Date: Wed, 29 Apr 2026 23:15:30 +0000 From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 90ca5afa56b2 - main - science/py-MDAnalysis: update 2.7.0=?utf-8?Q? =E2=86=92 2.1?=0.0 Message-ID: <69f29112.201ff.13e8d79f@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=90ca5afa56b253c97afbab2061dea2739a0d9d90 commit 90ca5afa56b253c97afbab2061dea2739a0d9d90 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2026-04-29 23:00:09 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2026-04-29 23:00:09 +0000 science/py-MDAnalysis: update 2.7.0 → 2.10.0 --- science/py-MDAnalysis/Makefile | 25 +++++++------- science/py-MDAnalysis/distinfo | 6 ++-- .../files/patch-MDAnalysis.egg-info_requires.txt | 10 ------ .../patch-MDAnalysis_lib_formats_src_xdrfile.c | 39 +++------------------- science/py-MDAnalysis/files/patch-setup.py | 19 ----------- 5 files changed, 20 insertions(+), 79 deletions(-) diff --git a/science/py-MDAnalysis/Makefile b/science/py-MDAnalysis/Makefile index fc5924e5d5ee..eaca51c4c354 100644 --- a/science/py-MDAnalysis/Makefile +++ b/science/py-MDAnalysis/Makefile @@ -1,9 +1,9 @@ PORTNAME= MDAnalysis -DISTVERSION= 2.7.0 -PORTREVISION= 3 +DISTVERSION= 2.10.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} +DISTNAME= ${PORTNAME:tl}-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Python library to analyze molecular dynamics trajectories @@ -12,26 +12,27 @@ WWW= https://www.mdanalysis.org LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE -BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy1>=1.16:math/py-numpy1@${PY_FLAVOR} \ +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}cython>=0.28:lang/cython@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}numpy>=1.26.0:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}packaging>=2.0:devel/py-packaging@${PY_FLAVOR} -RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy1>=1.16:math/py-numpy1@${PY_FLAVOR} \ +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}GridDataFormats>=0.4.0:math/py-GridDataFormats@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}biopython>=1.80:biology/py-biopython@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}gsd>3.0.0:science/py-gsd@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}joblib>=0.12:devel/py-joblib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>=1.5.1:math/py-matplotlib@${PY_FLAVOR} \ clustalw2:biology/clustalw \ rdkit>0:science/rdkit \ - ${PYTHON_PKGNAMEPREFIX}biopython>=1.71:biology/py-biopython@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}GridDataFormats>=0.4.0:math/py-GridDataFormats@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}fasteners>0:devel/py-fasteners@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}gsd>=1.9.3:science/py-gsd@${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} \ ${PYTHON_PKGNAMEPREFIX}networkx>=2.0:math/py-networkx@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}numpy>=1.26.0:math/py-numpy@${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 -USE_PYTHON= distutils cython autoplist +USE_PYTHON= distutils cython autoplist pytest + +# tests as of 2.10.0 .if !defined(WITH_DEBUG) LDFLAGS+= -s diff --git a/science/py-MDAnalysis/distinfo b/science/py-MDAnalysis/distinfo index 904a4e724ecb..b7a23bbd2a3b 100644 --- a/science/py-MDAnalysis/distinfo +++ b/science/py-MDAnalysis/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1714979275 -SHA256 (MDAnalysis-2.7.0.tar.gz) = 572e82945e5d058e3749ec5f18e6b3831ef7f2119cb54672567ae9a977201e93 -SIZE (MDAnalysis-2.7.0.tar.gz) = 3938260 +TIMESTAMP = 1777492771 +SHA256 (mdanalysis-2.10.0.tar.gz) = 5cef1f1eba4b25cbf9dd4045f08eeab293bb9577b970aa96132f14491312d877 +SIZE (mdanalysis-2.10.0.tar.gz) = 5263029 diff --git a/science/py-MDAnalysis/files/patch-MDAnalysis.egg-info_requires.txt b/science/py-MDAnalysis/files/patch-MDAnalysis.egg-info_requires.txt deleted file mode 100644 index ec795498a023..000000000000 --- a/science/py-MDAnalysis/files/patch-MDAnalysis.egg-info_requires.txt +++ /dev/null @@ -1,10 +0,0 @@ ---- MDAnalysis.egg-info/requires.txt.orig 2023-12-26 20:46:12 UTC -+++ MDAnalysis.egg-info/requires.txt -@@ -5,7 +5,6 @@ tqdm>=4.43.0 - scipy>=1.5.0 - matplotlib>=1.5.1 - tqdm>=4.43.0 --threadpoolctl - packaging - fasteners - 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 index e64cd135c92c..d9dee2efbac3 100644 --- a/science/py-MDAnalysis/files/patch-MDAnalysis_lib_formats_src_xdrfile.c +++ b/science/py-MDAnalysis/files/patch-MDAnalysis_lib_formats_src_xdrfile.c @@ -1,46 +1,15 @@ - 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.orig 2025-10-17 00:00:00 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); +- int64_t (*x_getpostn) (XDR *__xdrs); +- int (*x_setpostn) (XDR *__xdrs, int64_t __pos, int __whence); + off_t (*x_getpostn) (XDR *__xdrs); -+ off_t (*x_setpostn) (XDR *__xdrs, off_t __pos, int); ++ off_t (*x_setpostn) (XDR *__xdrs, off_t __pos, int __whence); 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 deleted file mode 100644 index b418f13e5dbc..000000000000 --- a/science/py-MDAnalysis/files/patch-setup.py +++ /dev/null @@ -1,19 +0,0 @@ ---- setup.py.orig 2023-12-26 20:45:53 UTC -+++ setup.py -@@ -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', '-O3', '-funroll-loops', -+ extra_compile_args = ['-std=c99', '-funroll-loops', - '-fsigned-zeros'] # see #2722 - define_macros = [] - if config.get('debug_cflags', default=False): -@@ -598,7 +598,6 @@ if __name__ == '__main__': - 'scipy>=1.5.0', - 'matplotlib>=1.5.1', - 'tqdm>=4.43.0', -- 'threadpoolctl', - 'packaging', - 'fasteners', - 'mda-xdrlib',home | help
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