Merge branch sage6.7.beta3 into ticket18128

Conflicts:
	src/sage/geometry/polyhedron/base.py
	src/sage/geometry/polyhedron/library.py

.gitignore

@@ -4,6 +4,7 @@
 /local
 /logs
 /upstream
+/src/mac-app/build
 
 #############################
 # Autotools generated files #

COPYING.txt

@@ -54,7 +54,6 @@ freetype                    FreeType License (similar to BSD; see below)
 gap                         GPLv2+
 gcc                         GPLv3+
 gd                          Custom (BSD-ish)
-gdmodule                    Custom (BSD-ish)
 genus2reduction             GPLv2+
 gfan                        GPLv2 or GPLv3
 gf2x                        GPLv2+
@@ -80,6 +79,7 @@ markupsafe                  Simplified BSD
 mathjax                     Apache License 2.0
 matplotlib                  Matplotlib License (BSD compatible, see below)
 maxima                      See below
+mistune                     Modified BSD
 mpc                         LGPLv3+
 mpfi                        COPYING is GPLv2, source files state LGPLv2.1+
 mpfr                        LGPLv3+
@@ -128,6 +128,7 @@ sympow                      Modified BSD
 sympy                       Modified BSD
 tachyon                     Modified BSD
 termcap                     GPLv2+
+threejs                     MIT License
 tornado                     Apache License
 zlib                        Custom (Modified BSD)
 zn_poly                     GPLv2 or GPLv3 (no later versions, see below)
@@ -948,19 +949,6 @@ documentation.
 
 ================================================================================
 
-gdmodule:
-(http://newcenturycomputers.net/projects/gdmodule.html)
-
-Permission granted for unlimited use, provided that the Quest Center
-at Cold Spring Harbor Labs is given credit for the library in the
-user-visible documentation of your software. If you modify gd, we ask
-that you share the modifications with us so they can be added to the
-distribution. See gd.html for details.  (The rest of the notice is in
-the package gdmodule spkg, which is a bzip2'd tarball included in the
-Sage source distribution.)
-
-================================================================================
-
 genus2reduction:
 (http://www.math.u-bordeaux.fr/~liu/G2R/)
 Copyright Qing LIU. See PARI for the license terms.

Makefile

@@ -20,7 +20,7 @@ build: logs configure
 	"../$(PIPE)" \
 		"env SAGE_PARALLEL_SPKG_BUILD='$(SAGE_PARALLEL_SPKG_BUILD)' ./install all 2>&1" \
 		"tee -a ../logs/install.log"
-	./sage -b
+	+./sage -b
 
 # Preemptively download all standard upstream source tarballs.
 download:

VERSION.txt

@@ -1 +1 @@
-Sage version 6.6.rc3, released 2015-04-12
+Sage version 6.7.beta3, released 2015-04-28

build/deps

@@ -47,7 +47,6 @@ all-sage: \
      $(INST)/$(FREETYPE) \
      $(INST)/$(GAP) \
      $(INST)/$(GD) \
-     $(INST)/$(GDMODULE) \
      $(INST)/$(GFAN) \
      $(INST)/$(GF2X) \
      $(INST)/$(GIVARO) \
@@ -72,6 +71,7 @@ all-sage: \
      $(INST)/$(MATHJAX) \
      $(INST)/$(MATPLOTLIB) \
      $(INST)/$(MAXIMA) \
+     $(INST)/$(MISTUNE) \
      $(INST)/$(MPC) \
      $(INST)/$(MPFI) \
      $(INST)/$(MPFR) \
@@ -316,6 +316,9 @@ $(INST)/$(LIBGAP): $(INST)/$(GAP)
 $(INST)/$(JSONSCHEMA): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
 	+$(PIPE) "$(SAGE_SPKG) $(JSONSCHEMA) 2>&1" "tee -a $(SAGE_LOGS)/$(JSONSCHEMA).log"
 
