Attachment 234753 Details for Bug 264716 – New patch to upgrade science/py-MDAnalysis and science/py-MDAnalysisTests disabling threadpoolctl

[patch] New patch to upgrade science/py-MDAnalysis and science/py-MDAnalysisTests disabling threadpoolctl

science_py-MDAnalysis+Tests.diff (text/plain), 11.54 KB, created by Thierry Thomas on 2022-06-17 16:59:11 UTC

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Creator: Thierry Thomas

Created: 2022-06-17 16:59:11 UTC

Size: 11.54 KB

patch

obsolete

>From 7ee73147f50558503cca3adf8986d9762c467afb Mon Sep 17 00:00:00 2001
>From: Thierry Thomas <thierry@FreeBSD.org>
>Date: Thu, 16 Jun 2022 18:10:38 +0200
>Subject: [PATCH 1/2] 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
><https://github.com/MDAnalysis/mdanalysis/pull/2950> for the impacts on
>performance.
>
>Releases notes at <https://github.com/MDAnalysis/mdanalysis/releases>.
>---
> science/py-MDAnalysis/Makefile                | 27 +++++++++++++------
> science/py-MDAnalysis/distinfo                |  6 ++---
> .../patch-MDAnalysis.egg-info_requires.txt    | 10 +++++++
> .../patch-MDAnalysis_transformations_base.py  | 23 ++++++++++++++++
> science/py-MDAnalysis/files/patch-setup.py    | 20 +++++++++-----
> 5 files changed, 69 insertions(+), 17 deletions(-)
> create mode 100644 science/py-MDAnalysis/files/patch-MDAnalysis.egg-info_requires.txt
> create mode 100644 science/py-MDAnalysis/files/patch-MDAnalysis_transformations_base.py
>
>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 <bsd.port.mk>
>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',
>-- 
>2.36.1
>
>
>From d591b8dec346b0ba89b8581cb68f31e772e6e0f8 Mon Sep 17 00:00:00 2001
>From: Thierry Thomas <thierry@FreeBSD.org>
>Date: Fri, 17 Jun 2022 18:10:51 +0200
>Subject: [PATCH 2/2] science/py-MDAnalysisTests: upgrade to 2.2.0
>
>Note: like for science/py-MDAnalysis, threadpoolctl has been disabled
>for the moment.
>---
> science/py-MDAnalysisTests/Makefile           |  7 ++-
> science/py-MDAnalysisTests/distinfo           |  6 +--
> ...nalysisTests_transformations_test__base.py | 54 +++++++++++++++++++
> 3 files changed, 60 insertions(+), 7 deletions(-)
> create mode 100644 science/py-MDAnalysisTests/files/patch-MDAnalysisTests_transformations_test__base.py
>
>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)
>-- 
>2.36.1
>

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Attachments on bug 264716: 234730 | 234731 | 234753