Merge branch 'develop' into t/20973/cartan_type_aoo

* develop: (155 commits)
  Updated SageMath version to 7.3.beta8
  py3 imports in manifolds and symbolic folders
  py3 imports in homology and tensor folders
  py3 imports in doctest, dynamics, quadratic_forms folders
  p3 imports in databases, quivers, repl, sets folders
  Fix formatting for examples in this file
  Trac 19779: fix references
  trac 14490 adding doctest
  trac 21011 adding not tested to raise statement
  These tests needed to be updated further since they also tested the number of lines in the test function (that happens to be 'banner', the length of which has changed).
  Restore the logic of not displaying any banner if SAGE_BANNER is explicitly 'no'
  trac 21008 fixing doctests in posets
  Banner text should be quoted
  trac 21008 utf8 encoding of file, plus nicer doctest
  Follow upstream and use inputenc only when building with pdftex
  trac 21011 details
  a few more python3 print
  trac 21008 allow unicode labels in graphs
  Trac 19779: more coherence in references
  Trac 19779: Python 3 print compatibility
  ...

VERSION.txt

@@ -1 +1 @@
-SageMath version 7.3.beta7, Release Date: 2016-07-08
+SageMath version 7.3.beta8, Release Date: 2016-07-14

build/pkgs/atlas/spkg-install

@@ -143,6 +143,7 @@ if 'SAGE_ATLAS_LIB' in os.environ:
 
     paths = [ ATLAS_LIB, os.path.join(ATLAS_LIB, 'lib64'), os.path.join(ATLAS_LIB, 'lib') ]
     ATLAS_LIB = None
+    libraries = []
     for libs in libraries_sets:
         for path in paths:
             if is_atlas_lib_path(path, libs):
@@ -209,7 +210,7 @@ if 'SAGE_ATLAS_LIB' in os.environ:
     for lib in libraries + libraries_optional:
         symlinkOSlibrary(prefix+lib)
 
-    if 'atlas' in libs:
+    if 'atlas' in libraries:
         write_pc_file(['cblas', 'atlas'], 'cblas')
         write_pc_file(['f77blas', 'atlas'], 'blas')
         # The inclusion of cblas is not a mistake. ATLAS' lapack include

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=f61a172a42a9f55c79bb6404290ee41163ccdad0
-md5=d342f35e46105c010e86cc3f733b85cd
-cksum=3230256794
+sha1=9bea2597a9ed11310446ffb2fef3f8df71893e75
+md5=aefa1d5044a5ed8eda8236bb637bb74c
+cksum=3931049725

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-172
+173

build/pkgs/frobby/SPKG.txt

@@ -0,0 +1,55 @@
+= Frobby =
+
+== Description ==
+The software package Frobby provides a number of computations on
+monomial ideals. The current main feature is the socle of a monomial
+ideal, which is largely equivalent to computing the maximal standard
+monomials, the Alexander dual or the irreducible decomposition.
+
+Operations on monomial ideals are much faster than algorithms designed
+for ideals in general, which is what makes a specialized library for
+these operations on monomial ideals useful.
+
+== License ==
+ * GPL version 2.0 or later
+
+== Maintainers ==
+ * Bjarke Hammersholt Roune (www.broune.com)
+
+== Upstream Contact ==
+ * Bjarke Hammersholt Roune (www.broune.com)
+
+== Dependencies ==
+ * GMP built with support for C++
+
+== Special Update/Build instructions ==
+Download Frobby at www.broune.com/ and then type "make spkg VER=blah" which wil create an spkg
+named frobby-VER.spkg in bin/. The files related to doing this is in the sage/ sub-directory of the
+Frobby source distribution.
+
+== Changelog ==
+
+=== frobby-0.9.0.p2 (Dima Pasechnik, Jun 30, 2016) ===
+ * convertion to new-style package
+ * integration of Macaulay2 patches
+ * fix linking (rpath)
+
+=== frobby-0.9.0.p1 (Dima Pasechnik, Sept 7, 2013) ===
+ * added <unistd.h> for getpid() 
+
+=== frobby-0.9.0 (Mike Hansen, May 24th, 2012) ===
+ * #13007: Update to 0.9.0.
+ * Add a patch to the Makefile so that the build succeeds with SAGE_CHECK="yes"
+
+=== frobby-0.7.6 (Bjarke Hammersholt Roune, May 20th, 2008) ===
+ * Move to Frobby 0.7.6 with Makefile improvements by Michale Abshoff.
+
+=== frobby-0.7.5.p1 (Michael Abshoff, May 19th, 2008) ===
+ * fix the main Makefile to set include and library directories correctly when some env variables are defined
+
+=== frobby-0.7.5.p0 (Michael Abshoff, May 19th, 2008) ===
+ * various cleanups, i.e. repo, .hgignore, missing SPKG.txt sections
+ * move all sources into src
+
+=== frobby-0.7.5 (Bjarke Hammersholt Roune) ===
+ * initial version

