Merge tag '8.8.beta3' into t/26340/public/26340

SageMath version 8.8.beta3, Release Date: 2019-04-18

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.8.beta2, Release Date: 2019-04-14
+SageMath version 8.8.beta3, Release Date: 2019-04-18

build/pkgs/4ti2/spkg-install

@@ -1,7 +1,7 @@
 cd src/
 CFLAGS="-I $SAGE_LOCAL/include -L$SAGE_LOCAL/lib $CFLAGS"
 export CFLAGS
-sdh_configure --with-gmp=$SAGE_LOCAL --with-glpk=$SAGE_LOCAL \
+sdh_configure $SAGE_CONFIGURE_GMP --with-glpk=$SAGE_LOCAL \
     --enable-shared=yes --enable-static=no
 sdh_make
 sdh_make_install

build/pkgs/arb/spkg-install

@@ -4,8 +4,8 @@ cd src
 # be removed in arb >= 2.8 when it is released
 export EXTRA_SHARED_FLAGS=$LDFLAGS
 
-./configure --disable-static --prefix="$SAGE_LOCAL" --with-flint="$SAGE_LOCAL" \
-    --with-gmp="$SAGE_LOCAL" --with-mpfr="$SAGE_LOCAL" || \
+./configure --disable-static --prefix="$SAGE_LOCAL" $SAGE_CONFIGURE_GMP \
+            --with-flint="$SAGE_LOCAL" --with-mpfr="$SAGE_LOCAL" || \
     sdh_die "Error configuring arb."
 
 sdh_make verbose

build/pkgs/barvinok/spkg-install

@@ -1,6 +1,10 @@
 cd src
 
-sdh_configure --with-gmp-prefix=${SAGE_LOCAL} \
+if [ -n "$SAGE_GMP_PREFIX" ];
+   GMP_CONFIGURE="--with-gmp-prefix=$SAGE_GMP_PREFIX"
+fi
+
+sdh_configure $GMP_CONFIGURE \
               --with-ntl-prefix=${SAGE_LOCAL} \
               --with-isl=system               \
               --with-polylib=system           \

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=4d2c15968d8e733ec129b75b4914310bb029ead8
-md5=c4e0b3aba2a4a030a3d6a31886eb2194
-cksum=2385275364
+sha1=1e7159211ed0f3b3d67271447eaffc0d19f3d241
+md5=3e2cd72a942df6a0bcaebcd4b5420019
+cksum=2626107527

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-315
+317

build/pkgs/deformation/spkg-install

@@ -3,7 +3,7 @@ cd src
 # Note: Not actually an autoconf-generated configure; doesn't support
 # all standard flags, so we can't use sdh_configure
 ./configure --prefix="$SAGE_LOCAL" --disable-static \
-            --with-gmp="$SAGE_LOCAL" --with-mpfr="$SAGE_LOCAL" \
+            $SAGE_CONFIGURE_GMP --with-mpfr="$SAGE_LOCAL" \
             --with-flint="$SAGE_LOCAL" || \
             sdh_die "Failed to configure deformation"
 sdh_make

build/pkgs/ecl/spkg-install

@@ -37,7 +37,7 @@ echo ""
 # Use newer version of config.guess and config.sub (see Trac #19732)
 cp "$SAGE_ROOT"/config/config.* src
 
-sdh_configure --with-gmp-prefix=$SAGE_LOCAL --disable-threads \
+sdh_configure $SAGE_CONFIGURE_GMP --disable-threads \
               --enable-unicode=yes $ECL_CONFIGURE
 
 # Before running make we touch build/TAGS so its building process is never triggered

build/pkgs/ecm/spkg-install

@@ -210,7 +210,10 @@ else
 fi
 echo "  --prefix=\"$SAGE_LOCAL\""
 echo "  --libdir=\"$SAGE_LOCAL/lib\""
-echo "  --with-gmp=\"$SAGE_LOCAL\""
+if [ -n "$SAGE_CONFIGURE_GMP" ]; then
+    echo "  --with-gmp=\"$SAGE_LOCAL\""
+fi
+
 for opt in $ECM_CONFIGURE; do
     echo "  $opt"
 done
@@ -221,7 +224,7 @@ if [ -z "$ECM_CONFIGURE" ]; then
 fi
 echo
 
