CVS commit: pkgsrc/math/py-scipy

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

Module Name:    pkgsrc
Committed By:   adam
Date:           Wed Feb 19 09:23:16 UTC 2025

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

Log Message:
py-scipy: updated to 1.15.2

Issues closed for 1.15.2

BUG: _lib: crash in uarray on interpreter exit with a free-threaded...
BUG: special: Unchecked calls of malloc() and calloc() in specfun.h
BUG: Segmentation Fault when passing a special array to ``scipy.cluster.hierarch``...
BUG: median_filter on 1D array crashes with memory corruption...
BUG: special: Potential memory leak in the function ``besy()``...
BUG: ndimage.median_filter: Heap corruption with scipy 1.15
BUG: signal.medfilt and ndimage.median_filter not returning correct...
BUG: special: Unchecked malloc in stirling2.h
BUG: Matrix multiplication of a coo_matrix with an invalid type...
BLD: libhighs.a static library is installed
BUG: interpolate test_bary_rational.TestAAA.test_basic_functions...
BUG: ``scipy.stats.zmap`` returns incorrect values for complex...
BUG: spatial.transform: ``Rotation.from_matrix()`` uses inaccurate...
BUG: io.loadmat thinks a file with a lot of zeros is valid
BUG: Slicing sparse matrix with ``None`` gives result different...
MAINT: scipy.stats: test_regressZEROX SIMD warning for certain...

Pull requests for 1.15.2

BUG: immortalize uarray global strings in order to prevent negative...
BUG: special: Fix unchecked memory allocations in ``specfun.h``
BUG: cluster: ``cophenet`` intercept invalid linkage matrix count
REL, MAINT: prep for 1.15.2
MAINT: stats.Mixture: make return type consistent when ``shape``...
MAINT: stats.Mixture: fix inverse functions when mean is undefined
BUG: special: Fix unchecked malloc in stirling2.h
TST: turn off dtype check due to endianness
BUG: sparse: fix selecting wrong dtype for coo coords
TST: interpolate: small tolerance bump to TestAAA.test_basic_functions
MAINT: Stop installing ``libhighs``
BUG: sparse.linalg.norm: add test for and fix return type
BUG: sparse: revert NotImplemented return values in dot and matmul
DOC: sparse.linalg: add two recent functions to namespace and...
BUG: wrap median_filter stability
MAINT: stats.zmap: restore support for complex data
MAINT: integrate.cumulative_simpson: bump test tolerance
BUG: scipy.spatial: Fix inaccurate orthonormalization in ``Rotation.from_matrix(``...
BUG: special: Fix a memory leak in the AMOS function besy().
CI: migrate Linux aarch64 jobs to GitHub Actions, add cp313t...
BUG: io.loadmat: throw error on file containing all zeros
BUG: sparse: fix spmatrix indexing with None and implicit padding...
MAINT: stats: pearsonr SIMD-related shim


To generate a diff of this commit:
cvs rdiff -u -r1.94 -r1.95 pkgsrc/math/py-scipy/Makefile
cvs rdiff -u -r1.31 -r1.32 pkgsrc/math/py-scipy/PLIST
cvs rdiff -u -r1.58 -r1.59 pkgsrc/math/py-scipy/distinfo
cvs rdiff -u -r1.1 -r1.2 \
    pkgsrc/math/py-scipy/patches/patch-scipy_special_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:1.94 pkgsrc/math/py-scipy/Makefile:1.95
--- pkgsrc/math/py-scipy/Makefile:1.94  Tue Jan 14 18:18:06 2025
+++ pkgsrc/math/py-scipy/Makefile       Wed Feb 19 09:23:15 2025
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.94 2025/01/14 18:18:06 gdt Exp $
+# $NetBSD: Makefile,v 1.95 2025/02/19 09:23:15 adam Exp $
 
-DISTNAME=      scipy-1.15.1
+DISTNAME=      scipy-1.15.2
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
-PKGREVISION=   1
 CATEGORIES=    math python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=s/scipy/}
 

Index: pkgsrc/math/py-scipy/PLIST
diff -u pkgsrc/math/py-scipy/PLIST:1.31 pkgsrc/math/py-scipy/PLIST:1.32
--- pkgsrc/math/py-scipy/PLIST:1.31     Sun Jan  5 08:58:47 2025
+++ pkgsrc/math/py-scipy/PLIST  Wed Feb 19 09:23:15 2025
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.31 2025/01/05 08:58:47 adam Exp $
+@comment $NetBSD: PLIST,v 1.32 2025/02/19 09:23:15 adam Exp $
 ${PYSITELIB}/${WHEEL_INFODIR}/LICENSE.txt
 ${PYSITELIB}/${WHEEL_INFODIR}/METADATA
 ${PYSITELIB}/${WHEEL_INFODIR}/RECORD
@@ -1513,7 +1513,6 @@ ${PYSITELIB}/scipy/optimize/_highspy/_hi
 ${PYSITELIB}/scipy/optimize/_highspy/_highs_wrapper.py
 ${PYSITELIB}/scipy/optimize/_highspy/_highs_wrapper.pyc
 ${PYSITELIB}/scipy/optimize/_highspy/_highs_wrapper.pyo
-${PYSITELIB}/scipy/optimize/_highspy/libhighs.a
 ${PYSITELIB}/scipy/optimize/_isotonic.py
 ${PYSITELIB}/scipy/optimize/_isotonic.pyc
 ${PYSITELIB}/scipy/optimize/_isotonic.pyo

