Merge #32046

.homebrew-build-env

@@ -31,7 +31,7 @@ for l in readline bzip2 ntl; do
         CPATH="$HOMEBREW/opt/$l/include:$CPATH"
     fi
 done
-for l in "gcc/lib/gcc/10 gcc/lib/gcc/9"; do
+for l in "gcc/lib/gcc/11 gcc/lib/gcc/10 gcc/lib/gcc/9"; do
     if [ -d "$HOMEBREW/opt/$l" ]; then
         LIBRARY_PATH="$HOMEBREW/opt/$l:$LIBRARY_PATH"
         break

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.4.beta5", 
-    "version": "9.4.beta5", 
+    "title": "sagemath/sage: 9.4.beta6", 
+    "version": "9.4.beta6", 
     "upload_type": "software", 
-    "publication_date": "2021-07-18", 
+    "publication_date": "2021-07-24", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.4.beta5", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.4.beta6", 
             "relation": "isSupplementTo"
         }, 
         {

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.4.beta5, Release Date: 2021-07-18
+SageMath version 9.4.beta6, Release Date: 2021-07-24

build/bin/write-dockerfile.sh

@@ -8,13 +8,14 @@ shopt -s extglob
 SAGE_PACKAGE_LIST_ARGS="${2:- --has-file=spkg-configure.m4 :standard:}"
 WITH_SYSTEM_SPKG="${3:-yes}"
 IGNORE_MISSING_SYSTEM_PACKAGES="${4:-no}"
+EXTRA_SAGE_PACKAGES="${5:-_bootstrap}"
 #
 STRIP_COMMENTS="sed s/#.*//;"
 SAGE_ROOT=.
 export PATH="$SAGE_ROOT"/build/bin:$PATH
 SYSTEM_PACKAGES=
 CONFIGURE_ARGS="--enable-option-checking "
-for PKG_BASE in $($SAGE_ROOT/sage -package list --has-file=distros/$SYSTEM.txt $SAGE_PACKAGE_LIST_ARGS) _bootstrap; do
+for PKG_BASE in $($SAGE_ROOT/sage -package list --has-file=distros/$SYSTEM.txt $SAGE_PACKAGE_LIST_ARGS) $EXTRA_SAGE_PACKAGES; do
     PKG_SCRIPTS="$SAGE_ROOT"/build/pkgs/$PKG_BASE
     if [ -d $PKG_SCRIPTS ]; then
        SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/distros/$SYSTEM.txt

build/pkgs/_prereq/distros/opensuse.txt

@@ -15,7 +15,10 @@ perl
 python3
 tar
 bc
+which
+glibc-locale-base
 gcc
+gcc-c++
 # Needed if we download some packages from a https upstream URL
 ca-certificates
 # gunzip needed for ppl spkg

build/pkgs/arb/package-version.txt

@@ -1 +1 @@
-2.19.0
+2.19.0.p0

build/pkgs/arb/patches/arb-flint-2.8-compatibility-b6c8032e2da1b19eb7c5a5f5c2f3372643e3d170.patch

@@ -0,0 +1,46 @@
+From b6c8032e2da1b19eb7c5a5f5c2f3372643e3d170 Mon Sep 17 00:00:00 2001
+From: fredrik <fredrik.johansson@gmail.com>
+Date: Mon, 15 Mar 2021 11:56:24 +0100
+Subject: [PATCH] compatibility fix for latest flint
+
+---
+ acb_modular/epsilon_arg.c | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/acb_modular/epsilon_arg.c b/acb_modular/epsilon_arg.c
+index e1332725..b42a64ad 100644
+--- a/acb_modular/epsilon_arg.c
++++ b/acb_modular/epsilon_arg.c
+@@ -12,7 +12,7 @@
+ #include "acb_modular.h"
+
+ static int
+-fmpz_kronecker(const fmpz_t a, const fmpz_t b)
++fmpz_kronecker1(const fmpz_t a, const fmpz_t b)
+ {
+     if (fmpz_sgn(b) < 0)
+     {
+@@ -20,7 +20,7 @@ fmpz_kronecker(const fmpz_t a, const fmpz_t b)
+         fmpz_t t;
+         fmpz_init(t);
+         fmpz_neg(t, b);
+-        r = fmpz_kronecker(a, t);
++        r = fmpz_kronecker1(a, t);
+         fmpz_clear(t);
+         return r;
+     }
+@@ -58,12 +58,12 @@ acb_modular_epsilon_arg(const psl2z_t g)
+
+         if (cc % 2 == 1)
+         {
+-            u = fmpz_kronecker(a, c);
++            u = fmpz_kronecker1(a, c);
+             aa = aa*bb + 2*aa*cc - 3*cc + cc*dd*(1-aa*aa);
+         }
+         else
+         {
+-            u = fmpz_kronecker(c, a);
++            u = fmpz_kronecker1(c, a);
+             aa = aa*bb - aa*cc + 3*aa - 3 + cc*dd*(1-aa*aa);
+         }
+

