Merge branch 'develop' into ticket/16908-maxima-5.34.1

VERSION.txt

@@ -1 +1 @@
-Sage version 6.4.beta2, released 2014-08-28
+Sage version 6.4.beta3, released 2014-09-10

build/pkgs/buckygen/SPKG.txt

@@ -0,0 +1,29 @@
+= Buckygen =
+
+== Description ==
+Buckygen is a program for the efficient generation of all nonisomorphic fullerenes. These are triangulations where all vertices have degree 5 or 6. Or if the dual representation is used: cubic plane graphs where all faces are pentagons or hexagons. 
+
+== License ==
+Buckygen is licensed under the GNU General Public License v3 ( June 2007 )
+
+== SPKG Maintainers ==
+Nico Van Cleemput (nico.vancleemput@gmail.com)
+
+== Upstream Contact ==
+Buckygen was mainly written by Jan Goedgebeur, jan.goedgebeur[at]ugent.be.
+http://caagt.ugent.be/buckygen/
+
+== Dependencies ==
+ * None
+
+== Changelog ==
+
+=== buckygen-1.0 (Nico Van Cleemput, 9th September 2014) ===
+ * #16945: Update for the sage-git directory layout.
+
+=== buckygen-1.0 (Nico Van Cleemput, 3rd September 2013) ===
+ * Fixed error in license info.
+
+=== buckygen-1.0 (Nico Van Cleemput, 25th May 2013) ===
+ * First release put into Sage.
+

build/pkgs/buckygen/checksums.ini

@@ -0,0 +1,4 @@
+tarball=buckygen-VERSION.tar.bz2
+sha1=db4fe52211e25b8964308f8bea19db32242c1f1d
+md5=d33ea8f76b95a69842a291f88ed501fb
+cksum=1430056194

build/pkgs/buckygen/package-version.txt

@@ -0,0 +1 @@
+1.0

build/pkgs/buckygen/spkg-install

@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+
+if [ -z "$SAGE_LOCAL" ]; then
+    echo >&2 "SAGE_LOCAL undefined ... exiting"
+    echo >&2 "Maybe run 'sage --sh'?"
+    exit 1
+fi
+
+cd src
+
+$MAKE
+if [ $? -ne 0 ]; then
+    echo >&2 "Error building buckygen."
+    exit 1
+fi
+
+echo >&2 "Copying buckygen..."
+cp buckygen $SAGE_LOCAL/bin/buckygen
+if [ $? -ne 0 ]; then
+    echo >&2 "Error installing buckygen."
+    exit 1
+fi
+

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=9f52b9a8917273a8b29a40c8e517ebb099cc0537
-md5=adfa272430f561682954687258364d5d
-cksum=3677976078
+sha1=deffea92fdb644888b8349efdc0a8c5da5b2690e
+md5=d58250c470893500de6fb86f10ea61b1
+cksum=3339214726

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-46
+47

build/pkgs/cython/checksums.ini

@@ -1,4 +1,4 @@
-tarball=Cython-VERSION.tar.gz
-sha1=e0f2c2094722bada54f24c33f5c792411778ba4f
-md5=52431696c64e618036537c4d9aa79d99
-cksum=3488695300
+tarball=cython-VERSION.tar.gz
+sha1=f5784539870715e33b51374e9c4451ff6ff21c7f
+md5=6c9c4d19ba485fe8cd88e23b57ac7886
+cksum=2221677113

build/pkgs/cython/package-version.txt

@@ -1 +1 @@
-0.20.1
+0.21

build/pkgs/database_cremona_ellcurve/checksums.ini

@@ -1,4 +1,4 @@
 tarball=database_cremona_ellcurve-VERSION.tar.bz2
-sha1=ab96f509574419c03d9f1c8820c4d96042a17a04
-md5=56956829063534142f9f12bc1274c01c
-cksum=2400753722
+sha1=01360c8292b9d2fb60cd5e4cb84c84d368c4eda4
+md5=627731f9fd5b0cc3e8a25dff329d2cbf
+cksum=2933014536