build/pkgs/frobby/checksums.ini

@@ -0,0 +1,4 @@
+tarball=frobby_v0.9.0.tar.gz
+sha1=513b6e2ef8e8670c0518d168c2e554df1f8d79b4
+md5=2204f340dad8fb7be156f9f7c403c4a0
+cksum=2889611419

build/pkgs/frobby/dependencies

@@ -0,0 +1 @@
+$(MP_LIBRARY)

build/pkgs/frobby/package-version.txt

@@ -0,0 +1 @@
+0.9.0.p2

build/pkgs/frobby/patches/HashMap.h.patch

@@ -0,0 +1,31 @@
+--- /tmp/HashMap.h 2011-09-23 16:09:12.000000000 -0400
++++ src/HashMap.h 2015-06-06 12:56:15.000000000 -0400
+@@ -35,10 +35,16 @@
+ class FrobbyHash {};
+
+ // *********************************************************
+-#ifdef __GNUC__ // Only GCC defines this macro
++#if defined(__GNUC__) || defined(__clang__)
++#if 0
+ #include "hash_map/hash_map"
+ #include <string>
++#endif
++#include <unordered_map>
++template<class Key, class Value>
++  class HashMap : public std::unordered_map<Key, Value, FrobbyHash<Key>> { };
+
++#if 0
+ template<>
+ class FrobbyHash<string> : public __gnu_cxx::hash<string> {
+ };
+@@ -47,9 +53,8 @@
+ class HashMap : public __gnu_cxx::hash_map<Key, Value,
+   FrobbyHash<Key> > {
+ };
+-
++#endif
+ #else
+-
+ // *********************************************************
+ #ifdef _MSC_VER // Only Microsoft C++ defines this macro
+ #include <hash_map>

build/pkgs/frobby/patches/Makefile.patch

@@ -0,0 +1,30 @@
+--- Makefile.orig	2011-09-23 21:09:12.000000000 +0100
++++ Makefile	2016-06-30 07:47:38.314034517 +0100
+@@ -70,8 +70,8 @@
+   BIN_INSTALL_DIR = "/usr/local/bin/"
+ endif
+
+-cflags = $(CFLAGS) $(CPPFLAGS) -Wall -ansi -pedantic -I $(GMP_INC_DIR)	\
+-         -Wno-uninitialized -Wno-unused-parameter
++cflags = $(CFLAGS) $(CPPFLAGS) -Wall -I $(GMP_INC_DIR)	\
++         -Wno-uninitialized -Wno-unused-parameter -std=c++11
+ program = frobby
+ library = libfrobby.a
+ benchArgs = $(FROBBYARGS)
+@@ -93,7 +93,7 @@
+ ifeq ($(MODE), debug)
+   rawSources := $(rawSources) $(rawTests)
+   outdir = bin/debug/
+-  cflags += -g -D DEBUG -fno-inline -Werror -Wextra -Wno-uninitialized \
++  cflags += -g -D DEBUG -fno-inline -Wextra -Wno-uninitialized \
+             -Wno-unused-parameter
+   MATCH=true
+ endif
+@@ -217,6 +217,7 @@
+ 	  $(patsubst $(outdir)main.o,,$(objs))
+ else
+ 	ar crs bin/$(library) $(patsubst $(outdir)main.o,,$(objs))
++	$(RANLIB) bin/$(library)
+ endif
+
+ # Compile and output object files.

build/pkgs/frobby/patches/StatisticsStrategy.cpp.patch

@@ -0,0 +1,11 @@
+--- /tmp/StatisticsStrategy.cpp     2011-09-23 16:09:12.000000000 -0400
++++ src/StatisticsStrategy.cpp    2013-05-18 17:22:09.000000000 -0400
+@@ -140,7 +140,7 @@
+   if (_nodeCount == 0)
+     return 0.0;
+   else {
+-    mpz_class q = mpq_class(_subGenSum) / _nodeCount;
++    mpq_class q = mpq_class(_subGenSum) / _nodeCount;
+     return q.get_d();
+   }
+ }

build/pkgs/frobby/patches/StringStream.patch

@@ -0,0 +1,24 @@
+--- /tmp/FrobbyStringStream.cpp    2011-09-23 15:09:12.000000000 -0500
++++ src/FrobbyStringStream.cpp    2013-05-10 11:42:01.840492200 -0500
+@@ -41,6 +41,11 @@
+   return *this;
+ }
+
++FrobbyStringStream& FrobbyStringStream::operator<<(unsigned long long integer) {
++  appendIntegerToString(_str, integer);
++  return *this;
++}
++
+ FrobbyStringStream& FrobbyStringStream::operator<<(unsigned long integer) {
+   appendIntegerToString(_str, integer);
+   return *this;
+--- /tmp/FrobbyStringStream.h      2011-09-23 15:09:12.000000000 -0500
++++ src/FrobbyStringStream.h      2013-05-10 11:42:01.843492400 -0500
+@@ -25,6 +25,7 @@
+  used for operations that need to be efficient. */
+ class FrobbyStringStream {
+  public:
++  FrobbyStringStream& operator<<(unsigned long long integer);
+   FrobbyStringStream& operator<<(unsigned long integer);
+   FrobbyStringStream& operator<<(unsigned int integer);
+   FrobbyStringStream& operator<<(const mpz_class& integer);

build/pkgs/frobby/patches/Term.h.patch

@@ -0,0 +1,24 @@
+--- /tmp/Term.h    2011-09-23 15:09:12.000000000 -0500
++++ src/Term.h    2013-05-10 11:42:01.846492600 -0500
+@@ -99,6 +99,10 @@
+     ASSERT(offset < _varCount);
+     return _exponents[offset];
+   }
++  Exponent operator[](unsigned long long offset) const {
++    ASSERT(offset < _varCount);
++    return _exponents[offset];
++  }
+
+   Exponent& operator[](int offset) {
+     ASSERT(0 <= offset);
+@@ -113,6 +117,10 @@
+     ASSERT(offset < _varCount);
+     return _exponents[offset];
+   }
++  Exponent& operator[](unsigned long long offset) {
++    ASSERT(offset < _varCount);
++    return _exponents[offset];
++  }
+
+   bool operator==(const Term& term) const {
+     ASSERT(_varCount == term._varCount);

build/pkgs/frobby/patches/VarNames.h.patch

@@ -0,0 +1,21 @@
+--- /tmp/VarNames.h      2011-09-23 16:09:12.000000000 -0400
++++ src/VarNames.h        2015-06-06 12:36:28.000000000 -0400
+@@ -21,7 +21,7 @@
+
+ #include <vector>
+ #include <string>
+-
++#include <unordered_map>
+ class Scanner;
+
+ /** Defines the variables of a polynomial ring and facilities IO
+@@ -102,7 +102,8 @@
+ private:
+   static bool compareNames(const string* a, const string* b);
+
+-  typedef HashMap<string, size_t> VarNameMap;
++  typedef unordered_map<string, size_t> VarNameMap;
++  //typedef HashMap<string, size_t> VarNameMap;
+   VarNameMap _nameToIndex;
+   vector<const string*> _indexToName;
+ };

build/pkgs/frobby/patches/main.cpp.patch

@@ -0,0 +1,13 @@
+*** /tmp/main.cpp	Sat Sep  7 14:09:12 2013
+--- src/main.cpp	Sat Sep  7 14:09:44 2013
+***************
+*** 24,29 ****
+--- 24,31 ----
+
+  #include <ctime>
+  #include <cstdlib>
++ #include <unistd.h> /* needed for getpid */
++
+
+  /** This function runs the Frobby console interface. the ::main
+      function calls this function after having set up DEBUG-specific

build/pkgs/frobby/patches/randomDataGenerators.cpp.patch

@@ -0,0 +1,12 @@
+*** /tmp/randomDataGenerators.cpp	Sat Sep  7 14:09:19 2013
+--- src/randomDataGenerators.cpp	Sat Sep  7 14:10:19 2013
+***************
+*** 25,30 ****
+--- 25,31 ----
+
+  #include <limits>
+  #include <ctime>
++ #include <unistd.h> /* needed for getpid */
+
+  void generateLinkedListIdeal(BigIdeal& ideal, size_t variableCount) {
+    VarNames names(variableCount);

build/pkgs/frobby/patches/stdinc.h.patch

@@ -0,0 +1,10 @@
+--- /tmp/stdinc.h        2011-09-23 16:09:12.000000000 -0400
++++ src/stdinc.h  2015-06-02 21:27:34.000000000 -0400
+@@ -29,6 +29,7 @@
+ // Some versions of GMP do not define gmp_fprintf unless cstdio is
+ // included first, so we have to include it here.
+ #include <cstdio>
++#include <cstddef>
+
+ #include <gmp.h>
+ #include <gmpxx.h>

