Merge branch 'master' into ticket/17729

Conflicts:
	src/sage/schemes/affine/affine_morphism.py

.gitignore

@@ -29,7 +29,9 @@
 .\#*
 
 # Vim
-*.s[a-w][a-z]
+*.swp
+*.swo
+*.swn
 *.un~
 .netrwhist
 

Makefile

@@ -59,6 +59,13 @@ doc: doc-html
 doc-html: build
 	$(PIPE) "./sage --docbuild --no-pdf-links all html $(SAGE_DOCBUILD_OPTS) 2>&1" "tee -a logs/dochtml.log"
 
+# 'doc-html-no-plot': build docs without building the graphics coming
+# from the '.. plot' directive, in case you want to save a few
+# megabytes of disk space. 'doc-clean' is a prerequisite because the
+# presence of graphics is cached in src/doc/output.
+doc-html-no-plot: build doc-clean
+	$(PIPE) "./sage --docbuild --no-pdf-links --no-plot all html $(SAGE_DOCBUILD_OPTS) 2>&1" "tee -a logs/dochtml.log"
+
 doc-html-mathjax: build
 	$(PIPE) "./sage --docbuild --no-pdf-links all html -j $(SAGE_DOCBUILD_OPTS) 2>&1" "tee -a logs/dochtml.log"
 

VERSION.txt

@@ -1 +1 @@
-Sage version 6.5.beta6, released 2015-01-24
+Sage version 6.6.beta0, released 2015-02-18

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=99eab7d6d7eabfb85e3efe2ce4b2096c836681ce
-md5=9823a583c3663035cdb47fdb6f334173
-cksum=2606347674
+sha1=fc6a6e09db9e9ef7877296947cfcc0929b6d08bf
+md5=ca43ab046439d42063bf4af39baecb18
+cksum=3453818239

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-64
+70

build/pkgs/cython/checksums.ini

@@ -1,4 +1,4 @@
-tarball=cython-VERSION.tar.gz
-sha1=02c6f25025923e5a5647e7876670a4cc7759371e
-md5=c59163d7c72c0a0ee5eb84edd17935ed
-cksum=3555036300
+tarball=cython-VERSION.tar.bz2
+sha1=89cf4f3d9a840e593da066a9f723b31a27d7c6a6
+md5=6fe7c9d93970ce602d60defd903188d8
+cksum=1851959595

build/pkgs/cython/package-version.txt

@@ -1 +1 @@
-0.21.1
+0.22

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/jmol/checksums.ini

@@ -1,4 +1,4 @@
 tarball=jmol-VERSION.tar.bz2
-sha1=0496d92d75efb91c2b332f59be48c0ee6a12a314
-md5=acc6c39a4b7787f53657310e9252fbf9
-cksum=389669432
+sha1=3def57106c750286af364cbbf040ed7e568b866e
+md5=8664c2b5c109c7dadcfcce9d4e30770b
+cksum=211082989

build/pkgs/jmol/package-version.txt

@@ -1 +1 @@
-14.2.4_2014.08.03
+14.2.11_2015.01.20

build/pkgs/maxima/package-version.txt

@@ -1 +1 @@
-5.35.1.p1
+5.35.1.p2

build/pkgs/maxima/patches/stdin-illegal-seek.patch

@@ -0,0 +1,32 @@
+#17667: Maxima parser fails on ==
+
+There is no == operator in Maxima, but on invalid input it does bad
+things to the C-level stream. On Linux (below) this is caught by
+gilbc, on OSX the Maxima process hangs indefinitely.
+
+Patch taken from the upstream repo:
+
+commit f7c388a0f030b2701ac982ea66cce61ce8002bf8
+tree 948ebe84ce56a76090e2b86403b18d7bc262e67c
+parent a57b4323587f6f4c1115a51915cfb096f4d820c2
+author Andrej Vodopivec <andrej.vodopivec@gmail.com> 1423041512 +0100
+committer Andrej Vodopivec <andrej.vodopivec@gmail.com> 1423041512 +0100
+
+    mread-synerr: don't report line/column for errors from user input.
+
+diff -ru src/src/nparse.lisp b/src/nparse.lisp
+--- src/src/nparse.lisp	2014-11-19 06:00:09.000000000 +0100
++++ b/src/nparse.lisp	2015-02-13 10:12:49.107785016 +0100
+@@ -37,8 +37,10 @@
+ (defmvar $report_synerr_info t "If T, report the syntax error details from all sources; otherwise, only report details from standard-input.")
+
+ (defun mread-synerr (format-string &rest l)
+-  (let ((fp (file-position *parse-stream*))
+-	(file (cadr *current-line-info*)))
++  (let ((fp (and (not (eq *parse-stream* *standard-input*))
++                 (file-position *parse-stream*)))
++	(file (and (not (eq *parse-stream* *standard-input*))
++                   (cadr *current-line-info*))))
+     (flet ((line-number ()
+ 	     ;; Fix me: Neither batch nor load track the line number
+ 	     ;; correctly. batch, via dbm-read, does not track the

build/pkgs/openssl/SPKG.txt

@@ -12,13 +12,10 @@ library in a variety of computer languages are available.
 
