Merge tag '9.4.beta6' into t/31881/realset__extend_constructors_so_th…

…at_they_can_build_manifold_objects

SageMath version 9.4.beta6, Release Date: 2021-07-24

.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/sage-dist-helpers

@@ -64,6 +64,10 @@
 #    If $SAGE_DESTDIR is not set then the command is run with $SAGE_SUDO, if
 #    set.
 #
+# - sdh_pip_uninstall [...]
+#
+#    Runs `pip uninstall` with the given arguments.  If unsuccessful, it displays a warning.
+#
 # - sdh_cmake [...]
 #
 #    Runs `cmake` in the current directory with the given arguments, as well as
@@ -266,6 +270,22 @@ sdh_store_and_pip_install_wheel() {
     fi
     $sudo sage-pip-install $root "$wheel" || \
         sdh_die "Error installing ${wheel##*/}"
+    if [ -n "${SAGE_PKG_DIR}" ]; then
+        # Record name of installed distribution name for uninstallation.
+        wheel=${wheel##*/}
+        echo "${wheel%%-*}" >> ${SAGE_PKG_DIR}/spkg-piprm-requirements.txt
+    fi
+}
+
+sdh_pip_uninstall() {
+    # --disable-pip-version-check: Don't periodically check PyPI to determine whether a new version of pip is available
+    # --no-input: Disable prompting for input.
+    # --yes: Don't ask for confirmation of uninstall deletions
+    # See sage-pip-install for a discussion of the other flags.
+    python3 -m pip uninstall --isolated --disable-pip-version-check --yes --no-input "$@"
+    if [ $? -ne 0 ]; then
+        echo "Warning: pip exited with status $?" >&2
+    fi
 }
 
 sdh_cmake() {

build/bin/sage-spkg

@@ -295,12 +295,6 @@ export SAGE_SPKG_INST="$SAGE_INST_LOCAL/var/lib/sage/installed"
 export SAGE_SPKG_SCRIPTS="$SAGE_INST_LOCAL/var/lib/sage/scripts"
 export SAGE_SPKG_WHEELS="$SAGE_INST_LOCAL/var/lib/sage/wheels"
 
-# USE_LOCAL_SCRIPTS is a flag that if non-empty will cause
-# this script to try to install the package using local metadata
-# i.e. use upstream tarballs (vs spkgs) and scripts located in build/pkgs/$PKG_BASE
-# the value of this flag is set in the next codeblock
-USE_LOCAL_SCRIPTS=
-
 # PKG_SRC should look like "package-VERSION" or just "package".
 # If VERSION matches the version in build/pkgs or there is no version
 # specified, use the local scripts; otherwise we try to find a package
@@ -315,7 +309,6 @@ if [ -z "$PKG_VER" ]; then
 else
     PKG_NAME="${PKG_BASE}-${PKG_VER}"
 fi
-USE_LOCAL_SCRIPTS=yes
 PKG_BASE_VER=`echo $PKG_VER | sed 's/\.p[0-9][0-9]*$//'`
 PKG_NAME_UPSTREAM=`lookup_param tarball "$PKG_SCRIPTS/checksums.ini" | sed "s/VERSION/$PKG_BASE_VER/"`
 
@@ -351,7 +344,7 @@ EOF
     fi
 fi
 
-if [ $INFO -ne 0 -a "$USE_LOCAL_SCRIPTS" = yes ]; then
+if [ $INFO -ne 0 ]; then
     exec sage-spkg-info $PKG_BASE
 fi
 
@@ -395,20 +388,6 @@ if [ -n "$SAGE_INSTALL_FETCH_ONLY" ]; then
     exit 0
 fi
 
-##################################################################
-# Handle --info
-##################################################################
-
-if [ $INFO -ne 0 -a -z "$USE_LOCAL_SCRIPTS" ]; then
-        cat "$PKG_SCRIPTS/SPKG.txt"
-    sage-uncompress-spkg "$PKG_SRC" "$PKG_NAME/SPKG.txt"
-    if [ $? -ne 0 ]; then
-        error_msg "Error: no file SPKG.txt in $PKG_NAME"
-        exit 1
-    fi
-    exit 0
-fi
-
 ##################################################################
 # Setup directories
 ##################################################################
@@ -467,19 +446,13 @@ fi
 # Extract the package
 ##################################################################
 
