Merge tag '8.8.beta6' into t/21161/public/repr_of_numberfields__the_p…

…arents__should_indicate_its_embedding_if_there_is_one

SageMath version 8.8.beta6, Release Date: 2019-05-22

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.8.beta5, Release Date: 2019-05-11
+SageMath version 8.8.beta6, Release Date: 2019-05-22

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=75b58f92f04eac5ac6d680de929111518e9769f4
-md5=c349a0f3533c5e8ec809b9a20eac89f2
-cksum=2447773146
+sha1=c91befc71803600bcfcfa5637b8330f65dcf594c
+md5=eee7fd54b6aa2131981ab46442fe09a0
+cksum=2162906054

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-319
+320

build/pkgs/jupymake/SPKG.txt

@@ -0,0 +1,20 @@
+= jupymake =
+
+== Description ==
+
+The Python module JuPyMake provides an interface to polymake.
+
+== License ==
+
+ * GPL v2
+
+== Upstream Contact ==
+
+ https://github.com/polymake/JuPyMake
+
+== Dependencies ==
+
+ * pip
+ * polymake
+
+== Special Update/Build Instructions ==

build/pkgs/jupymake/checksums.ini

@@ -0,0 +1,4 @@
+tarball=JuPyMake-VERSION.tar.gz
+sha1=0dc4e4a29afbdc733908249cd28b7ed4c4ab8b73
+md5=646f0c6c91166ea84e233587fc2dec1e
+cksum=4049738923

build/pkgs/jupymake/package-version.txt

@@ -0,0 +1 @@
+0.9

build/pkgs/jupymake/spkg-install

@@ -0,0 +1,15 @@
+if [ "$SAGE_LOCAL" = "" ]; then
+   echo "SAGE_LOCAL undefined ... exiting";
+   echo "Maybe run 'sage -sh'?"
+   exit 1
+fi
+
+#Install new version
+cd src
+
+sdh_pip_install .
+
+if [ $? -ne 0 ]; then
+   echo "Error installing JuPyMake."
+   exit 1
+fi

build/pkgs/jupymake/type

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

build/pkgs/libpng/SPKG.txt

@@ -27,9 +27,11 @@ This spkg depends on:
 
 == Special Update/Build Instructions ==
 
- * On Darwin, the symbolic links libpng.* created by libpng16 may
+ * On old versions of Darwin, the symbolic links libpng.* created by libpng16 may
    interfere with a system-wide libPng.dylib.
 
+   --- the following is very likely to be obsolete in 2014 ---
+
    This system-wide library is likely to be a different version and on
    top of that, the symbols exported there are prefixed with "_cg"
    (for "Core Graphics"). So even if by chance the functionalities of
@@ -46,6 +48,8 @@ This spkg depends on:
    - when Mercurial is built because it uses $EDITOR, cf. #4678;
    - when R is built and it finds -lpng, cf. #4409 and #11696.
 
+   --- this is no longer done, as of #27186 ---
+
    As not all of these problems are easily dealt with and new ones may
    arise, we chose to delete the $SAGE_LOCAL/lib/libpng.* symlinks.
    Therefore, some packages like Tachyon, which by default look for

build/pkgs/libpng/package-version.txt

@@ -1 +1 @@
-1.6.29.p0
+1.6.29.p1

build/pkgs/libpng/spkg-configure.m4

@@ -0,0 +1,16 @@
+SAGE_SPKG_CONFIGURE([libpng], [
+    AC_REQUIRE([SAGE_SPKG_CONFIGURE_ZLIB])
+    AC_MSG_CHECKING([Installing zlib? ])
+    if test x$sage_spkg_install_zlib = xyes; then
+      AC_MSG_RESULT([Yes. Install libpng as well.])
+      sage_spkg_install_libpng=yes
+    else
+      AC_MSG_RESULT([No.])
+      dnl First try checking for libpng with pkg-config
+      PKG_CHECK_MODULES([LIBPNG], [libpng >= 1.2], [], [
+        dnl Fallback to manually grubbing around for headers and libs
+        AC_CHECK_HEADERS([png.h], [break], [sage_spkg_install_libpng=yes])
+        AC_SEARCH_LIBS([png_get_io_ptr], [png], [], [sage_spkg_install_libpng=yes])
+      ])
+    fi
+])

build/pkgs/libpng/spkg-install

@@ -16,6 +16,3 @@ cd src
 sdh_configure --enable-shared=yes
 sdh_make
 sdh_make_install
-
-# Delete libpng.* symlinks, see SPKG.txt for details
-rm -f "$SAGE_DESTDIR_LOCAL"/lib/libpng.*