build/pkgs/database_cremona_ellcurve/package-version.txt

@@ -1 +1 @@
-20140512
+20140829

build/pkgs/ipython/SPKG.txt

@@ -35,3 +35,8 @@ ipython-user@scipy.org
 == Dependencies ==
 
  * Python
+
+== Patches ==
+
+* github_pr_5874.patch: https://github.com/ipython/ipython/pull/5874
+

build/pkgs/ipython/checksums.ini

@@ -1,4 +1,4 @@
 tarball=ipython-VERSION.tar.gz
-sha1=e80c30388cbe576038a78fc8ebb159cddae84fb4
-md5=785c7b6364c6a0dd34aa4ea970cf83b9
-cksum=2529846191
+sha1=ff8e3a2f756d62405f200a2c73aedfafd84076ac
+md5=b91d3724f655a8e16d022772f696cfd5
+cksum=2917965028

build/pkgs/ipython/package-version.txt

@@ -1 +1 @@
-2.1.0
+2.2.0

build/pkgs/ipython/patches/github_pr_5874.patch

@@ -0,0 +1,21 @@
+From cb1986230f78a936a905378f1aed92a4c67dba6d Mon Sep 17 00:00:00 2001
+From: Thomas Kluyver <takowl@gmail.com>
+Date: Fri, 16 May 2014 15:57:03 -0700
+Subject: [PATCH 2/2] Close database when HistorySavingThread stops
+
+---
+ IPython/core/history.py | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/IPython/core/history.py b/IPython/core/history.py
+index da10813..c9b8435 100644
+--- a/IPython/core/history.py
++++ b/IPython/core/history.py
+@@ -775,6 +775,7 @@ def run(self):
+             while True:
+                 self.history_manager.save_flag.wait()
+                 if self.stop_now:
++                    self.db.close()
+                     return
+                 self.history_manager.save_flag.clear()
+                 self.history_manager.writeout_cache(self.db)

build/pkgs/pari/package-version.txt

@@ -1 +1 @@
-2.7.1.p0
+2.7.1.p1

build/pkgs/pari/patches/README.txt

@@ -34,3 +34,5 @@ C files:
   determinant(), only collect garbage once per outer loop iteration.
   Better increase PARI stack size instead of collecting garbage too
   often.
+* nffactor.patch (Jeroen Demeyer, #16894): Fix an nffactor() bug, taken
+  from PARI git commit 7630f584371c3db43c5fd6f57900c70a2c832b8e.

