sagemath: update to 10.5

common/shlibs

@@ -4202,7 +4202,7 @@ libsimavrparts.so.1 simavr-1.6_2
 libsword-1.8.1.so libsword-1.8.1_6
 libgivaro.so.9 givaro-4.1.1_1
 liblinbox.so.0 linbox-1.6.3_1
-libpari-gmp-tls.so.8 pari-2.15.0_1
+libpari-gmp-tls.so.9 pari-2.17.0_1
 libtree-sitter.so.0.24 tree-sitter-0.24.3_1
 libplanarity.so.0 planarity-3.0.1.1_1
 libgap.so.9 gap-4.13.0_1
@@ -4211,7 +4211,7 @@ libxcvt.so.0 libxcvt-0.1.1_1
 libgf2x.so.3 gf2x-1.3.0_1
 libntl.so.44 ntl-11.5.1_1
 libflint.so.19 flintlib-3.1.0_1
-libec.so.10 eclib-20220621_1
+libec.so.14 eclib-20241112_1
 libsymmetrica.so.2 symmetrica-3.0.1_1
 libLfunction.so.1 lcalc-2.0.4_1
 liblrcalc.so.2 lrcalc-2.1_1

srcpkgs/eclib/patches/fix-32bit-modrat.patch

@@ -0,0 +1,15 @@
+new_modrat is broken on 32 bit, revert to old_modrat
+
+--- a/libsrc/arith.cc
++++ b/libsrc/arith.cc
+@@ -429,8 +430,8 @@ int new_modrat(long n, long m, long& a, long& b);
+
+ int modrat(long n, long m, long& a, long& b)
+ {
+-  // return old_modrat(n, m, a, b);
+-  return new_modrat(n, m, a, b);
++  return old_modrat(n, m, a, b);
++  //return new_modrat(n, m, a, b);
+ }
+
+ int old_modrat(long n, long m, long& a, long& b)

srcpkgs/eclib/template

@@ -1,6 +1,6 @@
 # Template file for 'eclib'
 pkgname=eclib
-version=20240408
+version=20241112
 revision=1
 build_style=gnu-configure
 configure_args="--with-flint --with-boost"
@@ -11,7 +11,7 @@ license="GPL-2.0-or-later"
 homepage="https://github.com/JohnCremona/eclib"
 changelog="https://github.com/JohnCremona/eclib/releases"
 distfiles="https://github.com/JohnCremona/eclib/releases/download/v${version}/eclib-${version}.tar.bz2"
-checksum=3ba908e2019de53fcba141449caa6fa82f03605bf83bf9da8092df538adabe7c
+checksum=30765c27ca1420141f83517897119d0185fea9b31132392170ddae40b060e46f
 
 eclib-devel_package() {
 	depends="${sourcepkg}>=${version}_${revision} ntl-devel"

srcpkgs/giac/template

@@ -1,6 +1,6 @@
 # Template file for 'giac'
 pkgname=giac
-version=1.9.0.995
+version=1.9.0.998
 revision=1
 build_style=gnu-configure
 configure_args="--disable-micropy --disable-quickjs"
@@ -15,7 +15,7 @@ license="GPL-3.0-or-later"
 homepage="https://www-fourier.ujf-grenoble.fr/~parisse/giac.html"
 changelog="https://www-fourier.ujf-grenoble.fr/~parisse/install_en#new"
 distfiles="https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/giac_${version%.*}-${version##*.}.tar.gz"
-checksum=b84b44287d260483ceea6703e12c5efcd67977b0f8f942e4fce20c31f837bcb3
+checksum=7f490a56af52c18cfdb53a2370f31fe05d9e96c8456090c541c3f51e049de1e4
 
 # need more than 4*65536 stack, see try_parse() in gen.cc line 11812
 LDFLAGS="-Wl,-z,stack-size=2097152"
@@ -40,7 +40,7 @@ post_extract() {
 	touch doc/en/tutoriel.stamp
 	# remove a binary that works only for a particular host
 	# the binary will be rebuilt using host compiler
-	rm src/mkjs
+	rm -f src/mkjs
 }
 
 pre_configure() {

srcpkgs/gp2c/template

@@ -1,6 +1,6 @@
 # Template file for 'gp2c'
 pkgname=gp2c
-version=0.0.13
+version=0.0.14
 revision=1
 build_style=gnu-configure
 hostmakedepends="perl"
@@ -10,6 +10,6 @@ short_desc="PARI/GP Computer Algebra System - gp2c compiler"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="GPL-2.0-or-later"
 homepage="http://pari.math.u-bordeaux.fr/"
-changelog="http://pari.math.u-bordeaux.fr/cgi-bin/gitweb.cgi?p=gp2c.git;a=blob_plain;f=ChangeLog;hb=HEAD"
+changelog="http://pari.math.u-bordeaux.fr/cgi-bin/sgitweb.cgi?p=gp2c.git;a=blob_plain;f=ChangeLog;hb=HEAD"
 distfiles="${homepage}pub/pari/GP2C/${pkgname}-${version}.tar.gz"
-checksum=261374eca73ebd76c112a9593dca28b64812aa762561fda5a4b2c2cd79a69d36
+checksum=af6112cc02940457e239da4433d1a0d8da60eeef29f7cc722f64cd4ac00b7b30