build/pkgs/lrslib/package-version.txt

@@ -1 +1 @@
-062+autotools-2017-03-03.p0
+062+autotools-2017-03-03.p1

build/pkgs/lrslib/spkg-install

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

build/pkgs/ninja_build/spkg-configure.m4

@@ -0,0 +1,15 @@
+SAGE_SPKG_CONFIGURE(
+    [ninja_build], [
+	AC_CACHE_CHECK([for ninja >= 1.7.2], [ac_cv_path_NINJA], [
+        AC_PATH_PROGS_FEATURE_CHECK([NINJA], [ninja], [
+            ninja_version=`$ac_path_NINJA --version 2>&1 \
+                | $SED -n -e 's/\([[0-9]]*\.[[0-9]]*\.[[0-9]]*\).*/\1/p'`
+            AS_IF([test -n "$ninja_version"], [
+                AX_COMPARE_VERSION([$ninja_version], [ge], [1.7.2], [
+                    ac_cv_path_NINJA="$ac_path_NINJA"
+                ])
+            ])
+        ])
+    ])
+    AS_IF([test -z "$ac_cv_path_NINJA"], [sage_spkg_install_ninja_build=yes])
+])

build/pkgs/normaliz/checksums.ini

@@ -1,4 +1,4 @@
 tarball=normaliz-VERSION.tar.gz
-sha1=5c8ba35446d2306ed6e2a7944776711c7569a80a
-md5=5f450845141a1d9baddb143b48a0cc3a
-cksum=289674826
+sha1=ab5c5c5653061e8223da511114871850e799f30d
+md5=504b249df9552a5d4a336c630fb9f4b4
+cksum=566272739

build/pkgs/normaliz/package-version.txt

@@ -1 +1 @@
-3.7.1
+3.7.2

build/pkgs/normaliz/spkg-install

@@ -3,7 +3,7 @@ cd src
 # Disable features that require packages SCIP and CoCoA, both of which
 # are experimental packages.
 
-# FLINT is a standard package and E-ANTIC is a standard pakcage.  We
+# FLINT is a standard package and E-ANTIC is an optional package.  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.

build/pkgs/polymake/SPKG.txt

@@ -35,7 +35,7 @@ On Ubuntu/Debian, use:
  sudo apt-get install libxml-libxslt-perl libxml-writer-perl libxml2-dev libperl-dev libfile-slurp-perl libjson-perl libsvg-perl libterm-readkey-perl libterm-readline-gnu-perl libmongodb-perl
 
 On Fedora 23, use:
- sudo yum install perl-ExtUtils-Embed perl-File-Slurp perl-JSON perl-MongoDB
+ sudo yum install perl-ExtUtils-Embed perl-File-Slurp perl-JSON perl-MongoDB perl-Term-ReadLine-Gnu
 
 On Gentoo, use
  emerge --ask XML-Writer XML-LibXML XML-LibXSLT File-Slurp dev-perl/Term-ReadLine-Gnu JSON SVG dev-perl/MongoDB

build/pkgs/polymake/patches/0001-bundled-libnormaliz-support-configure.pl-Conditional.patch

@@ -1,7 +1,7 @@
 From ddef1df5781ad60d65de71e7689b56dfad7288b5 Mon Sep 17 00:00:00 2001
 From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
 Date: Thu, 25 Apr 2019 14:59:19 +0200
-Subject: [PATCH] bundled/libnormaliz/support/configure.pl: Conditionalize
+Subject: [PATCH 1/3] bundled/libnormaliz/support/configure.pl: Conditionalize
 
     include of omp.h on _OPENMP
 ---

build/pkgs/polymake/patches/0002-Add-PERL_SET_CONTEXT-for-thread-correctness.patch