build/pkgs/frobby/patches/tests.patch

@@ -0,0 +1,53 @@
+--- /tmp/test/messages/runtest 2011-09-23 15:09:12.000000000 -0500
++++ test/messages/runtest 2013-05-10 11:42:01.825491400 -0500
+@@ -9,7 +9,7 @@
+ action="$1"
+ shift
+
+-tmpFile="/tmp/errorTestHelperTmp"
++tmpFile="./errorTestHelperTmp"
+ echo "$1" > $tmpFile
+ shift
+
+--- /tmp/test/testScripts/run_euler_test       2011-09-23 15:09:13.000000000 -0500
++++ test/testScripts/run_euler_test       2013-05-10 11:42:01.829491600 -0500
+@@ -3,9 +3,9 @@
+ frobby=../../bin/frobby
+ testhelper=../testScripts/testhelper
+ test="$1"
+-tmpFile=/tmp/frobbyEulerRadicalTmp
+-tmpFileInverted=/tmp/frobbyEulerRadicalInvertedTmp
+-tmpFileTransposed=/tmp/frobbyEulerRadicalTransposedTmp
++tmpFile=./frobbyEulerRadicalTmp
++tmpFileInverted=./frobbyEulerRadicalInvertedTmp
++tmpFileTransposed=./frobbyEulerRadicalTransposedTmp
+ genPivots="rarevar popvar maxsupp minsupp any random rarest raremax"
+ stdPivots="popvar rarevar popgcd any random"
+ shift
+--- /tmp/test/testScripts/testhelper   2011-09-23 15:09:13.000000000 -0500
++++ test/testScripts/testhelper   2013-05-10 11:42:01.833491800 -0500
+@@ -57,10 +57,10 @@
+
+ origParams="$*" # used for debug output below
+ origFrobby="../../bin/frobby"
+-origFrobbyOut="/tmp/frobbyTestScriptTemporary_standardOutput"
+-origFrobbyErr="/tmp/frobbyTestScriptTemporary_standardError"
+-frobbyChangedErr="/tmp/frobbyTestScriptTemporary_standardErrorChanged"
+-frobbyChangedInput="/tmp/frobbyTestScriptTemporary_standardInput"
++origFrobbyOut="./frobbyTestScriptTemporary_standardOutput"
++origFrobbyErr="./frobbyTestScriptTemporary_standardError"
++frobbyChangedErr="./frobbyTestScriptTemporary_standardErrorChanged"
++frobbyChangedInput="./frobbyTestScriptTemporary_standardInput"
+
+ frobby="$origFrobby"
+ frobbyOut="$origFrobbyOut"
+--- /tmp/test/internal/runtests      2011-09-23 13:09:12.000000000 -0700
++++ test/internal/runtests        2014-07-30 10:46:31.033944047 -0700
+@@ -7,6 +7,6 @@
+ fi
+
+ $frobby test 2> /dev/null > /dev/null
+-if [ $? == 0 ]; then exit 0; fi
++if [ $? = 0 ]; then exit 0; fi
+ echo "*** Internal test failed, rerunning tests with output ***"
+ $frobby test

build/pkgs/frobby/spkg-check

@@ -0,0 +1,14 @@
+#!/usr/bin/env sh
+
+if [ "$SAGE_LOCAL" = "" ]; then
+   echo "SAGE_LOCAL undefined ... exiting";
+   echo "Maybe run 'sage -sh'?"
+   exit 1
+fi
+
+GMP_INC_DIR="$SAGE_LOCAL/include"; export GMP_INC_DIR
+ldflags="-L$SAGE_LOCAL/lib/ -lgmpxx -lgmp"; export ldflags
+
+cd src/
+$MAKE test MODE=debug # run tests with assertions turned on
+$MAKE test MODE=release # test the binaries used by Sage

build/pkgs/frobby/spkg-install

@@ -0,0 +1,44 @@
+#!/usr/bin/env sh
+
+if [ "$SAGE_LOCAL" = "" ]; then
+   echo "SAGE_LOCAL undefined ... exiting";
+   echo "Maybe run 'sage -sh'?"
+   exit 1
+fi
+
+rm -rf "$SAGE_LOCAL/bin/frobby"
+
+GMP_INC_DIR="$SAGE_LOCAL/include"; export GMP_INC_DIR
+ldflags="-Wl,-rpath,$SAGE_LOCAL/lib -L$SAGE_LOCAL/lib/ -lgmpxx -lgmp"; export ldflags
+
+cd src
+
+# Apply fixes to upstream source
+echo "Applying patches..."
+for patch in ../patches/*.patch; do
+    [ -r "$patch" ] || continue  # Skip non-existing or non-readable patches
+    patch -p0 <"$patch"
+    if [ $? -ne 0 ]; then
+        echo >&2 "Error applying '$patch'"
+        exit 1
+    fi
+done
+
+$MAKE MODE=release
+
+if [ $? -ne 0 ]; then
+   echo "Error building Frobby."
+   exit 1
+fi
+
+if [ ! -f bin/release/frobby ]; then
+   echo "Frobby executable not found."
+   exit 1
+fi
+
+$CP bin/release/frobby "$SAGE_LOCAL/bin/"
+
+if [ ! -f "$SAGE_LOCAL/bin/frobby" ]; then
+   echo "Frobby executable not copied."
+   exit 1
+fi

build/pkgs/frobby/type

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