Merge branch 'develop' into public/refactor_integer_vectors-12453

* develop: (206 commits)
  Updated Sage version to 6.1.beta2
  fix latex
  fix documentation
  minor typography
  Trac 13101: mark doctest as "long time"
  trac 13101 better doctest
  Trac 13101: Fix bug in enumerate_totallyreal_fields_all
  #9706: review patch.
  trac 9706: Propose new class structure
  Symbolic Chebyshev polynomials: reviewer patch
  trac 9706: Collective patch. Bugfixes, extensions, optimizations, documentation, doctests for chebyshev_T, chebyshev_U and base class for ortho polys
  Updated Sage version to 6.1.beta1
  Fixing Whitespace errors
  Use bash as SHELL for build/Makefile
  allow numpy arrays in list_plot, line, points
  Run Jmol from current directory
  Trac #12322: Add a doctest for the correct behavior introduced in trac #12737.
  Trac #14186 coerce_binop errors with keyword arguments
  trac #15553: Broken links in the doc of graph/ and numerical/
  bug fix : importing BooleanPolynomialRing at the top-level prevents sage from starting
  ...

VERSION.txt

@@ -1 +1 @@
-Sage version 6.1.beta0, released 2013-12-19
+Sage version 6.1.beta2, released 2013-12-23

build/deps

@@ -109,10 +109,10 @@ all-sage: \
      $(INST)/$(NCURSES) \
      $(INST)/$(ZLIB) \
      $(INST)/$(ZNPOLY) \
-     scripts \
-     sage \
-     csage \
-     extcode
+     $(INST)/sage \
+     $(INST)/csage \
+     $(EXTCODE) \
+     $(SCRIPTS)
 
 # TOOLCHAIN consists of dependencies determined by build/install,
 # including for example the GCC package.
@@ -133,7 +133,7 @@ toolchain-deps:
 
 # Everything needed to start up Sage using "./sage".  Of course, not
 # every part of Sage will work.  It does not include Maxima for example.
-SAGERUNTIME = scripts sage $(INST)/$(SAGENB) $(INST)/$(IPYTHON) $(INST)/$(GAP)
+SAGERUNTIME = $(SCRIPTS) $(INST)/sage $(INST)/$(SAGENB) $(INST)/$(IPYTHON)
 
 ###############################################################################
 # Building the base system
@@ -308,7 +308,7 @@ $(INST)/$(SQLITE): $(INST)/$(READLINE)
 	+$(PIPE) "$(SAGE_SPKG) $(SQLITE) 2>&1" "tee -a $(SAGE_LOGS)/$(SQLITE).log"
 