build/pkgs/pari/patches/nffactor.patch

@@ -0,0 +1,59 @@
+commit 7630f584371c3db43c5fd6f57900c70a2c832b8e
+Author: Karim Belabas <Karim.Belabas@math.u-bordeaux1.fr>
+Date:   Tue Jun 17 13:24:37 2014 +0200
+
+    32- nffactor() could overflow the stack when default accuracy too low: e.g.
+       nffactor(y^2-22, x^2+926246528884912528275985458927067632*y-4344481316563541186659879867597013188)
+
+    due to logmax_modulus called with (approximate) polynomial T s.t. T(0) = 0
+
+diff --git a/src/basemath/rootpol.c b/src/basemath/rootpol.c
+index d63f8b3..f1ced73 100644
+--- a/src/basemath/rootpol.c
++++ b/src/basemath/rootpol.c
+@@ -652,7 +652,8 @@ lower_bound(GEN p, long *k, double eps)
+   avma = ltop; return R;
+ }
+
+-/* log of modulus of the largest root of p with relative error tau */
++/* log of modulus of the largest root of p with relative error tau. Assume
++ * P(0) != 0 and P non constant */
+ static double
+ logmax_modulus(GEN p, double tau)
+ {
+@@ -696,10 +697,12 @@ logmax_modulus(GEN p, double tau)
+   r = itor(r, DEFAULTPREC); shiftr_inplace(r, -M);
+   avma = ltop; return -rtodbl(r) * LOG2; /* -log(2) sum e_i 2^-i */
+ }
++/* assume P non constant */
+ GEN
+ logmax_modulus_bound(GEN P)
+ {
+-  return dblexp(logmax_modulus(P, 0.01) + 0.01);
++  (void)RgX_valrem_inexact(P,&P);
++  return lg(P)==3? gen_0: dblexp(logmax_modulus(P, 0.01) + 0.01);
+ }
+
+ /* log of modulus of the smallest root of p, with relative error tau */
+diff --git a/src/test/32/nffactor b/src/test/32/nffactor
+index 824ca6b..accbc30 100644
+--- a/src/test/32/nffactor
++++ b/src/test/32/nffactor
+@@ -729,4 +729,6 @@ x^6 + 10/7*x^5 - 867/49*x^4 - 76/245*x^3 + 3148/35*x^2 - 25944/245*x + 48771
+ 10
+ 10
+ [0]
+-Total time spent: 1385595334334
++[x + (-314226370217524044*y + 1473852319020386314), x + (314226370217524044*
++y - 1473852319020386314)]~
++Total time spent: 8061
+diff --git a/src/test/in/nffactor b/src/test/in/nffactor
+index 0992107..a3579a0 100644
+--- a/src/test/in/nffactor
++++ b/src/test/in/nffactor
+@@ -104,3 +104,5 @@ test(polcyclo(503),3)
+ test(polcyclo(211),18446744073709551667)
+
+ nfroots(a^2+1,x^2)
++
++do(y^2-22,x^2+926246528884912528275985458927067632*y-4344481316563541186659879867597013188)

src/bin/sage-banner

@@ -1,5 +1,5 @@
 ┌────────────────────────────────────────────────────────────────────┐
-│ Sage Version 6.4.beta2, Release Date: 2014-08-28                   │
+│ Sage Version 6.4.beta3, Release Date: 2014-09-10                   │
 │ Type "notebook()" for the browser-based notebook interface.        │
 │ Type "help()" for help.                                            │
 └────────────────────────────────────────────────────────────────────┘

src/bin/sage-preparse

@@ -11,6 +11,9 @@ AUTHOR:
 
 import os, sys, re
 
+from sage.misc.preparser import preparse_file
+from sage.misc.temporary_file import atomic_write
+
 # The spkg/bin/sage script passes the files to be preparsed as
 # arguments (but remove sys.argv[0]).
 files = sys.argv[1:]
@@ -115,7 +118,6 @@ def do_preparse(f, files_before=[]):
             F = '\n'.join(lines[:num] + lines[(num+1):])
 
     # Preparse it
-    from sage.misc.preparser  import preparse_file
     G = preparse_file(F)
 
     # Check for load/attach commands.
@@ -129,8 +131,10 @@ def do_preparse(f, files_before=[]):
     i = find_position_right_after_module_docstring(G)
     G = coding + G[:i] + insert + G[i:]
 
-    # Finally, write out the result.
-    open(fname, 'w').write(G)
+    # Finally, write out the result.  We use atomic_write to avoid
+    # race conditions (for example, the file will never be half written).
+    with atomic_write(fname) as f:
+        f.write(G)
 
 def find_position_right_after_module_docstring(G):
     """
@@ -215,9 +219,11 @@ def do_load_and_attach(G, file, files_before):
                    continue
                 if name.endswith('.sage'):
                     do_preparse(name, files_before + [file])
-                    s += lws + 'execfile("%s.py")\n'%name[:-5]
+                    s += lws + "exec(compile(open({0}.py).read(), {0}.py, \
+                            'exec'))\n".format(name[:-5])
                 elif name.endswith('.py'):
-                    s += lws + 'execfile("%s")\n'%name
+                    s += lws + "exec(compile(open({0}).read(), {0}, \
+                            'exec'))\n".format(name)
         else:
             s += t + '\n'
     return s

src/bin/sage-run

@@ -16,13 +16,12 @@ if fn.startswith('-'):
     print "Try 'sage -h' for more information."
     sys.exit(1)
 
