0.0:science/py-mmtf-python@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}mock>0:devel/py-mock@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}networkx>=1.0:math/py-networkx@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}scipy>=1.0.0:science/py-scipy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}six>=1.4.0:devel/py-six@${PY_FLAVOR} + ${PYTHON_PKGNAMEPREFIX}netCDF4>0:science/py-netCDF4@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}networkx>0:math/py-networkx@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scikit-learn>0:science/py-scikit-learn@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>=1.5.0:science/py-scipy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}seaborn>0:math/py-seaborn@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}six>=1.4.0:devel/py-six@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}tqdm>=4.43.0:misc/py-tqdm@${PY_FLAVOR} USES= compiler:c++11-lang python:3.7+ -USE_PYTHON= distutils autoplist +USE_PYTHON= cython distutils autoplist + +.if !defined(WITH_DEBUG) +LDFLAGS+= -s +.endif .include diff --git a/science/py-MDAnalysis/distinfo b/science/py-MDAnalysis/distinfo index 7399e8d0dd4a..1c316cf373ea 100644 --- a/science/py-MDAnalysis/distinfo +++ b/science/py-MDAnalysis/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1541970443 -SHA256 (MDAnalysis-0.19.2.tar.gz) = c5395bbafa5efca2e1aee4715d26129844140c47cb8301da0293106cb969de7d -SIZE (MDAnalysis-0.19.2.tar.gz) = 16457970 +TIMESTAMP = 1655365188 +SHA256 (MDAnalysis-2.2.0.tar.gz) = bf9c9b7a03404e65aad66215d4c2ff8834ab747551eeaee059ff3e599a99d322 +SIZE (MDAnalysis-2.2.0.tar.gz) = 3640167 diff --git a/science/py-MDAnalysis/files/patch-MDAnalysis.egg-info_requires.txt b/science/py-MDAnalysis/files/patch-MDAnalysis.egg-info_requires.txt new file mode 100644 index 000000000000..863978e58ce8 --- /dev/null +++ b/science/py-MDAnalysis/files/patch-MDAnalysis.egg-info_requires.txt @@ -0,0 +1,10 @@ +--- MDAnalysis.egg-info/requires.txt.orig 2022-06-02 18:49:39 UTC ++++ MDAnalysis.egg-info/requires.txt +@@ -7,7 +7,6 @@ joblib>=0.12 + scipy>=1.5.0 + matplotlib>=1.5.1 + tqdm>=4.43.0 +-threadpoolctl + packaging + fasteners + gsd>=1.9.3 diff --git a/science/py-MDAnalysis/files/patch-MDAnalysis_transformations_base.py b/science/py-MDAnalysis/files/patch-MDAnalysis_transformations_base.py new file mode 100644 index 000000000000..1f5068094130 --- /dev/null +++ b/science/py-MDAnalysis/files/patch-MDAnalysis_transformations_base.py @@ -0,0 +1,23 @@ +--- MDAnalysis/transformations/base.py.orig 2022-06-02 18:49:09 UTC ++++ MDAnalysis/transformations/base.py +@@ -26,8 +26,9 @@ Transformations Base Class --- :mod:`MDAnalysis.transf + + .. autoclass:: TransformationBase + +-""" ++Note: threadpoolctl does not yet run on FreeBSD + from threadpoolctl import threadpool_limits ++""" + + + class TransformationBase(object): +@@ -113,8 +114,7 @@ class TransformationBase(object): + The thread limit works as a context manager with given `max_threads` + wrapping the real :func:`_transform` function + """ +- with threadpool_limits(self.max_threads): +- return self._transform(ts) ++ return self._transform(ts) + + def _transform(self, ts): + """Transform the given `Timestep` diff --git a/science/py-MDAnalysis/files/patch-setup.py b/science/py-MDAnalysis/files/patch-setup.py index baad2ab31e0e..21db43b92b78 100644 --- a/science/py-MDAnalysis/files/patch-setup.py +++ b/science/py-MDAnalysis/files/patch-setup.py @@ -1,11 +1,19 @@ ---- setup.py.orig 2018-05-13 20:38:06 UTC +--- setup.py.orig 2022-06-02 18:49:09 UTC +++ setup.py -@@ -253,7 +253,7 @@ def extensions(config): - use_cython = config.get('use_cython', default=not