+$(INST)/$(MISTUNE): $(INST)/$(SETUPTOOLS) $(INST)/$(CYTHON)
+	+$(PIPE) "$(SAGE_SPKG) $(MISTUNE) 2>&1" "tee -a $(SAGE_LOGS)/$(MISTUNE).log"
+
 $(INST)/$(IPYTHON): $(INST)/$(PYTHON) $(INST)/$(JINJA2) $(INST)/$(TORNADO) $(INST)/$(PYZMQ)
 	+$(PIPE) "$(SAGE_SPKG) $(IPYTHON) 2>&1" "tee -a $(SAGE_LOGS)/$(IPYTHON).log"
 
@@ -325,9 +328,6 @@ $(INST)/$(PEXPECT): $(INST)/$(PYTHON)
 $(INST)/$(GD): $(INST)/$(LIBPNG) $(INST)/$(FREETYPE) $(INST)/$(ICONV)
 	+$(PIPE) "$(SAGE_SPKG) $(GD) 2>&1" "tee -a $(SAGE_LOGS)/$(GD).log"
 
-$(INST)/$(GDMODULE): $(INST)/$(PYTHON) $(INST)/$(GD) $(INST)/$(ICONV)
-	+$(PIPE) "$(SAGE_SPKG) $(GDMODULE) 2>&1" "tee -a $(SAGE_LOGS)/$(GDMODULE).log"
-
 $(INST)/$(SCONS): $(INST)/$(PYTHON)
 	+$(PIPE) "$(SAGE_SPKG) $(SCONS) 2>&1" "tee -a $(SAGE_LOGS)/$(SCONS).log"
 
@@ -375,7 +375,7 @@ $(INST)/$(FREETYPE): $(INST)/$(LIBPNG)
 $(INST)/$(LIBPNG): $(INST)/$(ZLIB)
 	+$(PIPE) "$(SAGE_SPKG) $(LIBPNG) 2>&1" "tee -a $(SAGE_LOGS)/$(LIBPNG).log"
 
-$(INST)/$(SIX): $(INST)/$(PYTHON)
+$(INST)/$(SIX): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
 	+$(PIPE) "$(SAGE_SPKG) $(SIX) 2>&1" "tee -a $(SAGE_LOGS)/$(SIX).log"
 
 $(INST)/$(DATEUTIL): $(INST)/$(PYTHON) $(INST)/$(SIX) $(INST)/$(SETUPTOOLS)
@@ -402,9 +402,8 @@ $(INST)/$(MATHJAX):
 
 $(INST)/$(MATPLOTLIB): $(INST)/$(PYTHON) $(INST)/$(NUMPY) \
                        $(INST)/$(FREETYPE) $(INST)/$(LIBPNG) \
-                       $(INST)/$(GDMODULE) $(INST)/$(DATEUTIL) \
-                       $(INST)/$(PYPARSING) $(INST)/$(SETUPTOOLS) \
-                       $(INST)/$(TORNADO) $(INST)/$(SIX)
+                       $(INST)/$(DATEUTIL) $(INST)/$(PYPARSING) \
+                       $(INST)/$(SETUPTOOLS) $(INST)/$(TORNADO) $(INST)/$(SIX)
 	+$(PIPE) "$(SAGE_SPKG) $(MATPLOTLIB) 2>&1" "tee -a $(SAGE_LOGS)/$(MATPLOTLIB).log"
 
 $(INST)/$(CDDLIB): $(INST)/$(SAGE_MP_LIBRARY)
@@ -523,7 +522,7 @@ $(INST)/sage: \
 		 $(INST)/csage
 	if [ -z "$$SAGE_INSTALL_FETCH_ONLY" ]; then \
 		cd $(SAGE_SRC) && source bin/sage-env && \
-		$(PIPE) 'time python setup.py install 2>&1' 'tee -a $(SAGE_LOGS)/sage-$(SAGE_VERSION).log' && \
+		$(PIPE) 'time $(MAKE) sage 2>&1' 'tee -a $(SAGE_LOGS)/sage-$(SAGE_VERSION).log' && \
 		touch $@; \
 	fi
 
