Merge tag '8.8.beta5' into t/21161/public/repr_of_numberfields__the_p…

…arents__should_indicate_its_embedding_if_there_is_one

SageMath version 8.8.beta5, Release Date: 2019-05-11

Makefile

@@ -149,7 +149,7 @@ PTEST_PYTHON3 = cat src/ext/doctest/python3-known-passing.txt | xargs ./sage -t
 # By default, include all tests marked 'dochtml' -- see
 # https://trac.sagemath.org/ticket/25345 and
 # https://trac.sagemath.org/ticket/26110.
-TESTALL_FLAGS = --optional=sage,dochtml,optional,external
+TESTALL_FLAGS = --optional=sage,dochtml,optional,external,build
 
 test: all
 	$(TESTALL) --logfile=logs/test.log

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.8.beta3, Release Date: 2019-04-18
+SageMath version 8.8.beta5, Release Date: 2019-05-11

build/pkgs/barvinok/spkg-install

@@ -1,6 +1,6 @@
 cd src
 
-if [ -n "$SAGE_GMP_PREFIX" ];
+if [ -n "$SAGE_GMP_PREFIX" ]; then
    GMP_CONFIGURE="--with-gmp-prefix=$SAGE_GMP_PREFIX"
 fi
 

build/pkgs/cmake/spkg-configure.m4

@@ -0,0 +1,15 @@
+SAGE_SPKG_CONFIGURE(
+    [cmake], [
+	AC_CACHE_CHECK([for cmake >= 3.4], [ac_cv_path_CMAKE], [
+        AC_PATH_PROGS_FEATURE_CHECK([CMAKE], [cmake], [
+            cmake_version=`$ac_path_CMAKE --version 2>&1 \
+                | $SED -n -e 's/cmake version *\([[0-9]]*\.[[0-9]]*\.[[0-9]]*\)/\1/p'`
+            AS_IF([test -n "$cmake_version"], [
+                AX_COMPARE_VERSION([$cmake_version], [ge], [3.4], [
+                    ac_cv_path_CMAKE="$ac_path_CMAKE"
+                ])
+            ])
+        ])
+    ])
+    AS_IF([test -z "$ac_cv_path_CMAKE"], [sage_spkg_install_cmake=yes])
+])

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=1e7159211ed0f3b3d67271447eaffc0d19f3d241
-md5=3e2cd72a942df6a0bcaebcd4b5420019
-cksum=2626107527
+sha1=75b58f92f04eac5ac6d680de929111518e9769f4
+md5=c349a0f3533c5e8ec809b9a20eac89f2
+cksum=2447773146

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-317
+319

build/pkgs/dot2tex/checksums.ini

@@ -1,4 +1,4 @@
 tarball=dot2tex-VERSION.tar.gz
-sha1=03f502c0922c2dc87b5dd38456021a6774e4c8be
-md5=2dbaeac905424d0410751235bde4b8b2
-cksum=1572429696
+sha1=5149c76e817b0592ea4dfd03f899495a394b8e90
+md5=b9ae1b7939409df221209098aaf11c97
+cksum=557736523

build/pkgs/dot2tex/package-version.txt

@@ -1 +1 @@
-2.9.0.p2
+2.11.3.p0

build/pkgs/dot2tex/patches/remove_test_semicolon.patch

@@ -1,7 +1,7 @@
 --- src/tests/test_dot2tex.py        2014-11-08 10:21:31.565955354 -0800
 +++ src/tests/test_dot2tex.py        2014-11-08 10:24:09.985964244 -0800
-@@ -137,29 +137,6 @@
-         self.failUnless(r'{1.2.3.4}' in source)
+@@ -138,29 +138,6 @@ class NeedsQuotesTests(unittest.TestCase):
+         self.assertTrue(r'{1.2.3.4}' in source)
 