Index: pkgsrc/math/py-scipy/distinfo
diff -u pkgsrc/math/py-scipy/distinfo:1.58 pkgsrc/math/py-scipy/distinfo:1.59
--- pkgsrc/math/py-scipy/distinfo:1.58  Tue Jan 14 18:18:06 2025
+++ pkgsrc/math/py-scipy/distinfo       Wed Feb 19 09:23:15 2025
@@ -1,8 +1,8 @@
-$NetBSD: distinfo,v 1.58 2025/01/14 18:18:06 gdt Exp $
+$NetBSD: distinfo,v 1.59 2025/02/19 09:23:15 adam Exp $
 
-BLAKE2s (scipy-1.15.1.tar.gz) = 5ec6b4743ca6bfab9c01acb2ac0a6eef61688904c3af6b18c85395c6a82bf705
-SHA512 (scipy-1.15.1.tar.gz) = 92cb6a2cdb5a305eef0aa81baea4b90c14c0084c09ffbf62f2d6ee8dd5a08791a838838e2d4907356b5b07d0b4f74a81a8e861f81628bd9e5c7e0216e3f77b17
-Size (scipy-1.15.1.tar.gz) = 59407493 bytes
+BLAKE2s (scipy-1.15.2.tar.gz) = ff2662850a82d0f7108a0829324bdf23ac2f09006e341adc6d5d917ce8a41290
+SHA512 (scipy-1.15.2.tar.gz) = e772aa040622ef457478e08eb41471af33784cafc2022f091a30563f6abed067cdbae424a5ae86f9dab8c1adc67276794b67cb7cb7c7963ca55a38529df63834
+Size (scipy-1.15.2.tar.gz) = 59417316 bytes
 SHA1 (patch-scipy_ndimage_src___rank__filter__1d.cpp) = 55fc9396ea8268c7ae5e346a70b4fe8e43134c32
 SHA1 (patch-scipy_spatial___ckdtree.pyx) = 09f79827790edb78204cca7bbe25b5f373834dd4
 SHA1 (patch-scipy_spatial_ckdtree_src_ckdtree__decl.h) = f05aa0f0ebbf49f119b17ce8646d2f496a557019
@@ -11,6 +11,6 @@ SHA1 (patch-scipy_special_boost__special
 SHA1 (patch-scipy_special_meson.build) = db22da79b31a0fb8dbdac96f398463f4d24adfe0
 SHA1 (patch-scipy_special_stirling2.h) = 0aee0ba3de639f7bb87ecb6ae5bf9bd6d583d2b0
 SHA1 (patch-scipy_special_wright.hh) = 56d65f9ed4bec96f0b927bbe42edd30fc6546454
-SHA1 (patch-scipy_special_xsf_amos_amos.h) = 4d757b98ab6c98bac2d6e3b6f01f4ad5d02c2afb
+SHA1 (patch-scipy_special_xsf_amos_amos.h) = 13b9831eaf944f44e4f90c332896eb9a6f8a2e8b
 SHA1 (patch-scipy_special_xsf_specfun_specfun.h) = 67fa2ad7980bb836a0d490a8bc7891b535c9bf35
 SHA1 (patch-scipy_stats___unuran_meson.build) = afa31bf66c9599c8ffc102f2013694305c7e8d03

Index: pkgsrc/math/py-scipy/patches/patch-scipy_special_xsf_amos_amos.h
diff -u pkgsrc/math/py-scipy/patches/patch-scipy_special_xsf_amos_amos.h:1.1 pkgsrc/math/py-scipy/patches/patch-scipy_special_xsf_amos_amos.h:1.2
--- pkgsrc/math/py-scipy/patches/patch-scipy_special_xsf_amos_amos.h:1.1        Sun Jan  5 08:58:47 2025
+++ pkgsrc/math/py-scipy/patches/patch-scipy_special_xsf_amos_amos.h    Wed Feb 19 09:23:15 2025
@@ -1,11 +1,11 @@
-$NetBSD: patch-scipy_special_xsf_amos_amos.h,v 1.1 2025/01/05 08:58:47 adam Exp $
+$NetBSD: patch-scipy_special_xsf_amos_amos.h,v 1.2 2025/02/19 09:23:15 adam Exp $
 
 Prefer C++ headers.
 Fix error: 'isinf' was not declared in this scope; did you mean 'std::isinf'?
 
---- scipy/special/xsf/amos/amos.h.orig 2025-01-02 22:53:29.000000000 +0000
+--- scipy/special/xsf/amos/amos.h.orig 2025-02-16 22:01:46.000000000 +0000
 +++ scipy/special/xsf/amos/amos.h
-@@ -94,8 +94,11 @@
+@@ -94,10 +94,13 @@
  
  #include <stdlib.h>
  
@@ -13,9 +13,11 @@ Fix error: 'isinf' was not declared in t
 -#include <complex.h>
 +#include <cmath>
 +#include <complex>
-+
+ #include <memory>     // unique_ptr
+ 
 +using std::isinf;
 +using std::isnan;
- 
++
  namespace xsf {
  namespace amos {
+