srcpkgs/lcalc/template

@@ -1,7 +1,7 @@
 # Template file for 'lcalc'
 pkgname=lcalc
 version=2.0.5
-revision=2
+revision=3
 build_style=gnu-configure
 configure_args="--with-pari"
 hostmakedepends="automake libtool pkg-config gengetopt"

srcpkgs/pari/patches/fix-nproc.patch

@@ -0,0 +1,18 @@
+Prefer "number of online processors" since some cpus will overreport
+the total number of cpus.
+
+See: https://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=2593#25
+
+--- a/src/mt/pthread.c
++++ b/src/mt/pthread.c
+@@ -139,7 +139,9 @@ void mt_broadcast(GEN code) {(void) code;}
+ void pari_mt_init(void)
+ {
+   pari_mt = NULL;
+-#ifdef _SC_NPROCESSORS_CONF
++#ifdef _SC_NPROCESSORS_ONLN
++  if (!pari_mt_nbthreads) pari_mt_nbthreads = sysconf(_SC_NPROCESSORS_ONLN);
++#elif _SC_NPROCESSORS_CONF
+   if (!pari_mt_nbthreads) pari_mt_nbthreads = sysconf(_SC_NPROCESSORS_CONF);
+ #elif defined(_WIN32)
+   if (!pari_mt_nbthreads) pari_mt_nbthreads = win32_nbthreads();

srcpkgs/pari/template

@@ -1,6 +1,6 @@
 # Template file for 'pari'
 pkgname=pari
-version=2.15.5
+version=2.17.1
 revision=1
 build_style=configure
 build_helper=qemu
@@ -17,9 +17,9 @@ short_desc="Fast computations library in number theory"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="GPL-2.0-or-later"
 homepage="https://pari.math.u-bordeaux.fr"
-changelog="https://pari.math.u-bordeaux.fr/cgi-bin/gitweb.cgi?p=pari.git;a=blob_plain;f=CHANGES;hb=refs/heads/pari-${version%.*}"
+changelog="https://pari.math.u-bordeaux.fr/cgi-bin/sgitweb.cgi?p=pari.git;a=blob_plain;f=CHANGES;hb=refs/heads/pari-${version%.*}"
 distfiles="https://pari.math.u-bordeaux.fr/pub/pari/unix/pari-${version}.tar.gz"
-checksum=0efdda7515d9d954f63324c34b34c560e60f73a81c3924a71260a2cc91d5f981
+checksum=67ba6f3071233725258541e4f174b5efbc64c65ae5115bade9edfc45f1fde5dc
 
 build_options="x11 pthreads"
 build_options_default="x11 pthreads"
@@ -56,6 +56,11 @@ pre_configure() {
 	if [ "$CROSS_BUILD" ]; then
 		export RUNTEST="/usr/bin/qemu-$XBPS_TARGET_QEMU_MACHINE-static"
 	fi
+	if [ "${XBPS_WORDSIZE}" = 32 ] && [ $(nproc) -gt 4 ]; then
+		# for 32 bit, limit nbthreads to 4, to avoid memory issues, see
+		# https://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=2593
+		export GPTESTOPT='-D nbthreads=4'
+	fi
 }
 
 pari-devel_package() {

srcpkgs/python3-cypari2/patches/165.patch

@@ -0,0 +1,38 @@
+See: https://github.com/sagemath/cypari2/pull/165
+and https://github.com/sagemath/sage/pull/38749
+
+From 0a5a7b42e53d065f8d78bdaa8181d6afa20d1f4f Mon Sep 17 00:00:00 2001
+From: Antonio Rojas <arojas@archlinux.org>
+Date: Tue, 1 Oct 2024 18:54:19 +0200
+Subject: [PATCH] Add pari_PRIMES declaration
+
+Needed to port sagemath to work with pari 2.17
+---
+ cypari2/paridecl.pxd | 1 +
+ cypari2/types.pxd    | 1 +
+ 2 files changed, 2 insertions(+)
+
+diff --git a/cypari2/paridecl.pxd b/cypari2/paridecl.pxd
+index 29cb8ef..9ccf336 100644
+--- a/cypari2/paridecl.pxd
++++ b/cypari2/paridecl.pxd
+@@ -118,6 +118,7 @@ cdef extern from *:     # PARI headers already included by types.pxd
+     extern PariOUT* pariOut
+     extern PariOUT* pariErr
+     extern byteptr diffptr
++    extern pari_prime* pari_PRIMES
+
+     ###############################################
+     #                                             #
+diff --git a/cypari2/types.pxd b/cypari2/types.pxd
+index 9ee4fe6..7f00b52 100644
+--- a/cypari2/types.pxd
++++ b/cypari2/types.pxd
+@@ -24,6 +24,7 @@ cdef extern from "pari/pari.h":
+     ctypedef long* GEN
+     ctypedef char* byteptr
+     ctypedef unsigned long pari_sp
++    ctypedef unsigned long pari_prime
+
+     # PARI types
+     enum: