Merge branch 'develop' into t/17678/special_values_of_bessel_functions

* develop: (121 commits)
  Updated Sage version to 6.5.rc0
  trac #17671: fix two doctests
  #17685 better regex for sage ^-n=.*
  trac #17671: fix float definition of gcd/lcm/xgcd
  trac #17671: fix typo in doc
  trac #17671: force the parent of gcd/lcm/xgcd
  trac #17671: gcd(2.0, 6.0) is now 1.0
  trac #17671: fix doctest in coercion_and_categories.rst
  trac #17671: revert changes in function_field.py
  trac #17671: (review) clearer doc in rings.arith.xgcd
  trac #17671: fix xgcd of polynomial_field_generic
  trac #17671: (review) fix gcd/xgcd in QuotientFields
  trac #17671: fix doctests
  trac #17671: compatibility of gcd and xgcd
  Updated Sage version to 6.5.beta6
  Minor typesetting issue in graph.py
  trac #17683: Subgraph of Hasse Diagram gives error
  trac #17616: Broken doctest
  17675: reviewer's patch: fix typo
  trac #17675: doc typo
  ...

VERSION.txt

@@ -1 +1 @@
-Sage version 6.5.beta6, released 2015-01-24
+Sage version 6.5.rc0, released 2015-01-29

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=99eab7d6d7eabfb85e3efe2ce4b2096c836681ce
-md5=9823a583c3663035cdb47fdb6f334173
-cksum=2606347674
+sha1=15e8210b4d0a90f83d1e25b4a02f9173a5b4daad
+md5=07dbcb4dc1f5bad86c8d813576b05f54
+cksum=1785342277

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-64
+65

build/pkgs/gdb/patches/yosemite-setjmp.patch

@@ -0,0 +1,13 @@
+Patch for building on OSX 10.10 taken from https://trac.macports.org/ticket/43973
+
+--- gdb-7.7.1/gdb/darwin-nat.c.orig	2014-06-15 10:49:39.000000000 -0700
++++ gdb-7.7.1/gdb/darwin-nat.c	2014-06-15 10:51:23.000000000 -0700
+@@ -42,7 +42,7 @@
+
+ #include <sys/ptrace.h>
+ #include <sys/signal.h>
+-#include <machine/setjmp.h>
++#include <setjmp.h>
+ #include <sys/types.h>
+ #include <unistd.h>
+ #include <signal.h>

build/pkgs/gdb/spkg-install

@@ -8,6 +8,16 @@ fi
 
 cd src
 
+# Apply patches.
+for patch in ../patches/*.patch; do
+    [ -r "$patch" ] || continue  # Skip non-existing or non-readable patches
+    patch -p1 <"$patch"
+    if [ $? -ne 0 ]; then
+        echo >&2 "Error applying '$patch'"
+        exit 1
+    fi
+done
+
 LDFLAGS="${LDFLAGS} -L${SAGE_LOCAL}/lib"
 export LDFLAGS
 

build/pkgs/pari/package-version.txt

@@ -1 +1 @@
-2.7.1.p1
+2.7.1.p2

build/pkgs/pari/patches/cb_pari_err_handle.patch

@@ -0,0 +1,105 @@
+Add cb_pari_err_handle() callback
+
+Backported from upstream commits
+e9e659dc9ecb5ca6a8296c7922528a4ecbb89cb0
+26a7ae0f42918407febe9901ded41faf26ef43a6
+
+diff -ru src/src/headers/paricom.h b/src/headers/paricom.h
+--- src/src/headers/paricom.h	2014-03-25 09:59:21.000000000 +0100
++++ b/src/headers/paricom.h	2015-01-13 19:41:47.430885048 +0100
+@@ -81,6 +81,7 @@
+ extern int  (*cb_pari_whatnow)(PariOUT *out, const char *, int);
+ extern void (*cb_pari_sigint)(void);
+ extern int (*cb_pari_handle_exception)(long);
++extern int (*cb_pari_err_handle)(GEN);
+ extern void (*cb_pari_pre_recover)(long);
+ extern void (*cb_pari_err_recover)(long);
+ extern const char *pari_library_path;
+diff -ru src/src/language/init.c b/src/language/init.c
+--- src/src/language/init.c	2015-01-13 19:40:30.643622993 +0100
++++ b/src/language/init.c	2015-01-13 19:41:47.431884833 +0100
+@@ -87,6 +87,7 @@
+
+ void (*cb_pari_ask_confirm)(const char *);
+ int  (*cb_pari_handle_exception)(long);
++int  (*cb_pari_err_handle)(GEN);
+ int  (*cb_pari_whatnow)(PariOUT *out, const char *, int);
+ void (*cb_pari_sigint)(void);
+ void (*cb_pari_pre_recover)(long);
+@@ -732,6 +733,8 @@
+ static void
+ dflt_err_recover(long errnum) { (void) errnum; pari_exit(); }
+
++static int pari_err_display(GEN err);
++
+ /* initialize PARI data. Initialize [new|old]fun to NULL for default set. */
+ void
+ pari_init_opts(size_t parisize, ulong maxprime, ulong init_opts)
+@@ -739,6 +742,8 @@
+   ulong u;
+
+   cb_pari_whatnow = NULL;
++  cb_pari_handle_exception = NULL;
++  cb_pari_err_handle = pari_err_display;
+   cb_pari_pre_recover = NULL;
+   cb_pari_sigint = dflt_sigint_fun;
+   if (init_opts&INIT_JMPm) cb_pari_err_recover = dflt_err_recover;
+@@ -887,9 +892,6 @@
+   evalstate_reset();
+   killallfiles();
+   pari_init_errcatch();
+-  out_puts(pariErr, "\n");
+-  pariErr->flush();
+-
+   cb_pari_err_recover(numerr);
+ }
+
+@@ -1266,21 +1268,22 @@
+   return NULL; /*NOT REACHED*/
+ }
+
+-static void
++static int
+ pari_err_display(GEN err)
+ {
+   long numerr=err_get_num(err);
++  err_init();
+   if (numerr==e_SYNTAX)
+   {
+     const char *msg = GSTR(gel(err,2));
+     const char *s     = (const char *) gmael(err,3,1);
+     const char *entry = (const char *) gmael(err,3,2);
+     print_errcontext(pariErr, msg, s, entry);
+-    return;
+   }
+   else
+   {
+     char *s = pari_err2str(err);
++    closure_err(0);
+     err_init_msg(numerr, e_USER);
+     pariErr->puts(s);
+     if (numerr==e_NOTFUNC)
+@@ -1295,6 +1298,8 @@
+     }
+     pari_free(s);
+   }
++  out_term_color(pariErr, c_NONE);
++  pariErr->flush(); return 0;
+ }
+
+ void
+@@ -1315,12 +1320,9 @@
+   global_err_data = E;
+   if (*iferr_env) longjmp(*iferr_env, numerr);
+   mt_err_recover(numerr);
+-  err_init();
+-  if (numerr != e_SYNTAX) closure_err(0);
+-  pari_err_display(E);
+-  out_term_color(pariErr, c_NONE);
+   va_end(ap);
+-  pariErr->flush();
++  if (cb_pari_err_handle &&
++      cb_pari_err_handle(E)) return;
+   if (cb_pari_handle_exception &&
+       cb_pari_handle_exception(numerr)) return;
+   err_recover(numerr);

build/pkgs/pari/spkg-install

@@ -187,6 +187,13 @@ install()
         exit 1
     fi
 
+    # Copy anal.h
+    cp -f "src/language/anal.h" "$SAGE_LOCAL/include/pari/anal.h"
+    if [ $? -ne 0 ]; then
+        echo >&2 "Error copying anal.h"
+        exit 1
+    fi
+
     cd "$CUR"
 
     if [ "$UNAME" = "Darwin" ]; then

src/bin/sage

@@ -632,7 +632,7 @@ build_sage() {
     sage-build "$@" || exit $?
 }
 
-if [[ "$1" =~ "--notebook="* || "$1" =~ "-n="* || "$1" =~ "-notebook="* ]]; then
+if [[ "$1" =~ ^--notebook=.* || "$1" =~ ^-n=.* || "$1" =~ ^-notebook=.* ]] ; then
     sage-cleaner &>/dev/null &
     exec sage-notebook "$@"
 fi

src/bin/sage-banner

@@ -1,5 +1,5 @@
 ┌────────────────────────────────────────────────────────────────────┐
-│ Sage Version 6.5.beta6, Release Date: 2015-01-24                   │
+│ Sage Version 6.5.rc0, Release Date: 2015-01-29                     │
 │ 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='6.5.beta6'
-SAGE_RELEASE_DATE='2015-01-24'
+SAGE_VERSION='6.5.rc0'
+SAGE_RELEASE_DATE='2015-01-29'

src/doc/en/reference/diophantine_approximation/conf.py

@@ -0,0 +1 @@
+../conf_sub.py

src/doc/en/reference/diophantine_approximation/index.rst

@@ -0,0 +1,13 @@
+Diophantine approximation
+=========================
+
+The diophantine approximation deals with the approximation of real numbers
+(or real vectors) with rational numbers (or rational vectors).
+See the article :wikipedia:`Diophantine_approximation` for more information.
+
+.. toctree::
+   :maxdepth: 2
+
+   sage/rings/continued_fraction
+
+.. include:: ../footer.txt

src/doc/en/reference/index.rst

@@ -74,6 +74,7 @@ Geometry and Topology
 Number Theory, Algebraic Geometry
 ---------------------------------
 
+* :doc:`Diophantine approximation <diophantine_approximation/index>`
 * :doc:`Quadratic Forms <quadratic_forms/index>`
 * :doc:`L-Functions <lfunctions/index>`
 * :doc:`Schemes <schemes/index>`