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Code Issues Releases Activity

science/py-MDAnalysis{,Tests}: update 2.3.0 → 2.7.0

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This commit is contained in:
Yuri Victorovich 2024-05-06 07:44:28 -07:00
parent 61f69b43d8
commit 947fb0ba70
7 changed files with 64 additions and 20 deletions
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3
science/py-MDAnalysis/Makefile
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@ -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}

6
science/py-MDAnalysis/distinfo
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@ -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

6
science/py-MDAnalysis/files/patch-MDAnalysis.egg-info_requires.txt
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@ -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

46
science/py-MDAnalysis/files/patch-MDAnalysis_lib_formats_src_xdrfile.c Normal file
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@ -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,

14
science/py-MDAnalysis/files/patch-setup.py
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@ -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',

3
science/py-MDAnalysisTests/Makefile
View File

@ -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}

6
science/py-MDAnalysisTests/distinfo
View File

@ -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