 # To build SageTeX, you just need Python, but to test (SAGE_CHECK=yes)
-# SageTeX, you actually need to run sage, produce plots,...
+# SageTeX, you actually need to run Sage, produce plots,...
 $(INST)/$(SAGETEX): $(INST)/$(PYTHON) \
                     $(SAGERUNTIME) $(INST)/$(MAXIMA) $(INST)/$(SCIPY) \
                     $(INST)/$(MATPLOTLIB) $(INST)/$(PIL) $(INST)/$(TACHYON)
@@ -418,7 +418,7 @@ $(INST)/$(PYGMENTS): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
 # on the one hand, programs needed for the build/install process of the
 # Sage library (e.g. JINJA2), and on the
 # other hand all dependencies for Cython files (e.g. PARI, NTL, MPIR).
-sage: \
+$(INST)/sage: \
 		 $(INST)/$(ATLAS) \
 		 $(INST)/$(CEPHES) \
 		 $(INST)/$(CLIQUER) \
@@ -456,21 +456,25 @@ sage: \
 		 $(INST)/$(SINGULAR) \
 		 $(INST)/$(SYMMETRICA) \
 		 $(INST)/$(ZNPOLY) \
-		 csage
-	$(PIPE) '{ if [ -z "$(SAGE_INSTALL_FETCH_ONLY)" ]; then cd $(SAGE_SRC) && . ./bin/sage-env && time python setup.py install; fi; } 2>&1' 'tee -a $(SAGE_LOGS)/sage-$(SAGE_VERSION).log'
-
-scripts: $(SCRIPT_TARGETS)
-
-extcode: $(EXTCODE_TARGETS)
-
-csage: $(INST)/$(SCONS) \
+		 $(INST)/csage
+	if [ -z "$$SAGE_INSTALL_FETCH_ONLY" ]; then \
+		cd $(SAGE_SRC) && source bin/sage-env && \
+		$(PIPE) 'time python setup.py install 2>&1' 'tee -a $(SAGE_LOGS)/sage-$(SAGE_VERSION).log' && \
+		touch $@; \
+	fi
+
+$(INST)/csage: $(INST)/$(SCONS) \
        $(INST)/$(MPIR) \
        $(INST)/$(NTL) \
        $(INST)/$(PARI) \
        $(INST)/$(POLYBORI) \
        $(INST)/$(PYNAC) \
        $(INST)/$(PYTHON)
-	$(PIPE) '{ if [ -z "$(SAGE_INSTALL_FETCH_ONLY)" ]; then cd $(SAGE_SRC)/c_lib && . ../bin/sage-env && time scons -Q install; fi; } 2>&1' 'tee -a $(SAGE_LOGS)/csage-$(SAGE_VERSION).log'
+	if [ -z "$$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' && \
+		touch $@; \
+	fi
 
 $(INST)/ccache: $(BASE) $(INST)/$(ZLIB)
 	+$(PIPE) "$(SAGE_SPKG) ccache 2>&1" "tee -a $(SAGE_LOGS)/ccache.log"

build/install

@@ -331,6 +331,11 @@ cat >&3 <<EOF
 
 EOF
 
+# Use bash as shell for the Makefile (bash obviously exists, since
+# this build/install script runs under bash).
+echo >&3 "SHELL = `command -v bash`"
+echo >&3
+
 # If the user (or the Makefile) has set SAGE_PARALLEL_SPKG_BUILD=no,
 # then turn off parallel building: disable just building multiple
 # packages at the same time.   Individual packages can still be built
@@ -490,7 +495,7 @@ for file in "$SAGE_SRC/bin/"*; do
     echo >&3 "                 \$(SAGE_SRC)${file#$SAGE_SRC} \\"
 done
 echo >&3
-echo >&3 'SCRIPT_TARGETS = \'
+echo >&3 'SCRIPTS = \'
 for file in "$SAGE_SRC/bin/"*; do
     echo >&3 "                 \$(SAGE_LOCAL)${file#$SAGE_SRC} \\"
 done
@@ -500,7 +505,7 @@ for file in `find "$SAGE_SRC"/ext -type f`; do
     echo >&3 "                  \$(SAGE_SRC)${file#$SAGE_SRC} \\"
 done
 echo >&3
-echo >&3 'EXTCODE_TARGETS = \'
+echo >&3 'EXTCODE = \'
 for file in `find "$SAGE_SRC"/ext -type f`; do
     echo >&3 "                  \$(SAGE_EXTCODE)${file#$SAGE_SRC/ext} \\"
 done

build/pkgs/cython/patches/gdbout.patch

@@ -0,0 +1,20 @@
+--- src.orig/Cython/Compiler/CmdLine.py	2013-05-11 07:46:55.000000000 +0200
++++ src/Cython/Compiler/CmdLine.py	2013-06-04 19:09:59.000000000 +0200
+@@ -28,6 +28,7 @@ Options:
+   -w, --working <directory>      Sets the working directory for Cython (the directory modules
+                                  are searched from)
+   --gdb                          Output debug information for cygdb
++  --gdb-outdir <directory>       Specify gdb debug information output directory. Implies --gdb.
+
+   -D, --no-docstrings            Strip docstrings from the compiled module.
+   -a, --annotate                 Produce a colorized HTML version of the source.
+@@ -138,6 +125,9 @@ def parse_command_line(args):
+             elif option == "--gdb":
+                 options.gdb_debug = True
+                 options.output_dir = os.curdir
++            elif option == "--gdb-outdir":
++                options.gdb_debug = True
++                options.output_dir = pop_arg()
+             elif option == '-2':
+                 options.language_level = 2
+             elif option == '-3':