@@ -534,8 +533,8 @@ $(INST)/csage: $(INST)/$(SCONS) \
        $(INST)/$(PYTHON) \
        $(CSAGE_SOURCES)
 	if [ -z "$$SAGE_INSTALL_FETCH_ONLY" ]; then \
-		cd $(SAGE_SRC) && source bin/sage-env && cd c_lib && \
-		$(PIPE) 'time scons -Q install 2>&1' 'tee -a $(SAGE_LOGS)/csage-$(SAGE_VERSION).log' && \
+		cd $(SAGE_SRC) && source bin/sage-env && \
+		$(PIPE) 'time $(MAKE) csage 2>&1' 'tee -a $(SAGE_LOGS)/csage-$(SAGE_VERSION).log' && \
 		touch $@; \
 	fi
 

build/install

@@ -322,7 +322,6 @@ FREETYPE=`newest_version freetype`
 GAP=`newest_version gap`
 GCC=`newest_version gcc`
 GD=`newest_version libgd`
-GDMODULE=`newest_version gdmodule`
 GFAN=`newest_version gfan`
 GF2X=`newest_version gf2x`
 GIT=`newest_version git`
@@ -347,6 +346,7 @@ MARKUPSAFE=`newest_version markupsafe`
 MATHJAX=`newest_version mathjax`
 MATPLOTLIB=`newest_version matplotlib`
 MAXIMA=`newest_version maxima`
+MISTUNE=`newest_version mistune`
 MPC=`newest_version mpc`
 MPFI=`newest_version mpfi`
 MPFR=`newest_version mpfr`

build/pkgs/bliss/package-version.txt

@@ -1 +1 @@
-0.72
+0.72.p1

build/pkgs/bliss/patches/digraph_heuristic.patch

@@ -1,11 +1,10 @@
---- bliss-0.72/graph.hh	2011-05-12 15:29:46.000000000 +0200
-+++ /home/azi/bliss-0.72/graph.hh	2014-12-30 11:14:20.917059666 +0100
-@@ -843,7 +843,7 @@
-   bool is_equitable() const;
+--- src/graph.cc	2015-02-11 13:20:39.922021355 +0100
++++ src-patched/graph_new.cc	2015-02-11 13:20:15.546020960 +0100
+@@ -1920,6 +1920,7 @@
+ Digraph::Digraph(const unsigned int nof_vertices)
+ {
+   vertices.resize(nof_vertices);
++  sh = shs_f;
+ }
+
 
-   /* Splitting heuristics, documented in more detail in the cc-file. */
--  SplittingHeuristic sh;
-+  SplittingHeuristic sh = shs_f;
-   Partition::Cell* find_next_cell_to_be_splitted(Partition::Cell *cell);
-   Partition::Cell* sh_first();
-   Partition::Cell* sh_first_smallest();

build/pkgs/bliss/spkg-install

@@ -6,9 +6,9 @@ if [ "$SAGE_LOCAL" = "" ]; then
    exit 1
 fi
 
-cd "src"
 
-for patch in patches/*.patch; do
+cd "src"
+for patch in ../patches/*.patch; do
     [ -r "$patch" ] || continue  # Skip non-existing or non-readable patches
     patch -p1 <"$patch"
     if [ $? -ne 0 ]; then
@@ -17,6 +17,7 @@ for patch in patches/*.patch; do
     fi
 done
 
+
 $MAKE && mv libbliss.a "$SAGE_LOCAL/lib" && mv *.hh "$SAGE_LOCAL/include"
 
 if [ $? -ne 0 ]; then

build/pkgs/cbc/SPKG.txt

@@ -0,0 +1,28 @@
+= COIN-OR / CBC =
+
+== Description ==
+
+The Computational Infrastructure for Operations Research (COIN-OR**,
+or simply COIN)  project is an initiative to spur the development of
+open-source software for the operations research community.
+
+The COIN Branch and Cut solver (CBC) is an open-source
+mixed-integer program (MIP) solver written in C++. CBC is intended to
+be used primarily as a callable library to create customized
+branch-and-cut solvers. A basic, stand-alone executable version is
+also available. CBC is an active open-source project led by John
+Forrest at www.coin-or.org.
+
+== License ==
+
+Eclipse Public License, Version 1.0 (EPL-1.0)
+(http://opensource.org/licenses/eclipse-1.0)
+
+== Upstream Contact ==
+
+ * John Forrest <jjforre@us.ibm.com>
+ * Robin Lougee-Heimer
+
+== Project Home Page ==
+
+ * https://projects.coin-or.org/Cbc