 
 -class MultipleStatements(unittest.TestCase):
@@ -24,9 +24,10 @@
 -                                  figonly=True, format='tikz', autosize=True)
 -        source2 = dot2tex.dot2tex(testgraph2,
 -                                  figonly=True, format='tikz', autosize=True)
--        self.failUnless(source1 == source2)
+-        self.assertEqual(source1, source2)
 -
 -
  class TestPositionsOutputFormat(unittest.TestCase):
      # http://code.google.com/p/dot2tex/issues/detail?id=20
      def test_floating_point_coordinates(self):
+

build/pkgs/dot2tex/spkg-check

@@ -14,7 +14,7 @@ for file in test_*.py; do
     echo "############################################################"
     echo "spkg-check: Running $file..."
     echo "############################################################"
-    python $file || passed=false
+    sage-python23 $file || passed=false
 done
 echo
 if $passed; then

build/pkgs/e_antic/SPKG.txt

@@ -0,0 +1,22 @@
+= e-antic =
+
+== Description ==
+
+e-antic is a C library for exact computations with real embedded number field
+maintained by Vincent Delecroix.
+
+Website: https://github.com/videlec/e-antic
+
+== License ==
+
+e-antic is licensed GPL v3.
+
+== Upstream Contact ==
+
+ * https://github.com/videlec/e-antic
+
+== Dependencies ==
+
+ * GMP/MPIR
+ * FLINT
+ * ARB

build/pkgs/e_antic/checksums.ini

@@ -0,0 +1,4 @@
+tarball=e-antic-VERSION.tar.gz
+sha1=27784c0cf5466d4a3bac505f2bcd1d94bcffc83d
+md5=00b7ae08bd9f631413f597bfaeaef8c3
+cksum=3800561068

build/pkgs/e_antic/dependencies

@@ -0,0 +1,5 @@
+$(MP_LIBRARY) flint arb
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

build/pkgs/e_antic/package-version.txt

@@ -0,0 +1 @@
+0.1.3b0

build/pkgs/e_antic/spkg-check

@@ -0,0 +1,8 @@
+###############################################################################
+#
+# e-antic Sage check script
+#
+###############################################################################
+
+cd src
+sdh_make check

build/pkgs/e_antic/spkg-install

@@ -0,0 +1,14 @@
+###############################################################################
+#
+# e-antic Sage install script
+#
+###############################################################################
+if [ "$SAGE_DEBUG" = "yes" ]; then
+    CFLAGS="-O0 -g $CFLAGS"; export CFLAGS
+fi
+
+cd src
+
+sdh_configure
+sdh_make
+sdh_make_install

build/pkgs/e_antic/type

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

build/pkgs/lidia/checksums.ini

@@ -1,4 +1,4 @@
 tarball=lidia-VERSION.tar.gz
-sha1=47fdccd2cc79db258403287cad755465d503e643
-md5=6a14186ce2d82dde6864c0fc3fa5af6b
-cksum=3334545601
+sha1=93da2f24e3caa4c10452b4f088382084da3ddfbd
+md5=2d75b417194e98be64dd85368e149cf4
+cksum=1175913571

build/pkgs/lidia/package-version.txt

@@ -1 +1 @@
-2.3.0+latte-patches-2014-10-04.p0
+2.3.0+latte-patches-2019-05-02

build/pkgs/lidia/spkg-install

@@ -1,8 +1,11 @@
 cd src/
 
+if [ -n "$SAGE_GMP_PREFIX" ]; then
+   GMP_CONFIGURE="--with-extra-includes=$SAGE_GMP_PREFIX/include --with-extra-libs=$SAGE_GMP_PREFIX/lib"
+fi
+
 sdh_configure --with-arithmetic=gmp \
-              --with-extra-includes="$SAGE_LOCAL/include" \
-              --with-extra-libs="$SAGE_LOCAL/lib" \
+              $GMP_CONFIGURE \
               --enable-shared=yes --enable-static=no
 sdh_make
 sdh_make_install