src/bin/sage-banner

@@ -1,5 +1,5 @@
 ┌────────────────────────────────────────────────────────────────────┐
-│ Sage Version 6.1.beta0, Release Date: 2013-12-19                   │
+│ Sage Version 6.1.beta2, Release Date: 2013-12-23                   │
 │ Type "notebook()" for the browser-based notebook interface.        │
 │ Type "help()" for help.                                            │
 └────────────────────────────────────────────────────────────────────┘

src/bin/sage-version.sh

@@ -1,4 +1,4 @@
 # Sage version information for shell scripts
 # This file is auto-generated by the sage-update-version script, do not edit!
-SAGE_VERSION='6.1.beta0'
-SAGE_RELEASE_DATE='2013-12-19'
+SAGE_VERSION='6.1.beta2'
+SAGE_RELEASE_DATE='2013-12-23'

src/c_lib/include/interrupt.h

@@ -307,13 +307,6 @@ static inline void _sig_off_(const char* file, int line)
 #define sig_str(message)   _sig_on_(message)
 #define sig_off()          _sig_off_(__FILE__, __LINE__)
 
-/* These deprecated macros provide backwards compatibility with
- * sage-4.6 and earlier */
-#define _sig_on        {if (!_sig_on_(NULL)) return 0;}
-#define _sig_str(s)    {if (!_sig_on_(s)) return 0;}
-#define _sig_off       {_sig_off_(__FILE__, __LINE__);}
-
-
 /* sig_check() should be functionally equivalent to sig_on(); sig_off();
  * but much faster.  Essentially, it checks whether we missed any
  * interrupts.

src/c_lib/src/interrupt.c

@@ -214,10 +214,11 @@ void sage_signal_handler(int sig)
 
 
 /* This calls the externally defined function _signals.raise_exception
- * to actually raise the exception. It may only be called synchronously
- * with the Global Interpreter Lock held. */
+ * to actually raise the exception. Since it uses the Python API, the
+ * GIL needs to be acquired first. */
 static void do_raise_exception(int sig)
 {
+    PyGILState_STATE gilstate_save = PyGILState_Ensure();
 #if ENABLE_DEBUG_INTERRUPT
     struct timeval raisetime;
     if (sage_interrupt_debug_level >= 2) {
@@ -235,6 +236,8 @@ static void do_raise_exception(int sig)
         _signals.raise_exception(sig, _signals.s);
         assert(PyErr_Occurred());
     }
+
+    PyGILState_Release(gilstate_save);
 }
 
 
@@ -268,7 +271,12 @@ void _sig_off_warning(const char* file, int line)
 {
     char buf[320];
     snprintf(buf, sizeof(buf), "sig_off() without sig_on() at %s:%i", file, line);
+
+    /* Raise a warning with the Python GIL acquired */
+    PyGILState_STATE gilstate_save = PyGILState_Ensure();
     PyErr_WarnEx(PyExc_RuntimeWarning, buf, 2);
+    PyGILState_Release(gilstate_save);
+
     print_backtrace();
 }
 

src/c_lib/src/mpn_pylong.c

@@ -4,16 +4,16 @@
  * Date:    March 2006
  * License: GPL v2 or later
  *
- * the code to change the base to 2^SHIFT is based on the function
+ * the code to change the base to 2^PyLong_SHIFT is based on the function
  * mpn_get_str from GNU MP, but the new bugs are mine
  *
  * this is free software: if it breaks, you get to keep all the pieces
  */
 
 #include "mpn_pylong.h"
 
-/* This code assumes that SHIFT < GMP_NUMB_BITS */
-#if SHIFT >= GMP_NUMB_BITS
+/* This code assumes that PyLong_SHIFT < GMP_NUMB_BITS */
+#if PyLong_SHIFT >= GMP_NUMB_BITS
 #error "Python limb larger than GMP limb !!!"
 #endif
 
