CVS commit: pkgsrc/math/py-scipy

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

Module Name:    pkgsrc
Committed By:   adam
Date:           Wed Jun 12 08:57:43 UTC 2024

Modified Files:
        pkgsrc/math/py-scipy: Makefile distinfo

Log Message:
py-scipy: updated to 1.13.1

Issues closed for 1.13.1

BUG: \`scipy.ndimage.value_indices\` returns empty dict for \`intc\`/\`uintc\` dtype on Windows
DOC, MAINT: .jupyterlite.doit.db shows up untracked
DOC: optimize.root(method='lm') option
BUG: csr_array can no longer be initialized with 1D array
BUG: \`TestEig.test_falker\` fails on windows + MKL as well as...
BUG: Cannot find \`OpenBLAS\` on Cygwin
BUG: special.spherical_in: derivative at \`z=0, n=1\` incorrect
BUG: \`eigh\` fails for size 1 array with driver=evd
BUG: warning from \`optimize.least_squares\` for astropy with...
BUG: spatial: error in \`Rotation.align_vectors()\` with an infinite...
MAINT, TST: two types of failures observed on maintenance/1.13.x...
BUG: scipy.special.factorial2 doesn't handle \`uint32\` dtypes
BUG: scipy.stats.wilcoxon in 1.13 fails on 2D array with nan...
BUG: scipy.spatial.Delaunay, scipy.interpolate.LinearNDInterpolator...
BUG: stats.yulesimon: incorrect kurtosis values
BUG: incorrect origin tuple handling in ndimage \`minimum_filter\`...
BUG: spatial: \`Rotation.align_vectors()\` incorrect for anti-parallel...
BUG: sparse matrix creation in 1.13 with indices not summing...
BUG: stats.zipf: incorrect pmf values
CI: scipy installation failing in umfpack tests

Pull requests for 1.13.1

MAINT: added doc/source/.jupyterlite.doit.db to .gitignore See...
BUG: sparse: align dok_array.pop() to dict.pop() for case with...
BUG: sync pocketfft again
REL, MAINT: prep for 1.13.1
DOC: optimize: fix wrong optional argument name in \`root(method="lm")\`.
DOC: add missing deprecations from 1.13.0 release notes
MAINT/DOC: fix syntax in 1.13.0 release notes
BUG: sparse: Clean up 1D input handling to sparse array/matrix...
DOC: remove spurious backtick from release notes
BUG: linalg: fix ordering of complex conj gen eigenvalues
TST: tolerance bumps for the conda-forge builds
TST: compare absolute values of U and VT in pydata-sparse SVD...
BUG: Include Python.h before system headers.
BUG: linalg: fix eigh(1x1 array, driver='evd') f2py check
BUG: \`spherical_in\` for \`n=0\` and \`z=0\`
BLD: Fix error message for f2py generation fail
TST: Adapt to \`__array__(copy=True)\`
BLD: Move Python-including files to start of source.
REV: 1.13.x: revert changes to f2py and tempita handling in meson.build...
update openblas to 0.3.27
BUG: Fix error with 180 degree rotation in Rotation.align_vectors()...
MAINT: optimize.linprog: fix bug when integrality is a list of...
MAINT: stats.wilcoxon: fix failure with multidimensional \`x\`...
MAINT: lint: temporarily disable UP031
BUG: handle uint arrays in factorial{,2,k}
BUG: prevent QHull message stream being closed twice
MAINT/DEV: lint: disable UP032
BUG: fix Vor/Delaunay segfaults
BUG: ndimage.value_indices: deal with unfixed types
BUG: ndimage: fix origin handling for \`{minimum, maximum}_filter\`
MAINT: stats.yulesimon: fix kurtosis
BUG: sparse: Fix summing duplicates for CSR/CSC creation from...
BUG: stats: Fix \`zipf.pmf\` and \`zipfian.pmf\` for int32 \`k\`
CI: pin Python for MacOS conda


To generate a diff of this commit:
cvs rdiff -u -r1.81 -r1.82 pkgsrc/math/py-scipy/Makefile
cvs rdiff -u -r1.51 -r1.52 pkgsrc/math/py-scipy/distinfo

