Date: Mon, 6 May 2024 21:08:17 GMT
From: Yuri Victorovich <yuri@FreeBSD.org>
To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-branches@FreeBSD.org
Subject: git: bf2a1f19116b - 2024Q2 - science/py-MDAnalysis{,Tests}: update 2.3.0 =?utf-8?Q?=E2=86=92?= 2.7.0
Message-ID: <202405062108.446L8HOb017419@gitrepo.freebsd.org>
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The branch 2024Q2 has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=bf2a1f19116b6ba8b2038a6780403a49330d44c2 commit bf2a1f19116b6ba8b2038a6780403a49330d44c2 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2024-05-06 14:44:28 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2024-05-06 21:08:12 +0000 science/py-MDAnalysis{,Tests}: update 2.3.0 → 2.7.0 (cherry picked from commit 947fb0ba70a8afb06c5ab834727a13dc6942097f) --- science/py-MDAnalysis/Makefile | 3 +- science/py-MDAnalysis/distinfo | 6 +-- .../files/patch-MDAnalysis.egg-info_requires.txt | 6 +-- .../patch-MDAnalysis_lib_formats_src_xdrfile.c | 46 ++++++++++++++++++++++ science/py-MDAnalysis/files/patch-setup.py | 14 +++---- science/py-MDAnalysisTests/Makefile | 3 +- science/py-MDAnalysisTests/distinfo | 6 +-- 7 files changed, 64 insertions(+), 20 deletions(-) diff --git a/science/py-MDAnalysis/Makefile b/science/py-MDAnalysis/Makefile index acb635f24fb4..70b9478a111a 100644 --- a/science/py-MDAnalysis/Makefile +++ b/science/py-MDAnalysis/Makefile @@ -1,6 +1,5 @@ PORTNAME= MDAnalysis -DISTVERSION= 2.3.0 -PORTREVISION= 1 +DISTVERSION= 2.7.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-MDAnalysis/distinfo b/science/py-MDAnalysis/distinfo index eefa396a1fd7..904a4e724ecb 100644 --- a/science/py-MDAnalysis/distinfo +++ b/science/py-MDAnalysis/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1662095086 -SHA256 (MDAnalysis-2.3.0.tar.gz) = 29579433c4ea87048278dc1d4019b52e6a19504162659447be7c79fbdbf508ff -SIZE (MDAnalysis-2.3.0.tar.gz) = 3701615 +TIMESTAMP = 1714979275 +SHA256 (MDAnalysis-2.7.0.tar.gz) = 572e82945e5d058e3749ec5f18e6b3831ef7f2119cb54672567ae9a977201e93 +SIZE (MDAnalysis-2.7.0.tar.gz) = 3938260 diff --git a/science/py-MDAnalysis/files/patch-MDAnalysis.egg-info_requires.txt b/science/py-MDAnalysis/files/patch-MDAnalysis.egg-info_requires.txt index 863978e58ce8..ec795498a023 100644 --- a/science/py-MDAnalysis/files/patch-MDAnalysis.egg-info_requires.txt +++ b/science/py-MDAnalysis/files/patch-MDAnalysis.egg-info_requires.txt @@ -1,10 +1,10 @@ ---- MDAnalysis.egg-info/requires.txt.orig 2022-06-02 18:49:39 UTC +--- MDAnalysis.egg-info/requires.txt.orig 2023-12-26 20:46:12 UTC +++ MDAnalysis.egg-info/requires.txt -@@ -7,7 +7,6 @@ joblib>=0.12 +@@ -5,7 +5,6 @@ tqdm>=4.43.0 scipy>=1.5.0 matplotlib>=1.5.1 tqdm>=4.43.0 -threadpoolctl packaging fasteners - gsd>=1.9.3 + mda-xdrlib diff --git a/science/py-MDAnalysis/files/patch-MDAnalysis_lib_formats_src_xdrfile.c b/science/py-MDAnalysis/files/patch-MDAnalysis_lib_formats_src_xdrfile.c new file mode 100644 index 000000000000..e64cd135c92c --- /dev/null +++ b/science/py-MDAnalysis/files/patch-MDAnalysis_lib_formats_src_xdrfile.c @@ -0,0 +1,46 @@ +- workaround for invalid C/C++ code, see https://github.com/MDAnalysis/mdanalysis/issues/4589 + +--- MDAnalysis/lib/formats/src/xdrfile.c.orig 2024-05-06 20:07:19 UTC ++++ MDAnalysis/lib/formats/src/xdrfile.c +@@ -132,8 +132,8 @@ struct XDR + int (*x_getbytes) (XDR *__xdrs, char *__addr, unsigned int __len); + int (*x_putbytes) (XDR *__xdrs, char *__addr, unsigned int __len); + /* two next