@@ -61,15 +61,15 @@ pylong_sizebits(digit *digits, py_size_t size) {
   unsigned long cnt;
   digit x;
   if (size==0) return 0;
-  cnt = (size - 1) * SHIFT;
+  cnt = (size - 1) * PyLong_SHIFT;
   x = digits[size - 1];
-#if SHIFT > 32
+#if PyLong_SHIFT > 32
   if ((x >> 32) != 0) { x >>= 32; cnt += 32; }
 #endif
-#if SHIFT > 16
+#if PyLong_SHIFT > 16
   if ((x >> 16) != 0) { x >>= 16; cnt += 16; }
 #endif
-#if SHIFT > 8
+#if PyLong_SHIFT > 8
   if ((x >>  8) != 0) { x >>=  8; cnt += 8; }
 #endif
   return cnt + ((x & 0x80) ? 8 : __sizebits_tab[x]);
@@ -81,7 +81,7 @@ pylong_sizebits(digit *digits, py_size_t size) {
 int
 mpn_pylong_size (mp_ptr up, mp_size_t un)
 {
-  return (mpn_sizebits(up, un) + SHIFT - 1) / SHIFT;
+  return (mpn_sizebits(up, un) + PyLong_SHIFT - 1) / PyLong_SHIFT;
 }
 
 /* this is based from GMP code in mpn/get_str.c */
@@ -106,19 +106,19 @@ mpn_get_pylong (digit *digits, py_size_t size, mp_ptr up, mp_size_t un)
 
   i = un - 1;
   n1 = up[i];
-  bit_pos = size * SHIFT - i * GMP_NUMB_BITS;
+  bit_pos = size * PyLong_SHIFT - i * GMP_NUMB_BITS;
 
   for (;;)
     {
-      bit_pos -= SHIFT;
+      bit_pos -= PyLong_SHIFT;
       while (bit_pos >= 0)
         {
-          *--s = (n1 >> bit_pos) & MASK;
-          bit_pos -= SHIFT;
+          *--s = (n1 >> bit_pos) & PyLong_MASK;
+          bit_pos -= PyLong_SHIFT;
         }
       if (i == 0)
         break;
-      n0 = (n1 << -bit_pos) & MASK;
+      n0 = (n1 << -bit_pos) & PyLong_MASK;
       n1 = up[--i];
       bit_pos += GMP_NUMB_BITS;
       *--s = n0 | (n1 >> bit_pos);
@@ -150,22 +150,22 @@ mpn_set_pylong (mp_ptr up, mp_size_t un, digit *digits, py_size_t size)
 
   i = un - 1;
   n1 = 0;
-  bit_pos = size * SHIFT - i * GMP_NUMB_BITS;
+  bit_pos = size * PyLong_SHIFT - i * GMP_NUMB_BITS;
 
   for (;;)
     {
-      bit_pos -= SHIFT;
+      bit_pos -= PyLong_SHIFT;
       while (bit_pos >= 0)
         {
           d = (mp_limb_t) *--s;
           n1 |= (d << bit_pos) & GMP_NUMB_MASK;
-          bit_pos -= SHIFT;
+          bit_pos -= PyLong_SHIFT;
         }
       if (i == 0)
         break;
       d = (mp_limb_t) *--s;
-      /* add some high bits of d; maybe none if bit_pos=-SHIFT */
-      up[i--] = n1 | (d & MASK) >> -bit_pos;
+      /* add some high bits of d; maybe none if bit_pos=-PyLong_SHIFT */
+      up[i--] = n1 | (d & PyLong_MASK) >> -bit_pos;
       bit_pos += GMP_NUMB_BITS;
       n1 = (d << bit_pos) & GMP_NUMB_MASK;
     }

src/c_lib/src/mpz_pylong.c

@@ -37,7 +37,7 @@ mpz_get_pylong(mpz_srcptr z)
   {
     mpn_get_pylong(l->ob_digit, size, z->_mp_d, abs(z->_mp_size));
     if (z->_mp_size < 0)
-      l->ob_size = -(l->ob_size);
+      Py_SIZE(l) = -Py_SIZE(l);
   }
 
   return (PyObject *) l;
@@ -68,13 +68,13 @@ mpz_set_pylong(mpz_ptr z, PyObject * ll)
     return -1;
   }
 
