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

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