-sdh_configure --with-gmp="$SAGE_LOCAL" $ECM_CONFIGURE
+sdh_configure $SAGE_CONFIGURE_GMP $ECM_CONFIGURE
 
 ###############################################################################
 # Now build ECM:

build/pkgs/elliptic_curves/SPKG.txt

@@ -4,9 +4,8 @@
 
 Includes two databases:
 
- * A small subset of the data in John Cremona's database of elliptic curves up
-   to conductor 10000. See http://www.warwick.ac.uk/~masgaj/ftp/data/ or
-   http://sage.math.washington.edu/cremona/INDEX.html
+ * A small subset of John Cremona's database of elliptic curves up
+   to conductor 10000.
  * William Stein's database of interesting curves
 
 == Upstream Contact ==
@@ -15,7 +14,7 @@ Includes two databases:
 
  * Author: John Cremona
  * Email: john.cremona@gmail.com
- * Website: http://www.warwick.ac.uk/~masgaj/ftp/data/
+ * Website: http://johncremona.github.io/ecdata/
 
 === ellcurves ===
 
@@ -29,6 +28,9 @@ Includes two databases:
 
 == Changelog ==
 
+=== elliptic_curves-0.8.1 (Frédéric Chapoton, 2019-03-01) ===
+ * #20717: remove macOS hidden files
+
 === elliptic_curves-0.8 (Simon Spicer, 2014-10-24) ===
  * #16773: add more examples of high rank curves
 

build/pkgs/elliptic_curves/checksums.ini

@@ -1,4 +1,4 @@
 tarball=elliptic_curves-VERSION.tar.bz2
-sha1=4de409b03002f5cb7b97f62a6797e33aa968bb80
-md5=fd9beee5a0e4a5ae330ffd6f1ab12112
-cksum=291102768
+sha1=1eb0d332be1d05aaee70cd03cce7299a1df95953
+md5=315564f43d9272a2659f91355e6b1d16
+cksum=3923089644

build/pkgs/elliptic_curves/package-version.txt

@@ -1 +1 @@
-0.8.p0
+0.8.1

build/pkgs/flint/spkg-install

@@ -16,7 +16,7 @@ echo "Configuring FLINT."
 ./configure \
     --disable-static \
     --prefix="$SAGE_LOCAL" \
-    --with-gmp="$SAGE_LOCAL" \
+    $SAGE_CONFIGURE_GMP \
     --with-mpfr="$SAGE_LOCAL" \
     --with-ntl="$SAGE_LOCAL" \
     $FLINT_CONFIGURE || sdh_die "Error: Failed to configure FLINT."

build/pkgs/gap/spkg-install

@@ -17,7 +17,7 @@ else
     export CFLAGS="-O2 -g $CFLAGS"
 fi
 
-sdh_configure --with-gmp="$SAGE_LOCAL"
+sdh_configure $SAGE_CONFIGURE_GMP
 sdh_make -j1
 
 # GAP's "make install" is work in progress; we use bits and pieces of it

build/pkgs/gcc/build-gcc

@@ -61,7 +61,7 @@ fi
 ../src/configure \
     --prefix="$SAGE_LOCAL" \
     --with-local-prefix="$SAGE_LOCAL" \
-    --with-gmp="$SAGE_LOCAL" --with-mpfr="$SAGE_LOCAL" --with-mpc="$SAGE_LOCAL" \
+    $SAGE_CONFIGURE_GMP --with-mpfr="$SAGE_LOCAL" --with-mpc="$SAGE_LOCAL" \
     --with-system-zlib \
     --disable-multilib \
     --disable-nls \

build/pkgs/gdb/spkg-install

@@ -6,6 +6,6 @@ export LDFLAGS="${LDFLAGS} -L${SAGE_LOCAL}/lib -ltinfo"
 sdh_configure \
     --with-mpc="$SAGE_LOCAL" \
     --with-mpfr="$SAGE_LOCAL" \
-    --with-gmp="$SAGE_LOCAL"
+    $SAGE_CONFIGURE_GMP
 sdh_make
 sdh_make_install

build/pkgs/givaro/spkg-install

@@ -9,6 +9,6 @@ if [ "$SAGE_FAT_BINARY" = yes ]; then
     GIVARO_CONFIGURE="--disable-sse --disable-sse2 --disable-sse3 --disable-ssse3 --disable-sse41 --disable-sse42 --disable-fma --disable-fma4 --disable-avx --disable-avx2  $GIVARO_CONFIGURE"
 fi
 