-binpath = os.path.join(os.environ['SAGE_LOCAL'], 'bin')
 
 if fn.endswith('.sage'):
-    if call(['sage', '-preparse', fn]) != 0:
+    if call(['sage-preparse', fn]) != 0:
         sys.exit(1)
-    os.execv(os.path.join(binpath, 'sage-python'), ['sage-python', fn[:-5] + '.py'] + opts)
+    os.execvp('sage-python', ['sage-python', fn[:-5] + '.py'] + opts)
 elif fn.endswith('.pyx') or fn.endswith('.spyx'):
-    os.execv(os.path.join(binpath, 'sage-run-cython'), ['sage-run-cython', fn] + opts)
+    os.execvp('sage-run-cython', ['sage-run-cython', fn] + opts)
 else:
-    os.execv(os.path.join(binpath, 'sage-python'), ['sage-python', fn] + opts)
+    os.execvp('sage-python', ['sage-python', fn] + opts)

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='6.4.beta2'
-SAGE_RELEASE_DATE='2014-08-28'
+SAGE_VERSION='6.4.beta3'
+SAGE_RELEASE_DATE='2014-09-10'

src/c_lib/SConstruct

@@ -134,7 +134,7 @@ cppFiles = Split( "ZZ_pylong.cpp  ntl_wrap.cpp" )
 srcFiles = cFiles + cppFiles
 incFiles = Split( "ccobject.h  convert.h  gmp_globals.h" ) + \
            Split( "interrupt.h  memory.h  mpn_pylong.h  mpz_longlong.h" ) + \
-           Split( "mpz_pylong.h  ntl_wrap.h  stdsage.h  ZZ_pylong.h" )
+           Split( "mpz_pylong.h  ntl_wrap.h  parisage.h  stdsage.h  ZZ_pylong.h" )
 
 lib = env.SharedLibrary( "csage", [ "src/" + x for x in srcFiles ],
                          LIBS=['ntl', 'pari', 'gmp', 'python$PYV'],

src/c_lib/include/ntl_wrap.h

@@ -45,8 +45,8 @@ struct ZZ;
 
 EXTERN int ZZ_to_int(const struct ZZ* x);
 EXTERN struct ZZ* int_to_ZZ(int value);
-EXTERN void ZZ_to_mpz(mpz_t* output, const struct ZZ* x);
-EXTERN void mpz_to_ZZ(struct ZZ *output, const mpz_t* x);
+EXTERN void ZZ_to_mpz(mpz_t output, const struct ZZ* x);
+EXTERN void mpz_to_ZZ(struct ZZ *output, const mpz_t x);
 EXTERN void ZZ_set_from_int(struct ZZ* x, int value);
 /*Random-number generation */
 //EXTERN void setSeed(const struct ZZ* n);
@@ -88,7 +88,7 @@ EXTERN char* ZZX_repr(struct ZZX* x);
 EXTERN struct ZZX* ZZX_copy(struct ZZX* x);
 EXTERN void ZZX_setitem_from_int(struct ZZX* x, long i, int value);
 EXTERN int ZZX_getitem_as_int(struct ZZX* x, long i);
-EXTERN void ZZX_getitem_as_mpz(mpz_t* output, struct ZZX* x, long i);
+EXTERN void ZZX_getitem_as_mpz(mpz_t output, struct ZZX* x, long i);
 EXTERN struct ZZX* ZZX_div(struct ZZX* x, struct ZZX* y, int* divisible);
 EXTERN void ZZX_quo_rem(struct ZZX* x, struct ZZX* other, struct ZZX** r, struct ZZX** q);
 EXTERN struct ZZX* ZZX_square(struct ZZX* x);