-if [ "$USE_LOCAL_SCRIPTS" = yes ]; then
-    # New-style package
-    echo "Setting up build directory for $PKG_NAME"
-    cp -RLp "$PKG_SCRIPTS" "$PKG_NAME"
-    cd "$PKG_NAME" || exit $?
+echo "Setting up build directory for $PKG_NAME"
+cp -RLp "$PKG_SCRIPTS" "$PKG_NAME"
+cd "$PKG_NAME" || exit $?
 
-    sage-uncompress-spkg -d src "$PKG_SRC"
-    if [ $? -ne 0 ]; then
-        error_msg "Error: failed to extract $PKG_SRC"
-        exit 1
-    fi
-else
-    echo >&2 "Error: Installing old-style SPKGs is no longer supported."
+sage-uncompress-spkg -d src "$PKG_SRC"
+if [ $? -ne 0 ]; then
+    error_msg "Error: failed to extract $PKG_SRC"
     exit 1
 fi
 
@@ -559,9 +532,12 @@ __EOF__
 }
 
 
-WRAPPED_SCRIPTS="build install check preinst postinst prerm postrm"
-INSTALLED_SCRIPTS="prerm postrm"
+INSTALLED_SCRIPTS="prerm piprm postrm"
+WRAPPED_SCRIPTS="build install check preinst postinst $INSTALLED_SCRIPTS"
 
+# Prepare script for uninstallation of packages that use sdh_pip_install
+# or sdh_store_and_pip_install_wheel.
+echo 'sdh_pip_uninstall -r $SAGE_SPKG_SCRIPTS/$PKG_BASE/spkg-piprm-requirements.txt' > spkg-piprm.in
 
 for script in $WRAPPED_SCRIPTS; do
     # 'Installed' scripts are not run immediately out of the package build
@@ -576,14 +552,7 @@ for script in $WRAPPED_SCRIPTS; do
     script="spkg-$script"
 
     if [ -f "$script.in" ]; then
-        if [ "$USE_LOCAL_SCRIPTS" = "yes" ]; then
             write_script_wrapper "$(pwd)/$script" "$script_dir"
-        else
-            if [ ! -x "$script" ]; then
-                echo >&2 "WARNING: $script is not executable, making it executable"
-                chmod +x "$script"
-            fi
-        fi
     fi
 done
 
@@ -741,6 +710,14 @@ unset SAGE_DESTDIR_LOCAL
 # $SAGE_SPKG_SCRIPTS; they are not included in the package's manifest, but are
 # removed by sage-spkg-uninstall
 INSTALLED_SCRIPTS_DEST="$SAGE_SPKG_SCRIPTS/$PKG_BASE"
+
+if [ -f spkg-piprm-requirements.txt ]; then
+    INSTALLED_SCRIPTS="$INSTALLED_SCRIPTS piprm-requirements.txt"
+else
+    # No packages to uninstall with pip, so remove the prepared uninstall script
+    rm -f spkg-piprm spkg-piprm.in
+fi
+
 for script in $INSTALLED_SCRIPTS; do
     script="spkg-$script"
 

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/make/Makefile.in

@@ -576,7 +576,7 @@ $(1)-no-deps:
 	$(AM_V_at)sage-logger -p 'sage --pip install -r "$$(SAGE_ROOT)/build/pkgs/$(1)/requirements.txt"' '$$(SAGE_LOGS)/$(1).log'
 
 $(1)-clean:
-	-sage --pip uninstall -y -r '$$(SAGE_ROOT)/build/pkgs/$(1)/requirements.txt'
+	-sage --pip uninstall --isolated --yes --no-input -r '$$(SAGE_ROOT)/build/pkgs/$(1)/requirements.txt'
 
 .PHONY: $(1) $(1)-clean $(1)-build-deps $(1)-no-deps
 endef

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