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=70b46d821bd601ddf3e6b6d6bfcfb288d81018d1
-md5=5d83741b640f1862df88c4d12bdc7220
-cksum=150019468
+sha1=c55867da552d5ed30328a35a480dc1ab14ec232c
+md5=5cbace690cae40b89993e3a71fe4200c
+cksum=912186647

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-5e648d88fead1ead94ca608e60c49c156e2291aa
+25ff4f4daf3cd93053f7b8c1e39117ce67e96b6c

build/pkgs/deformation/SPKG.rst

@@ -16,4 +16,7 @@ GLPv3
 Upstream Contact
 ----------------
 
--  Sebastian Pancratz: sebastian.pancratz@gmail.com
+-  Sebastian Pancratz: sebastian.pancratz@gmail.com, sage-devel@googlegroups.com
+
+-  We use the fork at https://github.com/sagemath/deformation
+   the fork uses GMP instead of MPIR, and Flint 2.7+.

build/pkgs/deformation/checksums.ini

@@ -1,4 +1,5 @@
 tarball=deformation-VERSION.tar.bz2
-sha1=317fb76c884fa4b6b92ed0b171a0b9fdb3bdc90f
-md5=e4af9b93ddc85ebb52d9fa1fedd75887
-cksum=4134074975
+sha1=0f5fd78a91da207d06b5be59bf466f16c2614eda
+md5=e2c365e20778117d402fb664fc145d72
+cksum=3789646827
+upstream_url=https://github.com/sagemath/deformation/archive/refs/tags/VERSION.tar.gz

build/pkgs/deformation/package-version.txt

@@ -1 +1 @@
-d05941b.p0
+20210503

build/pkgs/flint/spkg-configure.m4

@@ -1,14 +1,8 @@
 SAGE_SPKG_CONFIGURE([flint], [
-    AC_REQUIRE([SAGE_SPKG_CONFIGURE_MPFR])
-    AC_REQUIRE([SAGE_SPKG_CONFIGURE_NTL])
-    AC_MSG_CHECKING([installing mpfr or ntl? ])
-    if test x$sage_spkg_install_mpfr = xyes -o x$sage_spkg_install_ntl = xyes; then
-        AC_MSG_RESULT([yes; install flint as well])
-        sage_spkg_install_flint=yes
-    else
+    SAGE_SPKG_DEPCHECK([mpfr ntl], [
         AC_CHECK_HEADER(flint/flint.h, [
-          dnl fmpz_mat_is_hadamard appears in Flint 2.5.0
-          AC_SEARCH_LIBS([fmpz_mat_is_hadamard], [flint], [
+          dnl fmpz_mod_ctx_init appears in Flint 2.6.0
+          AC_SEARCH_LIBS([fmpz_mod_ctx_init], [flint], [
             dnl check that NTL is linked in
             AC_SEARCH_LIBS([fmpz_poly_get_ZZX], [flint], [
 
@@ -27,13 +21,11 @@ SAGE_SPKG_CONFIGURE([flint], [
             ], [sage_spkg_install_flint=yes])
           ], [sage_spkg_install_flint=yes])
         ], [sage_spkg_install_flint=yes])
-    fi
+    ])
 ], [], [], [
      if test x$sage_spkg_install_flint = xyes; then
         AC_SUBST(SAGE_FLINT_PREFIX, ['$SAGE_LOCAL'])
-        AC_MSG_RESULT([using Sage's flint SPKG])
      else
         AC_SUBST(SAGE_FLINT_PREFIX, [''])
-        AC_MSG_RESULT([using flint library from the system])
      fi
 ])

