diff options
| -rw-r--r-- | science/py-MDAnalysis/Makefile | 27 | ||||
| -rw-r--r-- | science/py-MDAnalysis/distinfo | 6 | ||||
| -rw-r--r-- | science/py-MDAnalysis/files/patch-MDAnalysis.egg-info_requires.txt | 10 | ||||
| -rw-r--r-- | science/py-MDAnalysis/files/patch-MDAnalysis_transformations_base.py | 23 | ||||
| -rw-r--r-- | science/py-MDAnalysis/files/patch-setup.py | 20 | ||||
| -rw-r--r-- | science/py-MDAnalysisTests/Makefile | 7 | ||||
| -rw-r--r-- | science/py-MDAnalysisTests/distinfo | 6 | ||||
| -rw-r--r-- | science/py-MDAnalysisTests/files/patch-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 <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', 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) |