is_release) +@@ -274,7 +274,7 @@ def extensions(config): + use_cython = config.get('use_cython', default=cython_found) use_openmp = config.get('use_openmp', default=True) -- extra_compile_args = ['-std=c99', '-ffast-math', '-O3', '-funroll-loops'] -+ extra_compile_args = ['-std=c99', '-ffast-math', '-funroll-loops'] +- extra_compile_args = ['-std=c99', '-ffast-math', '-O3', '-funroll-loops', ++ extra_compile_args = ['-std=c99', '-ffast-math', '-funroll-loops', + '-fsigned-zeros'] # see #2722 define_macros = [] if config.get('debug_cflags', default=False): - extra_compile_args.extend(['-Wall', '-pedantic']) +@@ -599,7 +599,6 @@ if __name__ == '__main__': + 'scipy>=1.5.0', + 'matplotlib>=1.5.1', + 'tqdm>=4.43.0', +- 'threadpoolctl', + 'packaging', + 'fasteners', + 'gsd>=1.9.3', diff --git a/science/py-MDAnalysisTests/Makefile b/science/py-MDAnalysisTests/Makefile index f115652c408f..c2e7061e5787 100644 --- a/science/py-MDAnalysisTests/Makefile +++ b/science/py-MDAnalysisTests/Makefile @@ -1,6 +1,5 @@ PORTNAME= MDAnalysisTests -DISTVERSION= 0.19.2 -PORTREVISION= 2 +DISTVERSION= 2.2.0 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -13,12 +12,12 @@ LICENSE_FILE= ${WRKSRC}/LICENSE RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}MDAnalysis>0:science/py-MDAnalysis@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pytest>=3.1.2:devel/py-pytest@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}fasteners>0:devel/py-fasteners@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}hypothesis>0:devel/py-hypothesis@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}psutil>=4.0.2:sysutils/py-psutil@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}mock>=2.0.0:devel/py-mock@${PY_FLAVOR} -USES= python:3.7+ +USES= pytest python:3.8+ USE_PYTHON= distutils autoplist NO_ARCH= yes diff --git a/science/py-MDAnalysisTests/distinfo b/science/py-MDAnalysisTests/distinfo index ca9108dddcda..71df2dd44f64 100644 --- a/science/py-MDAnalysisTests/distinfo +++ b/science/py-MDAnalysisTests/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1541975333 -SHA256 (MDAnalysisTests-0.19.2.tar.gz) = be4c27a11d3f55a00dfe54149508ea6df2d816bd25f57c2bebb8804abf4e927e -SIZE (MDAnalysisTests-0.19.2.tar.gz) = 46131381 +TIMESTAMP = 1655455829 +SHA256 (MDAnalysisTests-2.2.0.tar.gz) = 28d17b8c4ac0be3fe424acc9ac250e7bbbad6496eba21d915c58eb389ce04eb2 +SIZE (MDAnalysisTests-2.2.0.tar.gz) = 52452140 diff --git a/science/py-MDAnalysisTests/files/patch-MDAnalysisTests_transformations_test__base.py b/science/py-MDAnalysisTests/files/patch-MDAnalysisTests_transformations_test__base.py new file mode 100644 index 000000000000..02b82d1edb7e --- /dev/null +++ b/science/py-MDAnalysisTests/files/patch-MDAnalysisTests_transformations_test__base.py @@ -0,0 +1,54 @@ +--- MDAnalysisTests/transformations/test_base.py.orig 2022-06-02 18:49:13 UTC ++++ MDAnalysisTests/transformations/test_base.py +@@ -23,7 +23,8 @@ from numpy.testing import assert_equal + import numpy as np + import pytest + from numpy.testing import assert_equal +-from threadpoolctl import threadpool_info ++# threadpoolctl is not yet usable on FreeBSD ++#from threadpoolctl import threadpool_info + + import MDAnalysis as mda + from MDAnalysisTests.datafiles import PSF, DCD +@@ -36,7 +37,7 @@ class DefaultTransformation(TransformationBase): + super().__init__() + + def _transform(self, ts): +- self.runtime_info = threadpool_info() ++ """self.runtime_info = threadpool_info()""" + ts.positions = ts.positions + 1 + return ts + +@@ -54,7 +55,7 @@ class CustomTransformation(TransformationBase): + parallelizable=parallelizable) + + 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)