build/pkgs/gcc/spkg-configure.m4

@@ -149,8 +149,8 @@ SAGE_SPKG_CONFIGURE_BASE([gcc], [
                     # Install our own GCC if the system-provided one is older than gcc-4.8.
                     SAGE_SHOULD_INSTALL_GCC([you have $CXX version $GXX_VERSION, which is quite old])
                 ],
-                [1[[1-9]].*], [
-                    # Install our own GCC if the system-provided one is newer than 10.x.
+                [1[[2-9]].*], [
+                    # Install our own GCC if the system-provided one is newer than 11.x.
                     # See https://trac.sagemath.org/ticket/29456
                     SAGE_SHOULD_INSTALL_GCC([$CXX is g++ version $GXX_VERSION, which is too recent for this version of Sage])
                 ],

build/pkgs/llvm/SPKG.rst

@@ -0,0 +1,22 @@
+llvm: The LLVM Compiler Infrastructure, including the Clang C/C++/Objective-C compiler
+======================================================================================
+
+Description
+-----------
+
+The LLVM Project is a collection of modular and reusable compiler and toolchain technologies.
+
+Clang is an "LLVM native" C/C++/Objective-C compiler.
+
+The libc++ and libc++ ABI projects provide a standard conformant and high-performance
+implementation of the C++ Standard Library, including full support for C++11 and C++14.
+
+License
+-------
+
+Apache 2.0 License with LLVM exceptions
+
+Upstream Contact
+----------------
+
+https://llvm.org/

build/pkgs/llvm/distros/alpine.txt

@@ -0,0 +1 @@
+clang

build/pkgs/llvm/distros/arch.txt

@@ -0,0 +1 @@
+clang

build/pkgs/llvm/distros/cygwin.txt

@@ -0,0 +1 @@
+clang

build/pkgs/llvm/distros/debian.txt

@@ -0,0 +1 @@
+llvm-toolchain

build/pkgs/llvm/distros/fedora.txt

@@ -0,0 +1 @@
+clang

build/pkgs/llvm/distros/freebsd.txt

@@ -0,0 +1 @@
+devel/llvm

build/pkgs/llvm/distros/gentoo.txt

@@ -0,0 +1 @@
+sys-devel/clang

build/pkgs/llvm/distros/homebrew.txt

@@ -0,0 +1 @@
+llvm

build/pkgs/llvm/distros/macports.txt

@@ -0,0 +1 @@
+clang

build/pkgs/llvm/distros/nix.txt

@@ -0,0 +1 @@
+clang

build/pkgs/llvm/distros/openbsd.txt

@@ -0,0 +1 @@
+devel/llvm

build/pkgs/llvm/distros/opensuse.txt

@@ -0,0 +1 @@
+llvm

build/pkgs/llvm/distros/slackware.txt

@@ -0,0 +1 @@
+llvm

build/pkgs/llvm/distros/void.txt

@@ -0,0 +1 @@
+clang

build/pkgs/llvm/spkg-configure.m4

@@ -0,0 +1,3 @@
+SAGE_SPKG_CONFIGURE([llvm], [
+  sage_require_llvm=no
+])

build/pkgs/llvm/spkg-install

@@ -0,0 +1,4 @@
+#! /usr/bin/env bash
+echo Error: llvm is not installed.
+echo Please install it, for example using the system packages recommended by ./configure
+exit 1

build/pkgs/llvm/type

@@ -0,0 +1 @@
+optional

build/pkgs/lrslib/checksums.ini

@@ -1,4 +1,5 @@
 tarball=lrslib-VERSION.tar.gz
-sha1=c644600ca4a51eb08e61ba175e1d4ec999dc3e4b
-md5=bb435ccdd5faf292102e246827926680
-cksum=3830123478
+sha1=4723f2b96e4b59d8366316b84214d6221b7ee7ce
+md5=b379d2bdef0f5200c6274d9c50361b7c
+cksum=1216904185
+upstream_url=https://github.com/mkoeppe/lrslib/releases/download/lrslib-VERSION/lrslib-VERSION.tar.gz

