CVS commit: pkgsrc/math/py-scipy

["Adam Ciarcinski" <adam%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   adam
Date:           Thu Oct 30 14:58:40 UTC 2025

Modified Files:
        pkgsrc/math/py-scipy: Makefile distinfo
        pkgsrc/math/py-scipy/patches:
            patch-subprojects_xsf_include_xsf_amos_amos.h

Log Message:
py-scipy: updated to 1.16.3

Issues closed for 1.16.3

BUG: linalg: wrong handling of args/kwargs in ``_apply_over_batch``
BUG: huge speed and quality regression for stats.multivariate_normal.cdf
BUG: ``lqmn(1,1,0)`` and ``lqmn(1,1,0j)`` return incompatible...
CI: meson setup fails with "invalid int value: 'Sentinel.UNSET'"
BUG: ``special.expi(inf)`` is ``nan``\ , should be ``inf``
MAINT, TST: optimize test_input_validation torch failure
TST, MAINT: boxcox_llf failing again

Pull requests for 1.16.3

REL, MAINT: prepare for SciPy 1.16.3
TST, MAINT: backports, restore lfilter
BUG: linalg:solve...are: fix bug when optional array is skipped
MAINT: optimize: fix usage of ``nextafter(..., where=)`` without...
CI: pin Python 3.11.13 in CircleCI job
BUG:optimize:SLSQP: Use double negative in an if condition for...
ENH: scipy.stats: speed up bivariate normal cdf
BUG/TST: Bump xsf to v0.1.3 add tests for expi limits
CI: optimize: allow new Pytorch message
MAINT: patch vendored qhull source for security fix
TST: stats.boxcox_llf: bump test tolerance


To generate a diff of this commit:
cvs rdiff -u -r1.102 -r1.103 pkgsrc/math/py-scipy/Makefile
cvs rdiff -u -r1.62 -r1.63 pkgsrc/math/py-scipy/distinfo
cvs rdiff -u -r1.1 -r1.2 \
    pkgsrc/math/py-scipy/patches/patch-subprojects_xsf_include_xsf_amos_amos.h

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/py-scipy/Makefile
diff -u pkgsrc/math/py-scipy/Makefile:1.102 pkgsrc/math/py-scipy/Makefile:1.103
--- pkgsrc/math/py-scipy/Makefile:1.102 Thu Oct  9 07:57:49 2025
+++ pkgsrc/math/py-scipy/Makefile       Thu Oct 30 14:58:40 2025
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.102 2025/10/09 07:57:49 wiz Exp $
+# $NetBSD: Makefile,v 1.103 2025/10/30 14:58:40 adam Exp $
 
-DISTNAME=      scipy-1.16.2
+DISTNAME=      scipy-1.16.3
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
 CATEGORIES=    math python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=s/scipy/}

Index: pkgsrc/math/py-scipy/distinfo
diff -u pkgsrc/math/py-scipy/distinfo:1.62 pkgsrc/math/py-scipy/distinfo:1.63
--- pkgsrc/math/py-scipy/distinfo:1.62  Tue Sep 23 17:42:23 2025
+++ pkgsrc/math/py-scipy/distinfo       Thu Oct 30 14:58:40 2025
@@ -1,11 +1,11 @@
-$NetBSD: distinfo,v 1.62 2025/09/23 17:42:23 adam Exp $
+$NetBSD: distinfo,v 1.63 2025/10/30 14:58:40 adam Exp $
 
-BLAKE2s (scipy-1.16.2.tar.gz) = 46ebacdfe9bd52de90ff6b2f66e711c9124d637ba9cf35159056a007652b4876
-SHA512 (scipy-1.16.2.tar.gz) = 6b5c1ab6236af5d40850f8b77f8d47494dda9bccf814908ba306b4b3710359d18eb0dd880c05dc4f334cc298d0a2d54d271d5cd5b519190fcfba58524b1d8dce
-Size (scipy-1.16.2.tar.gz) = 30580599 bytes
+BLAKE2s (scipy-1.16.3.tar.gz) = 35b23ca11884eb3823b40220f990969306d2624565f452052b0bbb8c4d5a8432
+SHA512 (scipy-1.16.3.tar.gz) = 7386670d2be598f46425a5f2ac0194748c83ec006be0b0395a850a613bc12731669469aefe503c9db2521aba956325d44e7a75fa82e4c1e629202cafd1966aa5
+Size (scipy-1.16.3.tar.gz) = 30597883 bytes
 SHA1 (patch-scipy_ndimage_src___rank__filter__1d.cpp) = 55fc9396ea8268c7ae5e346a70b4fe8e43134c32
 SHA1 (patch-scipy_spatial___ckdtree.pyx) = 09f79827790edb78204cca7bbe25b5f373834dd4
 SHA1 (patch-scipy_special_boost__special__functions.h) = 9a345a5e81c090d16c6394e641624c504efbf4ea
 SHA1 (patch-scipy_special_wright.hh) = 56d65f9ed4bec96f0b927bbe42edd30fc6546454
 SHA1 (patch-scipy_stats___unuran_meson.build) = afa31bf66c9599c8ffc102f2013694305c7e8d03
-SHA1 (patch-subprojects_xsf_include_xsf_amos_amos.h) = bf8b0c344f9a8aaa825d2d1bb30684c8d4a8b020
+SHA1 (patch-subprojects_xsf_include_xsf_amos_amos.h) = c42696279efed5929ffdf73c59137ed3a7d724d0

Index: pkgsrc/math/py-scipy/patches/patch-subprojects_xsf_include_xsf_amos_amos.h
diff -u pkgsrc/math/py-scipy/patches/patch-subprojects_xsf_include_xsf_amos_amos.h:1.1 pkgsrc/math/py-scipy/patches/patch-subprojects_xsf_include_xsf_amos_amos.h:1.2
--- pkgsrc/math/py-scipy/patches/patch-subprojects_xsf_include_xsf_amos_amos.h:1.1      Wed Aug 20 12:19:24 2025
+++ pkgsrc/math/py-scipy/patches/patch-subprojects_xsf_include_xsf_amos_amos.h  Thu Oct 30 14:58:40 2025
@@ -1,16 +1,14 @@
-$NetBSD: patch-subprojects_xsf_include_xsf_amos_amos.h,v 1.1 2025/08/20 12:19:24 adam Exp $
+$NetBSD: patch-subprojects_xsf_include_xsf_amos_amos.h,v 1.2 2025/10/30 14:58:40 adam Exp $
 
 Prefer C++ headers.
 
---- subprojects/xsf/include/xsf/amos/amos.h.orig       2025-04-26 00:49:42.000000000 +0000
+--- subprojects/xsf/include/xsf/amos/amos.h.orig       2025-10-10 18:07:54.000000000 +0000
 +++ subprojects/xsf/include/xsf/amos/amos.h
-@@ -94,8 +94,8 @@
- 
+@@ -95,7 +95,7 @@
  #include <stdlib.h>
  
--#include <complex.h>
+ #include <complex>
 -#include <math.h>
-+#include <complex>
 +#include <cmath>
  #include <memory> // unique_ptr