build/pkgs/mpir/spkg-configure.m4

@@ -1,22 +1,4 @@
 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)
@@ -36,7 +18,37 @@ dnl Implement cases for what to do on different options here
             SAGE_MP_LIBRARY=gmp
             ;;
     esac
+], [], [
+    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 parse the options here
+    case "$with_mp" in
+        system) ;;
+        MPIR|mpir) with_mp=mpir;;
+        GMP|gmp) with_mp=gmp;;
+        "") with_mp=system;;
+        *)
+            AC_MSG_ERROR([allowed values for --with-mp are system, mpir, or gmp]);;
+    esac
+
+dnl Set SAGE_MP_LIBRARY depending on the with_mp option
+    case "$with_mp" in
+    mpir|system)
+        SAGE_MP_LIBRARY=mpir
+        ;;
+    gmp)
+        SAGE_MP_LIBRARY=gmp
+        ;;
+    esac
+
+    AC_SUBST([SAGE_MP_LIBRARY], [$SAGE_MP_LIBRARY])
+], [
     if test x$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, ['$SAGE_LOCAL/include'])
@@ -56,7 +68,5 @@ dnl Implement cases for what to do on different options here
         AC_SUBST(SAGE_GMP_PREFIX, [''])
         AC_MSG_RESULT([using GMP-compatible library from the system])
     fi
-
-    AC_SUBST([SAGE_MP_LIBRARY], [$SAGE_MP_LIBRARY])
 ])
 

build/pkgs/normaliz/checksums.ini

@@ -1,4 +1,4 @@
 tarball=normaliz-VERSION.tar.gz
-sha1=76e2fc02cf2eb9b2d05c9b26f64a90015fb3292b
-md5=0cd4efb6d6f7177ce83955785a59dd6d
-cksum=1666633916
+sha1=5c8ba35446d2306ed6e2a7944776711c7569a80a
+md5=5f450845141a1d9baddb143b48a0cc3a
+cksum=289674826

build/pkgs/normaliz/dependencies

@@ -1,4 +1,4 @@
-$(MP_LIBRARY) singular boost_cropped flint
+$(MP_LIBRARY) singular boost_cropped flint e_antic
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/normaliz/package-version.txt

@@ -1 +1 @@
-3.6.3
+3.7.1

build/pkgs/normaliz/spkg-install

@@ -3,10 +3,11 @@ cd src
 # Disable features that require packages SCIP and CoCoA, both of which
 # are experimental packages.
 
-# FLINT is a standard package.  We pass --enable-flint to configure so
-# that an error will be signalled if FLINT cannot be found, rather
+# FLINT is a standard package and E-ANTIC is a standard pakcage.  We
+# pass --enable-flint and --enable-enfnormaliz to configure so
+# that an error will be signalled if FLINT or E-ANTIC cannot be found, rather
 # than building normaliz without it.
 
-sdh_configure --disable-scip --disable-nmzintegrate --enable-flint
+sdh_configure --disable-scip --disable-nmzintegrate --enable-flint --enable-enfnormaliz
 sdh_make
 sdh_make_install

build/pkgs/notebook/package-version.txt

@@ -1 +1 @@
-5.7.6
+5.7.6.p0

build/pkgs/notebook/patches/0001-Workaround-for-wrong-errno-on-socket-bind-permission.patch

@@ -0,0 +1,36 @@
+From 82a681e0e876a7e45357c5cf3b041ae9113e55f8 Mon Sep 17 00:00:00 2001
+From: "Erik M. Bray" <erik.bray@lri.fr>
+Date: Tue, 23 Apr 2019 14:34:05 +0200
+Subject: [PATCH] Workaround for wrong errno on socket bind permission errors
+ on Cygwin.
+
+---
+ notebook/notebookapp.py | 9 ++++++++-
+ 1 file changed, 8 insertions(+), 1 deletion(-)
+
+diff --git a/notebook/notebookapp.py b/notebook/notebookapp.py
+index 6b680ed9a..f332aeb6a 100755
+--- a/notebook/notebookapp.py
++++ b/notebook/notebookapp.py
+@@ -1406,10 +1406,17 @@ class NotebookApp(JupyterApp):
+             try:
+                 self.http_server.listen(port, self.ip)
+             except socket.error as e:
++                eacces = (errno.EACCES, getattr(errno, 'WSAEACCES', errno.EACCES))
++                if sys.platform == 'cygwin':
++                    # Cygwin has a bug that causes EPERM to be returned in this
++                    # case instead of EACCES:
++                    # https://cygwin.com/ml/cygwin/2019-04/msg00160.html
++                    eacces += (errno.EPERM,)
++
+                 if e.errno == errno.EADDRINUSE:
+                     self.log.info(_('The port %i is already in use, trying another port.') % port)
+                     continue
+-                elif e.errno in (errno.EACCES, getattr(errno, 'WSAEACCES', errno.EACCES)):
++                elif e.errno in eacces:
+                     self.log.warning(_("Permission to listen on port %i denied") % port)
+                     continue
+                 else:
+-- 
+2.15.1
+