build/pkgs/lrslib/package-version.txt

@@ -1 +1 @@
-062+autotools-2017-03-03.p1
+071b+autotools-2021-07-13

build/pkgs/lrslib/spkg-configure.m4

@@ -2,6 +2,24 @@ SAGE_SPKG_CONFIGURE([lrslib], [
     dnl System lrslib may already be 7.x, which may be compiled with FLINT
     SAGE_SPKG_DEPCHECK([gmp mpir flint], [
         AC_CHECK_PROGS([LRSNASH], [lrsnash])
-        AS_IF([test -z "$LRSNASH"], [sage_spkg_install_lrslib=yes])
+        AS_IF([test -z "$LRSNASH"], [
+            sage_spkg_install_lrslib=yes
+        ], [
+            AC_MSG_CHECKING([whether $LRSNASH can handle the new input format])
+            cat > conftest.lrsnash <<EOF
+1 1
+
+0
+
+0
+EOF
+            AS_IF([$LRSNASH conftest.lrsnash >& AS_MESSAGE_LOG_FD 2>&1], [
+                AC_MSG_RESULT([yes])
+            ], [
+                AC_MSG_RESULT([no])
+                sage_spkg_install_lrslib=yes
+            ])
+            rm -f conftest.lrsnash
+        ])
     ])
 ])

build/pkgs/lrslib/spkg-install.in

@@ -1,4 +1,4 @@
 cd src/
-sdh_configure CPPFLAGS="-DLRS_QUIET $CPPFLAGS"
+sdh_configure
 sdh_make
 sdh_make_install

build/pkgs/ntl/spkg-configure.m4

@@ -47,8 +47,14 @@ SAGE_SPKG_CONFIGURE([ntl], [
         ntl_inc_ntl_dir=`AS_DIRNAME(["$gl_cv_absolute_NTL_ZZ_h"])`
         ntl_inc_dir=`AS_DIRNAME(["$ntl_inc_ntl_dir"])`
         ntl_prefix=`AS_DIRNAME(["$ntl_inc_dir"])`
-        AC_SUBST(NTL_INCDIR, [$ntl_inc_dir])
-        AC_SUBST(NTL_LIBDIR, [$ntl_prefix/lib])
+        PKG_CHECK_VAR([ntl_includedir], [ntl], [includedir])
+        AS_IF([test "x$ntl_includedir" = x], [AC_SUBST(NTL_INCDIR, [$ntl_inc_dir])],
+              [AC_SUBST(NTL_INCDIR, [$ntl_includedir])]
+             )
+        PKG_CHECK_VAR([ntl_libdir], [ntl], [libdir])
+        AS_IF([test "x$ntl_libdir" = x], [AC_SUBST(NTL_LIBDIR, [$ntl_prefix/lib])],
+              [AC_SUBST(NTL_LIBDIR, [$ntl_libdir])]
+             )
     fi
 ])
 

build/pkgs/numpy/lapack_conf.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env sage-bootstrap-python
+#!/usr/bin/env python3
 
 import pkgconfig, os
 

build/pkgs/pip/install-requires.txt

@@ -1 +1,2 @@
-pip >=20.2.3
+pip >=21.1.0
+# for use of "pip --use-feature=in-tree-build" by the Sage distribution

build/pkgs/polymake/SPKG.rst

@@ -51,7 +51,7 @@ you will need the local::lib Perl module installed::
    cpan -i XML::Writer XML::LibXML XML::LibXSLT File::Slurp Term::ReadLine::Gnu JSON SVG MongoDB
 
 Several Sage packages should be installed before installing the polymake
-package to give a more featureful Polymake installation:
+package to give a more featureful Polymake installation::
 
    sage -i 4ti2 latte_int topcom qhull
 
@@ -65,6 +65,13 @@ Information on missing Polymake prerequisites after installing polymake::
    (sage-sh) $ polymake
    polytope> show_unconfigured;
 
+It is strongly recommended to also install JuPyMake::
+
+  sage -i jupymake
+
+When JuPyMake is present, Sage is able to use a more robust interface
+to Polymake.
+
 
 Debugging polymake install problems
 -----------------------------------

build/pkgs/polymake/checksums.ini

@@ -1,4 +1,5 @@
 tarball=polymake-VERSION-minimal.tar.bz2
-sha1=e02bc7590910cff633c612cd95baa0c3aeade036
-md5=b0c6332c148060741d84b6f0eaed8343
-cksum=1380625742
+sha1=5370b16300ff8aed4eb5fa6bb5232d25935e6303
+md5=8f6a8e87e3b8bf5ccf22f26790a4dd1a
+cksum=1398515202
+upstream_url=https://polymake.org/lib/exe/fetch.php/download/polymake-VERSION-minimal.tar.bz2

build/pkgs/polymake/package-version.txt

@@ -1 +1 @@
-3.4
+4.4