-  size = mpn_size_from_pylong(l->ob_digit, abs(l->ob_size));
+  size = mpn_size_from_pylong(l->ob_digit, abs(Py_SIZE(l)));
 
   if (z->_mp_alloc < size)
     _mpz_realloc (z, size);
 
-  mpn_set_pylong(z->_mp_d, size, l->ob_digit, abs(l->ob_size));
-  z->_mp_size = l->ob_size < 0 ? -size : size;
+  mpn_set_pylong(z->_mp_d, size, l->ob_digit, abs(Py_SIZE(l)));
+  z->_mp_size = Py_SIZE(l) < 0 ? -size : size;
 
   return size;
 }

src/c_lib/src/stdsage.c

@@ -33,13 +33,13 @@ void init_global_empty_tuple(void) {
 /*
   This function gets called whenever NTL calls Error().
   s is the error message generated by NTL.
-  We just copy the error message into a global buffer, and then abort() to run
-  the usual interrupt machinery.
+  We raise a RuntimeError and then call sig_error() such that the
+  exception will be seen by sig_on().
  */
 void global_NTL_error_callback(const char* s, void* context)
 {
-    set_sage_signal_handler_message(s);
-    abort();
+    PyErr_SetString(PyExc_RuntimeError, s);
+    sig_error();
 }
 
 

src/doc/en/constructions/linear_codes.rst

@@ -22,7 +22,7 @@ Sage can compute Hamming codes
 
 ::
 
-    sage: C = HammingCode(3,GF(3))
+    sage: C = codes.HammingCode(3,GF(3))
     sage: C
     Linear code of length 13, dimension 10 over Finite Field of size 3
     sage: C.minimum_distance()
@@ -46,7 +46,7 @@ the four Golay codes
 
 ::
 
-    sage: C = ExtendedTernaryGolayCode()
+    sage: C = codes.ExtendedTernaryGolayCode()
     sage: C
     Linear code of length 12, dimension 6 over Finite Field of size 3
     sage: C.minimum_distance()
@@ -74,7 +74,7 @@ a check matrix, and the dual code:
 
 ::
 
-    sage: C = HammingCode(3,GF(2))
+    sage: C = codes.HammingCode(3,GF(2))
     sage: Cperp = C.dual_code()
     sage: C; Cperp
     Linear code of length 7, dimension 4 over Finite Field of size 2
@@ -90,7 +90,7 @@ a check matrix, and the dual code:
       [0 0 0 1 1 1 1]
     sage: C.dual_code()
     Linear code of length 7, dimension 3 over Finite Field of size 2
-    sage: C = HammingCode(3,GF(4,'a'))
+    sage: C = codes.HammingCode(3,GF(4,'a'))
     sage: C.dual_code()
     Linear code of length 21, dimension 3 over Finite Field in a of size 2^2
 
@@ -102,7 +102,7 @@ implemented.
 
 ::
 
-    sage: C = HammingCode(3,GF(2))
+    sage: C = codes.HammingCode(3,GF(2))
     sage: MS = MatrixSpace(GF(2),1,7)
     sage: F = GF(2); a = F.gen()
     sage: v1 = [a,a,F(0),a,a,F(0),a]
@@ -120,7 +120,7 @@ can use the matplotlib package included with Sage:
 
 ::
 
-    sage: C = HammingCode(4,GF(2))
+    sage: C = codes.HammingCode(4,GF(2))
     sage: C
      Linear code of length 15, dimension 11 over Finite Field of size 2
     sage: w = C.weight_distribution(); w