routines are not 64-bit IO safe - don't use! */ +- unsigned int (*x_getpostn) (XDR *__xdrs); +- int (*x_setpostn) (XDR *__xdrs, unsigned int __pos); ++ off_t (*x_getpostn) (XDR *__xdrs); ++ off_t (*x_setpostn) (XDR *__xdrs, off_t __pos, int); + void (*x_destroy) (XDR *__xdrs); + } + *x_ops; +@@ -2519,8 +2519,8 @@ static int xdrstdio_putbytes (XDR *, char *, unsigned + static int xdrstdio_putlong (XDR *, int32_t *); + static int xdrstdio_getbytes (XDR *, char *, unsigned int); + static int xdrstdio_putbytes (XDR *, char *, unsigned int); +-static int64_t xdrstdio_getpos (XDR *); +-static int xdrstdio_setpos (XDR *, int64_t, int); ++static off_t xdrstdio_getpos (XDR *); ++static off_t xdrstdio_setpos (XDR *, int64_t, int); + static void xdrstdio_destroy (XDR *); + + /* +@@ -2602,7 +2602,7 @@ xdrstdio_putbytes (XDR *xdrs, char *addr, unsigned int + } + + +-static int64_t ++static off_t + xdrstdio_getpos (XDR *xdrs) + { + #ifdef _WIN32 +@@ -2612,8 +2612,8 @@ xdrstdio_getpos (XDR *xdrs) + #endif + } + +-static int +-xdrstdio_setpos (XDR *xdrs, int64_t pos, int whence) ++static off_t ++xdrstdio_setpos (XDR *xdrs, off_t pos, int whence) + { + /* A reason for failure can be filesystem limits on allocation units, + * before the actual off_t overflow (ext3, with a 4K clustersize, diff --git a/science/py-MDAnalysis/files/patch-setup.py b/science/py-MDAnalysis/files/patch-setup.py index 21db43b92b78..b418f13e5dbc 100644 --- a/science/py-MDAnalysis/files/patch-setup.py +++ b/science/py-MDAnalysis/files/patch-setup.py @@ -1,19 +1,19 @@ ---- setup.py.orig 2022-06-02 18:49:09 UTC +--- setup.py.orig 2023-12-26 20:45:53 UTC +++ setup.py -@@ -274,7 +274,7 @@ def extensions(config): - use_cython = config.get('use_cython', default=cython_found) +@@ -266,7 +266,7 @@ def extensions(config): use_openmp = config.get('use_openmp', default=True) + annotate_cython = config.get('annotate_cython', default=False) -- extra_compile_args = ['-std=c99', '-ffast-math', '-O3', '-funroll-loops', -+ extra_compile_args = ['-std=c99', '-ffast-math', '-funroll-loops', +- extra_compile_args = ['-std=c99', '-O3', '-funroll-loops', ++ extra_compile_args = ['-std=c99', '-funroll-loops', '-fsigned-zeros'] # see #2722 define_macros = [] if config.get('debug_cflags', default=False): -@@ -599,7 +599,6 @@ if __name__ == '__main__': +@@ -598,7 +598,6 @@ if __name__ == '__main__': 'scipy>=1.5.0', 'matplotlib>=1.5.1', 'tqdm>=4.43.0', - 'threadpoolctl', 'packaging', 'fasteners', - 'gsd>=1.9.3', + 'mda-xdrlib', diff --git a/science/py-MDAnalysisTests/Makefile b/science/py-MDAnalysisTests/Makefile index ee722a2cd5b2..b560f72a9b9f 100644 --- a/science/py-MDAnalysisTests/Makefile +++ b/science/py-MDAnalysisTests/Makefile @@ -1,6 +1,5 @@ PORTNAME= MDAnalysisTests -DISTVERSION= 2.3.0 -PORTREVISION= 1 +DISTVERSION= 2.7.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-MDAnalysisTests/distinfo b/science/py-MDAnalysisTests/distinfo index 28d4454038e0..f39c637c7f98 100644 --- a/science/py-MDAnalysisTests/distinfo +++ b/science/py-MDAnalysisTests/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1662099346 -SHA256 (MDAnalysisTests-2.3.0.tar.gz) = b4dcdbbc6e216a59feb7c3e8cb5c7d9251dbd7aa7ab35f04ad81e93a301c12dc -SIZE (MDAnalysisTests-2.3.0.tar.gz) = 52461472 +TIMESTAMP = 1715029181 +SHA256 (MDAnalysisTests-2.7.0.tar.gz) = 326d65d7f14da8d1b047aab87ca312a68459a5fd18ddf6d8cb9ac9c3ca51d9e5 +SIZE (MDAnalysisTests-2.7.0.tar.gz) = 55704756
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