build/pkgs/cbc/checksums.ini

@@ -0,0 +1,4 @@
+tarball=cbc-VERSION.tar.gz
+sha1=d937d6af1ee8838d44659ebd4cf7bbb1b20372ce
+md5=2134576233cc95cdfedc63991a4944ec
+cksum=1215468781

build/pkgs/cbc/package-version.txt

@@ -0,0 +1 @@
+2.9.4

build/pkgs/cbc/spkg-install

@@ -0,0 +1,22 @@
+if [ "$SAGE_LOCAL" = "" ]; then
+   echo >&2 "SAGE_LOCAL undefined ... exiting";
+   echo >&2 "Maybe run 'sage -sh'?"
+   exit 1
+fi
+
+export LDFLAGS="$LDFLAGS -lz -lbz2"
+#export CPPFLAGS="-DHAVE_CLOCK_GETTIME=0"
+
+# See discussion on #12220
+#
+#-> Mac and Linux behave differently according to the presence of librt, and a
+#   good way around if to make the computer believe that it does not exist
+#   locally, or more precisely that it does not contain the clock_gettime
+#   function. Cbc uses an alternative method to do the job, and it looks like
+#   all this is required when Cbc solves LP with several threads.
+#
+cd src &&
+sed -i -e "s/clock\_gettime ()/Grrrrrrrrrrrr\ ()/g" Cbc/configure &&
+./configure --prefix="$SAGE_LOCAL" "${args[@]}" --enable-cbc-parallel --enable-parallel --enable-gnu-packages --enable-static &&
+make &&
+make install

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=beac54655b8d0fbff44d578bcb2b4f676d40b3c9
-md5=ac8c8051aebfe3d45bf36bdf498c9b59
-cksum=3023873269
+sha1=d0a00ec9d7e49ef6e758aee29f60cd399b2a8ff9
+md5=cbf68f077445ecb657e52276762d7e44
+cksum=3915828491