@@ -0,0 +1,128 @@
+From 51f36ef29e7d2482c23ea4da697e626cc61da611 Mon Sep 17 00:00:00 2001
+From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
+Date: Thu, 2 May 2019 13:31:00 +0200
+Subject: [PATCH 2/3] Add PERL_SET_CONTEXT for thread correctness
+
+---
+ lib/callable/src/perl/methods.cc | 14 ++++++++++++++
+ 1 file changed, 14 insertions(+)
+
+diff --git a/lib/callable/src/perl/methods.cc b/lib/callable/src/perl/methods.cc
+index 11beefb2..fccf63b7 100644
+--- a/lib/callable/src/perl/methods.cc
++++ b/lib/callable/src/perl/methods.cc
+@@ -40,6 +40,7 @@ const char Extension[]="Polymake::Core::Extension";
+ void Main::set_application(const AnyString& appname)
+ {
+    dTHXa(pi);
++   PERL_SET_CONTEXT(pi);
+    PmStartFuncall(1);
+    mPUSHp(appname.ptr, appname.len);
+    PUTBACK;
+@@ -49,6 +50,7 @@ void Main::set_application(const AnyString& appname)
+ void Main::set_application_of(const Object& x)
+ {
+    dTHXa(pi);
++   PERL_SET_CONTEXT(pi);
+    PmStartFuncall(1);
+    PUSHs(x.obj_ref);
+    PUTBACK;
+@@ -58,6 +60,7 @@ void Main::set_application_of(const Object& x)
+ void Main::add_extension(const AnyString& path)
+ {
+    dTHXa(pi);
++   PERL_SET_CONTEXT(pi);
+    PmStartFuncall(2);
+    mPUSHp(Extension, sizeof(Extension)-1);
+    mPUSHp(path.ptr, path.len);
+@@ -83,6 +86,7 @@ void Main::reset_preference(const AnyString& label_exp)
+ SV* Main::lookup_extension(const AnyString& path)
+ {
+    dTHXa(pi);
++   PERL_SET_CONTEXT(pi);
+    PmStartFuncall(2);
+    mPUSHp(Extension, sizeof(Extension)-1);
+    mPUSHp(path.ptr, path.len);
+@@ -93,6 +97,7 @@ SV* Main::lookup_extension(const AnyString& path)
+ void Main::call_app_method(const char* method, const AnyString& arg)
+ {
+    dTHXa(pi);
++   PERL_SET_CONTEXT(pi);
+    PmStartFuncall(2);
+    SV* const app=glue::get_current_application(aTHX);
+    PUSHs(app);
+@@ -104,6 +109,7 @@ void Main::call_app_method(const char* method, const AnyString& arg)
+ void Main::set_custom_var(const AnyString& name, const AnyString& key, Value& x)
+ {
+    dTHXa(pi);
++   PERL_SET_CONTEXT(pi);
+    PmStartFuncall(3);
+    mPUSHp(name.ptr, name.len);
+    if (key.ptr) mPUSHp(key.ptr, key.len);
+@@ -115,6 +121,7 @@ void Main::set_custom_var(const AnyString& name, const AnyString& key, Value& x)
+ void Main::reset_custom(const AnyString& name, const AnyString& key)
+ {
+    dTHXa(pi);
++   PERL_SET_CONTEXT(pi);
+    PmStartFuncall(2);
+    mPUSHp(name.ptr, name.len);
+    if (key.ptr) mPUSHp(key.ptr, key.len);
+@@ -125,6 +132,7 @@ void Main::reset_custom(const AnyString& name, const AnyString& key)
+ Scope Main::newScope()
+ {
+    dTHXa(pi);
++   PERL_SET_CONTEXT(pi);
+    PmStartFuncall(0);
+    return Scope(this, call_func_scalar(aTHX_ new_scope_cv));
+ }
+@@ -137,6 +145,7 @@ void Scope::prefer_now(const AnyString& labels) const
+ void Scope::set_custom_var(const AnyString& name, const AnyString& key, Value& x) const
+ {
+    dTHXa(pm_main->pi);
++   PERL_SET_CONTEXT(pm_main->pi);
+    PmStartFuncall(3);
+    mPUSHp(name.ptr, name.len);
+    if (key.ptr) mPUSHp(key.ptr, key.len);
+@@ -148,6 +157,7 @@ void Scope::set_custom_var(const AnyString& name, const AnyString& key, Value& x
+ std::string Main::greeting(int verbose)
+ {
+    dTHXa(pi);
++   PERL_SET_CONTEXT(pi);
+    PmStartFuncall(1);
+    mPUSHi(verbose);
+    PUTBACK;
+@@ -157,6 +167,7 @@ std::string Main::greeting(int verbose)
+ void Main::shell_enable()
+ {
+    dTHXa(pi);
++   PERL_SET_CONTEXT(pi);
+    PmStartFuncall(0);
+    glue::call_func_void(aTHX_ shell_enable_cv);
+ }
+@@ -167,6 +178,7 @@ Main::shell_execute_t Main::shell_execute(const std::string& input)
+       return shell_execute_t(true, input, input, input);
+
+    dTHXa(pi);
++   PERL_SET_CONTEXT(pi);
+    PmStartFuncall(1);
+    mPUSHp(input.c_str(), input.size());
+    PUTBACK;
+@@ -187,6 +199,7 @@ Main::shell_execute_t Main::shell_execute(const std::string& input)
+ Main::shell_complete_t Main::shell_complete(const std::string& input)
+ {
+    dTHXa(pi);
++   PERL_SET_CONTEXT(pi);
+    PmStartFuncall(1);
+    mPUSHp(input.c_str(), input.size());
+    PUTBACK;
+@@ -209,6 +222,7 @@ Main::shell_complete_t Main::shell_complete(const std::string& input)
+ std::vector<std::string> Main::shell_context_help(const std::string& input, size_t pos, bool full, bool html)
+ {
+    dTHXa(pi);
++   PERL_SET_CONTEXT(pi);
+    PmStartFuncall(4);
+    mPUSHp(input.c_str(), input.size());
+    if (pos == std::string::npos)
+-- 
+2.19.0
+