-sdh_configure --with-gmp="$SAGE_LOCAL" --enable-shared $GIVARO_CONFIGURE
+sdh_configure $SAGE_CONFIGURE_GMP --enable-shared $GIVARO_CONFIGURE
 sdh_make
 sdh_make_install

build/pkgs/glpk/spkg-install

@@ -6,7 +6,7 @@ cp "$SAGE_ROOT"/config/config.* .
 # Note: The following doesn't work with spaces in `$SAGE_LOCAL`, but we don't
 #       support that anyway, since many upstream packages don't.
 #       On the other hand, the only packages GLPK uses that Sage provides are
-#       GMP/MPIR and zlib, so we should just use `--with-gmp="$SAGE_LOCAL"` and
+#       GMP/MPIR and zlib, so we should just use `$SAGE_CONFIGURE_GMP` and
 #       `--with-zlib="$SAGE_LOCAL"` below (which is safe), and omit the fol-
 #       lowing two lines. (TODO)
 #

build/pkgs/gmp/spkg-configure.m4

@@ -0,0 +1,6 @@
+SAGE_SPKG_CONFIGURE([gmp], [
+    AC_REQUIRE([SAGE_SPKG_CONFIGURE_MPIR])
+    if test x"$with_mp" = xgmp; then
+        sage_spkg_install_gmp=yes
+    fi
+])

build/pkgs/iml/spkg-install

@@ -7,8 +7,15 @@ else
     export CFLAGS="-O3 -g $CFLAGS"
 fi
 
+# When using GMP from a standard system location it shouldn't really
+# matter what we put here, but iml's configure script requires we
+# provide *something*, and this should be reasonable in most cases
+SAGE_GMP_LIB="`echo "$SAGE_GMP_INCLUDE" | sed 's|/include|/lib|'`"
+
 sdh_configure --enable-shared \
               --with-default="$SAGE_LOCAL" \
+              --with-gmp-include="$SAGE_GMP_INCLUDE" \
+              --with-gmp-lib="$SAGE_GMP_LIB" \
               --with-cblas="$(pkg-config --libs cblas)" \
               --with-cblas-include="$(pkg-config --cflags cblas)" \
               "$IML_CONFIGURE"

build/pkgs/latte_int/spkg-install

@@ -1,7 +1,7 @@
 cd src
 
 sdh_configure --enable-shared=yes --enable-static=false \
-              --with-gmp=$SAGE_LOCAL --with-ntl=$SAGE_LOCAL \
+              $SAGE_CONFIGURE_GMP --with-ntl=$SAGE_LOCAL \
               --with-cddlib=$SAGE_LOCAL --with-4ti2=$SAGE_LOCAL \
               --with-lidia=$SAGE_LOCAL
 sdh_make

build/pkgs/mpc/spkg-install

@@ -13,7 +13,7 @@ if [ $UNAME = "CYGWIN" ]; then
 fi
 
 # Building
-sdh_configure --with-gmp="$SAGE_LOCAL" --with-mpfr="$SAGE_LOCAL" $EXTRA
+sdh_configure $SAGE_CONFIGURE_GMP --with-mpfr="$SAGE_LOCAL" $EXTRA
 sdh_make
 
 # Cleaning

build/pkgs/mpfi/spkg-install

@@ -5,7 +5,7 @@ cd src
 # Use newer version of config.guess and config.sub (see Trac #19716)
 cp "$SAGE_ROOT"/config/config.* .
 