build/pkgs/pari/package-version.txt

@@ -1 +1 @@
-2.11.1.p1
+2.11.1.p2

build/pkgs/pari/patches/QX_factor.patch

@@ -0,0 +1,28 @@
+See https://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=2125
+
+commit 943b45c148e06bb0f2f2bd7ff14f3ef99fa6e81a
+Author: Bill Allombert <Bill.Allombert@math.u-bordeaux1.fr>
+Date:   Tue Mar 5 14:59:43 2019 +0100
+
+    factor: fix 'bug in gerepile' (from Jeroen) [#2125]
+
+    ? p1 = (289*x^4 + 1)^8; p2 = (19*x^2 + 1)^16;
+    ? factor(p1);
+    ? factor(p2);
+      ***   at top-level: factor(p2)
+      ***                 ^----------
+      *** factor: bug in gerepile, significant pointers lost, please report.
+
+diff --git a/src/basemath/QX_factor.c b/src/basemath/QX_factor.c
+index 173b424..ee71ee5 100644
+--- a/src/basemath/QX_factor.c
++++ b/src/basemath/QX_factor.c
+@@ -892,7 +892,7 @@ ZX_squff(GEN f, GEN *ex)
+       GEN U;
+       if (!dW) { set_avma(av); break; }
+       while ( (U = ZX_divides(T, V)) ) { k++; T = U; }
+-      T = gerepileupto(av, T);
++      T = gerepilecopy(av, T);
+     }
+     else
+     {

build/pkgs/pcre/spkg-configure.m4

@@ -0,0 +1,18 @@
+SAGE_SPKG_CONFIGURE([pcre], [
+    AC_REQUIRE([SAGE_SPKG_CONFIGURE_BZIP2])
+    AC_MSG_CHECKING([Installing bzip2? ])
+    if test x$sage_spkg_install_bzip2 = xyes; then
+       AC_MSG_RESULT([Yes. Install pcre as well.])
+       sage_spkg_install_pcre=yes
+    else
+       AC_MSG_RESULT([No.])
+       dnl First try checking for pcre with pkg-config
+       PKG_CHECK_MODULES([PCRE], [libpcre >= 8.39 libpcreposix libpcrecpp], [], [
+           dnl Fallback to manually grubbing around for headers and libs
+           AC_CHECK_HEADERS([pcre.h pcrecpp.h pcreposix.h], [
+              AC_SEARCH_LIBS([regexec], [pcreposix], [], [sage_spkg_install_pcre=yes])],
+	   [sage_spkg_install_pcre=yes])
+       ])
+    fi
+])
+

build/pkgs/perl_term_readline_gnu/spkg-configure.m4

@@ -0,0 +1,13 @@
+SAGE_SPKG_CONFIGURE(
+    [perl_term_readline_gnu], [dnl direct testing for Term::ReadLine::Gnu does not work
+    AX_PROG_PERL_MODULES( Term::ReadLine, [dnl check that it's a GNU one
+      AC_MSG_CHECKING( Term::ReadLine module...)
+      $PERL -e "use Term::ReadLine; Term::ReadLine->get_all_function_names" > /dev/null 2>&1
+      if test $? -ne 0; then
+        AC_MSG_RESULT(non-GNU)
+        sage_spkg_install_perl_term_readline_gnu=yes
+      else
+        AC_MSG_RESULT(GNU)
+      fi
+     ],[sage_spkg_install_perl_term_readline_gnu=yes])
+])