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 <MDAnalysis/mdanalysis#2950> for the impacts on performance. Releases notes at <https://github.com/MDAnalysis/mdanalysis/releases>. PR: 264716 Approved by: yuri (maintainer)
freebsd · Jun 21, 2022 · 40568ca · 40568ca
1 parent 5734bd6
commit 40568ca
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Showing 8 changed files with 129 additions and 24 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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)