src/c_lib/include/parisage.h

@@ -0,0 +1,5 @@
+/* Include the relevant PARI includes in a safe way */
+#include <pari/paricfg.h>
+#include <pari/pari.h>
+
+#undef coeff  /* Conflicts with NTL */

src/c_lib/src/ZZ_pylong.cpp

@@ -23,7 +23,7 @@ PyObject * ZZ_get_pylong(ZZ &z)
     mpz_t temp;
     PyObject *val;
     mpz_init(temp);
-    ZZ_to_mpz( &temp, &z );
+    ZZ_to_mpz( temp, &z );
     val = mpz_get_pylong( temp );
     mpz_clear( temp );
     return val;
@@ -35,7 +35,7 @@ int ZZ_set_pylong(ZZ &z, PyObject * ll)
     mpz_t temp;
     mpz_init(temp);
     mpz_set_pylong( temp, ll );
-    mpz_to_ZZ( &z, &temp );
+    mpz_to_ZZ( &z, temp );
     mpz_clear( temp );
     return 0;
 }

src/c_lib/src/ntl_wrap.cpp

@@ -40,17 +40,17 @@ struct ZZ* int_to_ZZ(int value)
    Assumes output has been mpz_init'd.
    AUTHOR: David Harvey
            Joel B. Mohler moved the ZZX_getitem_as_mpz code out to this function (2007-03-13) */
-void ZZ_to_mpz(mpz_t* output, const struct ZZ* x)
+void ZZ_to_mpz(mpz_t output, const struct ZZ* x)
 {
     unsigned char stack_bytes[4096];
     int use_heap;
     unsigned long size = NumBytes(*x);
     use_heap = (size > sizeof(stack_bytes));
     unsigned char* bytes = use_heap ? (unsigned char*) malloc(size) : stack_bytes;
     BytesFromZZ(bytes, *x, size);
-    mpz_import(*output, size, -1, 1, 0, 0, bytes);
+    mpz_import(output, size, -1, 1, 0, 0, bytes);
     if (sign(*x) < 0)
-        mpz_neg(*output, *output);
+        mpz_neg(output, output);
     if (use_heap)
         free(bytes);
 }
@@ -61,19 +61,18 @@ void ZZ_to_mpz(mpz_t* output, const struct ZZ* x)
 
 /* Copies the mpz_t into the ZZ
    AUTHOR: Joel B. Mohler (2007-03-15) */
-// This should be changed to an mpz_t not an mpz_t*
-void mpz_to_ZZ(struct ZZ* output, const mpz_t *x)
+void mpz_to_ZZ(struct ZZ* output, const mpz_t x)
 {
     unsigned char stack_bytes[4096];
     int use_heap;
-    size_t size = (mpz_sizeinbase(*x, 2) + bits_in_byte-1) / bits_in_byte;
+    size_t size = (mpz_sizeinbase(x, 2) + bits_in_byte-1) / bits_in_byte;
     use_heap = (size > sizeof(stack_bytes));
     void* bytes = use_heap ? malloc(size) : stack_bytes;
     size_t words_written;
-    mpz_export(bytes, &words_written, -1, 1, 0, 0, *x);
+    mpz_export(bytes, &words_written, -1, 1, 0, 0, x);
     clear(*output);
     ZZFromBytes(*output, (unsigned char *)bytes, words_written);
-    if (mpz_sgn(*x) < 0)
+    if (mpz_sgn(x) < 0)
         NTL::negate(*output, *output);
     if (use_heap)
         free(bytes);
@@ -246,7 +245,7 @@ int ZZX_getitem_as_int(struct ZZX* x, long i)
 /* Copies ith coefficient of x to output.
    Assumes output has been mpz_init'd.
    AUTHOR: David Harvey (2007-02) */
-void ZZX_getitem_as_mpz(mpz_t* output, struct ZZX* x, long i)
+void ZZX_getitem_as_mpz(mpz_t output, struct ZZX* x, long i)
 {
     const ZZ& z = coeff(*x, i);
     ZZ_to_mpz(output, &z);