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-81
+89

build/pkgs/cython/package-version.txt

@@ -1 +1 @@
-0.22
+0.22.p2

build/pkgs/cython/patches/c_tuple_type_memleak.patch

@@ -0,0 +1,124 @@
+commit bb4d9c2de71b7c7e1e02d9dfeae53f4547fa9d7d
+Author: Stefan Behnel <stefan_ml@behnel.de>
+Date:   Fri Apr 24 17:57:23 2015 +0200
+
+    replace the incorrect and leaky global c-tuple type cache by a per-module one
+
+diff --git a/Cython/Compiler/ExprNodes.py b/Cython/Compiler/ExprNodes.py
+index 0fed86a..cce5c50 100644
+--- a/Cython/Compiler/ExprNodes.py
++++ b/Cython/Compiler/ExprNodes.py
+@@ -6539,9 +6539,7 @@ class TupleNode(SequenceNode):
+         if any(type.is_pyobject or type.is_unspecified or type.is_fused for type in arg_types):
+             return tuple_type
+         else:
+-            type = PyrexTypes.c_tuple_type(arg_types)
+-            env.declare_tuple_type(self.pos, type)
+-            return type
++            return env.declare_tuple_type(self.pos, arg_types).type
+
+     def analyse_types(self, env, skip_children=False):
+         if len(self.args) == 0:
+@@ -6552,8 +6550,7 @@ class TupleNode(SequenceNode):
+             if not skip_children:
+                 self.args = [arg.analyse_types(env) for arg in self.args]
+             if not self.mult_factor and not any(arg.type.is_pyobject or arg.type.is_fused for arg in self.args):
+-                self.type = PyrexTypes.c_tuple_type(arg.type for arg in self.args)
+-                env.declare_tuple_type(self.pos, self.type)
++                self.type = env.declare_tuple_type(self.pos, (arg.type for arg in self.args)).type
+                 self.is_temp = 1
+                 return self
+             else:
+diff --git a/Cython/Compiler/Nodes.py b/Cython/Compiler/Nodes.py
+index d6700d0..3ee9e9a 100644
+--- a/Cython/Compiler/Nodes.py
++++ b/Cython/Compiler/Nodes.py
+@@ -1180,10 +1180,9 @@ class CTupleBaseTypeNode(CBaseTypeNode):
+                 error(c.pos, "Tuple types can't (yet) contain Python objects.")
+                 return error_type
+             component_types.append(type)
+-        type = PyrexTypes.c_tuple_type(component_types)
+-        entry = env.declare_tuple_type(self.pos, type)
++        entry = env.declare_tuple_type(self.pos, component_types)
+         entry.used = True
+-        return type
++        return entry.type
+
+
+ class FusedTypeNode(CBaseTypeNode):
+diff --git a/Cython/Compiler/PyrexTypes.py b/Cython/Compiler/PyrexTypes.py
+index a4fc38d..bc61b6f 100644
+--- a/Cython/Compiler/PyrexTypes.py
++++ b/Cython/Compiler/PyrexTypes.py
+@@ -3684,13 +3684,11 @@ class CTupleType(CType):
+         env.use_utility_code(self._convert_from_py_code)
+         return True
+
+-c_tuple_types = {}
++
+ def c_tuple_type(components):
+     components = tuple(components)
+-    tuple_type = c_tuple_types.get(components)
+-    if tuple_type is None:
+-        cname = Naming.ctuple_type_prefix + type_list_identifier(components)
+-        tuple_type = c_tuple_types[components] = CTupleType(cname, components)
++    cname = Naming.ctuple_type_prefix + type_list_identifier(components)
++    tuple_type = CTupleType(cname, components)
+     return tuple_type
+
+
+diff --git a/Cython/Compiler/Symtab.py b/Cython/Compiler/Symtab.py
+index 7409420..c2f3ac8 100644
+--- a/Cython/Compiler/Symtab.py
++++ b/Cython/Compiler/Symtab.py
+@@ -610,8 +610,8 @@ class Scope(object):
+         self.sue_entries.append(entry)
+         return entry
+
+-    def declare_tuple_type(self, pos, type):
+-        return self.outer_scope.declare_tuple_type(pos, type)
++    def declare_tuple_type(self, pos, components):
++        return self.outer_scope.declare_tuple_type(pos, components)
+
+     def declare_var(self, name, type, pos,
+                     cname = None, visibility = 'private',
+@@ -1056,6 +1056,7 @@ class ModuleScope(Scope):
+         self.cached_builtins = []
+         self.undeclared_cached_builtins = []
+         self.namespace_cname = self.module_cname
++        self._cached_tuple_types = {}
+         for var_name in ['__builtins__', '__name__', '__file__', '__doc__', '__path__']:
+             self.declare_var(EncodedString(var_name), py_object_type, None)
+
+@@ -1075,18 +1076,24 @@ class ModuleScope(Scope):
+
+         return self.outer_scope.lookup(name, language_level=language_level)
+
+-    def declare_tuple_type(self, pos, type):
+-        cname = type.cname
++    def declare_tuple_type(self, pos, components):
++        components = tuple(components)
++        try:
++            ttype = self._cached_tuple_types[components]
++        except KeyError:
++            ttype = self._cached_tuple_types[components] = PyrexTypes.c_tuple_type(components)
++        cname = ttype.cname
+         entry = self.lookup_here(cname)
+         if not entry:
+             scope = StructOrUnionScope(cname)
+-            for ix, component in enumerate(type.components):
++            for ix, component in enumerate(components):
+                 scope.declare_var(name="f%s" % ix, type=component, pos=pos)
+-            struct_entry = self.declare_struct_or_union(cname + '_struct', 'struct', scope, typedef_flag=True, pos=pos, cname=cname)
++            struct_entry = self.declare_struct_or_union(
++                cname + '_struct', 'struct', scope, typedef_flag=True, pos=pos, cname=cname)
+             self.type_entries.remove(struct_entry)
+-            type.struct_entry = struct_entry
+-            entry = self.declare_type(cname, type, pos, cname)
+-        type.entry = entry
++            ttype.struct_entry = struct_entry
++            entry = self.declare_type(cname, ttype, pos, cname)
++        ttype.entry = entry
+         return entry
+
+     def declare_builtin(self, name, pos):