-sdh_configure --with-mpfr="$SAGE_LOCAL" --with-gmp="$SAGE_LOCAL"
+sdh_configure --with-mpfr="$SAGE_LOCAL" $SAGE_CONFIGURE_GMP
 sdh_make
 sdh_make_install
 

build/pkgs/mpfr/spkg-install

@@ -57,7 +57,7 @@ mpfr_configure()
     ###########################################################################
     echo "Checking what CC and CFLAGS MPFR would use if they were empty..."
     if (unset CC CFLAGS CPPFLAGS CXXFLAGS &&
-        ./configure --with-gmp="$SAGE_LOCAL" $SAGE_CONF_OPTS $MPFR_CONFIGURE) &>/dev/null;
+        ./configure $SAGE_CONFIGURE_GMP $SAGE_CONF_OPTS $MPFR_CONFIGURE) &>/dev/null;
     then
         mpfr_config_file=config.status
         if mpfr_get_upstream_selected_cflags "$mpfr_config_file"; then
@@ -131,16 +131,18 @@ mpfr_configure()
     fi
     echo "  --prefix=\"$SAGE_LOCAL\""
     echo "  --libdir=\"$SAGE_LOCAL/lib\""
-    echo "  --with-gmp=\"$SAGE_LOCAL\""
+    if [ -n "$SAGE_CONFIGURE_GMP" ]; then
+        echo "  --with-gmp=\"$SAGE_LOCAL\""
+    fi
+
     for opt in $SAGE_CONF_OPTS $MPFR_CONFIGURE; do
         echo "  $opt"
     done
     if [ -z "$MPFR_CONFIGURE" ]; then
         echo "You can set MPFR_CONFIGURE to pass additional parameters."
     fi
 
-    sdh_configure --with-gmp="$SAGE_LOCAL" \
-                $SAGE_CONF_OPTS $MPFR_CONFIGURE
+    sdh_configure $SAGE_CONFIGURE_GMP $SAGE_CONF_OPTS $MPFR_CONFIGURE
 }
 
 mpfr_build()

build/pkgs/mpfrcx/spkg-install

@@ -1,6 +1,6 @@
 cd src
 
-sdh_configure --with-gmp="$SAGE_LOCAL" --with-mpfr="$SAGE_LOCAL" \
+sdh_configure $SAGE_CONFIGURE_GMP --with-mpfr="$SAGE_LOCAL" \
               --with-mpc="$SAGE_LOCAL" --disable-static --enable-shared
 sdh_make
 sdh_make_install

build/pkgs/mpir/spkg-configure.m4

@@ -0,0 +1,62 @@
+SAGE_SPKG_CONFIGURE([mpir], [
+    AC_ARG_WITH([mp],
+    [AS_HELP_STRING([--with-mp=system],
+        [use the system GMP as multiprecision library, if possible (default)])]
+    [AS_HELP_STRING([--with-mp=mpir],
+        [use the Sage SPKG for MPIR as multiprecision library])]
+    [AS_HELP_STRING([--with-mp=gmp],
+        [use the Sage SPKG for GMP as multiprecision library])])
+
+dnl Just part the options here
+    case "$with_mp" in
+        system) ;;
+        MPIR|mpir) with_mp=mpir;;
+        GMP|gmp) with_mp=gmp;;
+        "") with_mp=system;;
+        *)
+            AC_MSG_ERROR([allowed values for --with-mp are system, mpir, or gmp]);;
+    esac
+
+dnl Implement cases for what to do on different options here
+    case "$with_mp" in
+        system)
+            AC_CHECK_HEADER(gmp.h, [], [sage_spkg_install_mpir=yes])
+            AC_CHECK_HEADER(gmpxx.h, [], [sage_spkg_install_mpir=yes])
+            dnl mpq_cmp_z appeared in GMP 6.1.0 and is used by pynac
+            AC_SEARCH_LIBS([__gmpq_cmp_z], [gmp], [break],
+                [sage_spkg_install_mpir=yes])
+            SAGE_MP_LIBRARY=mpir
+            ;;
+        mpir)
+            sage_spkg_install_mpir=yes
+            SAGE_MP_LIBRARY=mpir
+            ;;
+        gmp)
+            sage_spkg_install_gmp=yes
+            SAGE_MP_LIBRARY=gmp
+            ;;
+    esac
+
+    if test x$sage_spkg_install_mpir = xyes -o x$sage_spkg_install_gmp = xyes; then
+        AC_SUBST(SAGE_GMP_PREFIX, ['$SAGE_LOCAL'])
+        AC_SUBST(SAGE_GMP_INCLUDE, ['$SAGE_LOCAL/include'])
+        AC_MSG_RESULT([using $SAGE_MP_LIBRARY SPKG (via --with-mp=$SAGE_MP_LIBRARY)])
+    else
+        dnl If found, we want to get the absolute path to where we
+        dnl found it for use with some packages (e.g. iml) that need
+        dnl this information at configure time
+        AX_ABSOLUTE_HEADER([gmp.h])
+        if test x$gl_cv_absolute_gmp_h = x; then
+            AC_MSG_ERROR(m4_normalize([
+                failed to find absolute path to gmp.h despite it being reported
+                found
+            ]))
+        fi
+        AC_SUBST(SAGE_GMP_INCLUDE, [`AS_DIRNAME($gl_cv_absolute_gmp_h)`])
+        AC_SUBST(SAGE_GMP_PREFIX, [''])
+        AC_MSG_RESULT([using GMP-compatible library from the system])
+    fi
+
+    AC_SUBST([SAGE_MP_LIBRARY], [$SAGE_MP_LIBRARY])
+])
+