build/pkgs/polymake/patches/0003-Shell-Mock-Add-compile_scope.patch

@@ -0,0 +1,24 @@
+From 50ce55eea115b74eae9421de43a4405e254ef579 Mon Sep 17 00:00:00 2001
+From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
+Date: Fri, 10 May 2019 14:59:44 +0200
+Subject: [PATCH 3/3] Shell::Mock: Add compile_scope
+
+---
+ perllib/Polymake/Core/ShellMock.pm | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/perllib/Polymake/Core/ShellMock.pm b/perllib/Polymake/Core/ShellMock.pm
+index 46d59654..137f0b24 100644
+--- a/perllib/Polymake/Core/ShellMock.pm
++++ b/perllib/Polymake/Core/ShellMock.pm
+@@ -34,6 +34,7 @@ use Polymake::Struct (
+
+ sub term { shift }
+ sub interactive { 0 }
++sub compile_scope { undef }
+
+ sub complete {
+    my ($self, $string)=@_;
+-- 
+2.19.0
+

build/pkgs/polymake/spkg-install

@@ -12,9 +12,11 @@ if [ `uname` = Darwin ]; then
 fi
 
 # We disable SoPlex to avoid linking errors (#24905).
+# Since polymake v3.4, it does not find our lrs installation if we do not provide --with-lrs explicitly.
 ./configure --without-java \
             --without-javaview \
             --without-soplex \
+            --with-lrs="$SAGE_LOCAL" \
             --prefix="$SAGE_LOCAL" \
             --exec-prefix="$SAGE_LOCAL" \
             --includedir="$SAGE_LOCAL"/include \

build/pkgs/pynormaliz/checksums.ini

@@ -1,4 +1,4 @@
 tarball=PyNormaliz-VERSION.tar.gz
-sha1=880da253bf0785ae49efa12d2649e955034064f6
-md5=c157e80f4995690a2065cefc5e773ef0
-cksum=902471877
+sha1=cca8ea11f3ce3cf68455611e883da34b11c16949
+md5=97941329304064aef5fd1ead9776d33b
+cksum=1286083212

build/pkgs/pynormaliz/package-version.txt

@@ -1 +1 @@
-2.1
+2.5

build/pkgs/pynormaliz/spkg-check

@@ -0,0 +1,2 @@
+cd src
+sage-python23 setup.py test

build/pkgs/r/checksums.ini

@@ -1,4 +1,4 @@
 tarball=R-VERSION.tar.gz
-sha1=057ea91daed3e68a12b2a473ee1283cf26f360e2
-md5=3e4b40b2bbd4a2f8133ac45dbef6a485
-cksum=3313280655
+sha1=c8a1949e763d22ec3b1dbdd251afcb0f1d2d5c76
+md5=65601eac6d353f7efb5b48c29097c2fb
+cksum=3870442260

build/pkgs/r/package-version.txt

@@ -1 +1 @@
-3.5.2.p0
+3.6.0

build/pkgs/rw/spkg-configure.m4

@@ -0,0 +1,16 @@
+SAGE_SPKG_CONFIGURE([rw], [
+  # Check for "rw.h" in the system's include directory...
+  AC_CHECK_HEADER([rw.h],
+                  [sage_spkg_install_rw=no],
+                  [sage_spkg_install_rw=yes])
+
+  #...and ensure that we have at least one function "calculate_level"
+  # that we need from librw. If either check fails, we want to set
+  # sage_spkg_install_rw=yes. However if both checks succeed, the
+  # first will set sage_spkg_install_rw=no and the second will do
+  # nothing.
+  AC_SEARCH_LIBS([calculate_level],
+                 [rw],
+                 [],
+                 [sage_spkg_install_rw=yes])
+])

build/pkgs/tachyon/patches/Make-config.patch

@@ -71,7 +71,7 @@
 -PNGLIB=
 +USEPNG= -DUSEPNG
 +PNGINC= -I$(SAGE_LOCAL)/include
-+PNGLIB= -L$(SAGE_LOCAL)/lib -lpng16 -lz
++PNGLIB= -L$(SAGE_LOCAL)/lib -lpng -lz
 
 -# Uncomment the following lines to enable PNG support
 -#USEPNG= -DUSEPNG