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:1.81 pkgsrc/math/py-scipy/Makefile:1.82
--- pkgsrc/math/py-scipy/Makefile:1.81  Tue Jun  4 20:46:45 2024
+++ pkgsrc/math/py-scipy/Makefile       Wed Jun 12 08:57:43 2024
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.81 2024/06/04 20:46:45 markd Exp $
+# $NetBSD: Makefile,v 1.82 2024/06/12 08:57:43 adam Exp $
 
-DISTNAME=      scipy-1.13.0
+DISTNAME=      scipy-1.13.1
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
 CATEGORIES=    math python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=s/scipy/}
@@ -14,10 +14,9 @@ TOOL_DEPENDS+=       ${PYPKGPREFIX}-cython>=3.
 # Package directly expresses a meson minimum; we need higher to pick up our
 # multi-version build fixes.
 TOOL_DEPENDS+= meson>=1.2.2nb1:../../devel/meson
-TOOL_DEPENDS+= ${PYPKGPREFIX}-meson_python-[0-9]*:../../devel/py-meson_python
+TOOL_DEPENDS+= ${PYPKGPREFIX}-meson_python>=0.15.0:../../devel/py-meson_python
 TOOL_DEPENDS+= ${PYPKGPREFIX}-wheel-[0-9]*:../../devel/py-wheel
-DEPENDS+=      ${PYPKGPREFIX}-pybind11>=2.12:../../devel/py-pybind11
-DEPENDS+=      ${PYPKGPREFIX}-pythran>=0.12.0:../../math/py-pythran
+TOOL_DEPENDS+= ${PYPKGPREFIX}-pythran>=0.14.0:../../math/py-pythran
 TEST_DEPENDS+= ${PYPKGPREFIX}-hypothesis-[0-9]*:../../devel/py-hypothesis
 TEST_DEPENDS+= ${PYPKGPREFIX}-mpmath-[0-9]*:../../math/py-mpmath
 TEST_DEPENDS+= ${PYPKGPREFIX}-pooch-[0-9]*:../../devel/py-pooch

Index: pkgsrc/math/py-scipy/distinfo
diff -u pkgsrc/math/py-scipy/distinfo:1.51 pkgsrc/math/py-scipy/distinfo:1.52
--- pkgsrc/math/py-scipy/distinfo:1.51  Fri Apr 19 19:24:25 2024
+++ pkgsrc/math/py-scipy/distinfo       Wed Jun 12 08:57:43 2024
@@ -1,8 +1,8 @@
-$NetBSD: distinfo,v 1.51 2024/04/19 19:24:25 adam Exp $
+$NetBSD: distinfo,v 1.52 2024/06/12 08:57:43 adam Exp $
 
-BLAKE2s (scipy-1.13.0.tar.gz) = a46f63222f9d7e9447f680bd460c5390cb851355fa8ad7571e144247d31ecb6a
-SHA512 (scipy-1.13.0.tar.gz) = 9bd6fd3f76742a07e5bb003edf4c0e3a82edf749077502fbce3d16fe595d455846edcf57db12ec0a9d4792803e974355362d919047414badfcaededf1e4343f7
-Size (scipy-1.13.0.tar.gz) = 57204550 bytes
+BLAKE2s (scipy-1.13.1.tar.gz) = 62fb276532801ee896d00a3886122f9fa9b146834d148086f226e9fc71bf3858
+SHA512 (scipy-1.13.1.tar.gz) = 28aafdbcae7229a3d11f192683b703cb485d45e4d90413d6564df3d9005bc8fd4df8bd92caffe657666828cd7253e7e0363c0948c74a1b8f3f3b7d4f4cfd9b36
+Size (scipy-1.13.1.tar.gz) = 57210720 bytes
 SHA1 (patch-scipy_spatial___ckdtree.pyx) = 09f79827790edb78204cca7bbe25b5f373834dd4
 SHA1 (patch-scipy_spatial_ckdtree_src_ckdtree__decl.h) = f05aa0f0ebbf49f119b17ce8646d2f496a557019
 SHA1 (patch-scipy_special_Faddeeva.hh) = 9f6c0bb808fc9be0a1c1b7e65395d29f13821233