build/pkgs/pari/spkg-install

@@ -132,8 +132,9 @@ export CFLAGS
 # anyway, it doesn't hurt either. -- jdemeyer
 #
 # Note that "--graphic=none" is (usually) added to PARI_CONFIGURE:
+#--with-gmp-include="/usr/include/x86_64-linux-gnu" \
 bash ./Configure --prefix="$SAGE_LOCAL" \
-    --with-readline="$SAGE_LOCAL" --with-gmp="$SAGE_LOCAL" \
+    --with-readline="$SAGE_LOCAL" $SAGE_CONFIGURE_GMP \
     --with-runtime-perl="/usr/bin/env perl" \
     --kernel=gmp $PARI_CONFIGURE || \
     sdh_die "Error configuring PARI with readline and GMP kernel failed."

build/pkgs/ppl/spkg-install

@@ -4,19 +4,17 @@ export CXXFLAGS="$CXXFLAGS -I$SAGE_LOCAL/include"
 cd src
 
 # Enable only what's needed for Sage
-GMP_PATHS=( "--with-gmp-include=$SAGE_LOCAL/include"
-"--with-gmp-lib=$SAGE_LOCAL/lib" )
 PPL_CONFIGURE="--enable-coefficients=mpz --disable-fpmath $PPL_CONFIGURE"
 
 # First try configuring both the C and C++ interfaces.
 # If that fails (for example, because of a broken version of m4),
 # try to configure again with only the C++ interface, which is
 # sufficient for Sage.  See #11391 and #12672.
-if ! (sdh_configure --enable-interfaces=c,c++ "${GMP_PATHS[@]}" \
+if ! (sdh_configure --enable-interfaces=c,c++ $SAGE_CONFIGURE_GMP \
                     $PPL_CONFIGURE); then
     echo >&2 "Error configuring PPL with both C and C++ interfaces, trying"
     echo >&2 "again with only the C++ interface."
-    sdh_configure --enable-interfaces=c++ "${GMP_PATHS[@]}" $PPL_CONFIGURE
+    sdh_configure --enable-interfaces=c++ $SAGE_CONFIGURE_GMP $PPL_CONFIGURE
 fi
 
 # Workaround to disable PPL's "watchdog timer", preventing it from clobbering

build/pkgs/singular/spkg-install

@@ -77,7 +77,7 @@ config()
     #    may be ignored.
     sdh_configure --exec-prefix="$SAGE_LOCAL" \
                   --bindir="$SAGE_LOCAL/bin" \
-                  --with-gmp="$SAGE_LOCAL" \
+                  $SAGE_CONFIGURE_GMP \
                   --with-ntl="$SAGE_LOCAL" \
                   --with-flint="$SAGE_LOCAL" \
                   --enable-gfanlib \

build/pkgs/topcom/spkg-install

@@ -8,7 +8,7 @@ cd src
 ./configure \
     --prefix="$SAGE_LOCAL" \
     --libdir="$SAGE_LOCAL/lib" \
-    --with-gmp="$SAGE_LOCAL" \
+    $SAGE_CONFIGURE_GMP \
     --with-cdd="$SAGE_LOCAL"
 if [ $? -ne 0 ]; then
    echo "Error configuring TOPCOM."