  * Custom GPL-incompatible license
 
-== Maintainers ==
-
- * William Stein
-
 == Upstream Contact ==
 
- * None yet
+ * http://openssl.org/
+ * http://openssl.org/support/community.html
 
 === Patches ===
 

build/pkgs/openssl/checksums.ini

@@ -1,4 +1,4 @@
 tarball=openssl-VERSION.tar.gz
-sha1=cff86857507624f0ad42d922bb6f77c4f1c2b819
-md5=f7175c9cd3c39bb1907ac8bba9df8ed3
-cksum=490651201
+sha1=2f264f7f6bb973af444cd9fc6ee65c8588f610cc
+md5=38373013fc85c790aabf8837969c5eba
+cksum=3003646357

build/pkgs/openssl/package-version.txt

@@ -1 +1 @@
-1.0.1j
+1.0.2

build/pkgs/pari/package-version.txt

@@ -1 +1 @@
-2.7.1.p1
+2.7.1.p3

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

@@ -187,27 +187,15 @@ install()
         exit 1
     fi
 
-    cd "$CUR"
-
-    if [ "$UNAME" = "Darwin" ]; then
-        # The following is a hack to get the library installed correctly
-        # on Mac OS X:
-        echo "Applying Mac OS X hack -- deleting and reinstalling libpari.a ..."
-        rm -f Odarwin-ppc/*lib*
-        $MAKE install-lib-sta
-        if [ $? -ne 0 ]; then
-            echo >&2 "Error reinstalling PARI's static libraries (OS X trick)"
-            exit 1
-        fi
-
-        cd "`config/objdir`" && cp -f libpari* "$SAGE_LOCAL/lib"
-        if [ $? -ne 0 ]; then
-            echo >&2 "Error copying PARI's libraries (OS X trick)"
-            exit 1
-        fi
-        cd "$CUR"
+    # 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"
+
     # Copy gprc.expect to $SAGE_LOCAL/etc
     cp -f "$TOP/gprc.expect" "$SAGE_LOCAL/etc"
     if [ $? -ne 0 ]; then

build/pkgs/sagenb/checksums.ini

@@ -1,4 +1,4 @@
 tarball=sagenb-VERSION.tar
-sha1=c9426b9a7a2827f30cc78d7d6968c45318d75bc9
-md5=5df4791218cbad45970b0a7ab0be533b
-cksum=1503702642
+sha1=66593ecf18cbf77115279f6f1564854eb9b93df5
+md5=facdc06b94fcf0a85b76aa861c6e646f
+cksum=2719820378

build/pkgs/sagenb/package-version.txt

@@ -1 +1 @@
-0.11.2
+0.11.4

src/bin/math-readline

@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+
+# Cleverly run Mathematica with the benefit of readline, which
+# is something the usual commercial mathematica doesn't provide!
+# See
+#    http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/363500
+
+import os, sys
+f1 = os.popen('math ', 'w')
+f1.flush()
+try:
+    while True:
+        sys.stdout.write('')
+        try:
+            line = raw_input()
+            f1.writelines(line+'\n')
+            f1.flush()
+        except KeyboardInterrupt:
+            f1.close()
+            break
+except EOFError:
+    pass
+sys.stdout.write('\n')
+sys.exit()

src/bin/sage

@@ -632,15 +632,14 @@ 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
 
 if [ "$1" = "-notebook" -o "$1" = '--notebook' -o "$1" = '-n' ]; then
-    shift
     sage-cleaner &>/dev/null &
-    exec sage-notebook --notebook=default "$@"
+    exec sage-notebook "$@"
 fi
 
 if [ "$1" = "-bn" -o "$1" = "--build-and-notebook" ]; then

src/bin/sage-banner

@@ -1,5 +1,5 @@
 ┌────────────────────────────────────────────────────────────────────┐
-│ Sage Version 6.5.beta6, Release Date: 2015-01-24                   │
+│ Sage Version 6.6.beta0, Release Date: 2015-02-18                   │
 │ Type "notebook()" for the browser-based notebook interface.        │
 │ Type "help()" for help.                                            │
 └────────────────────────────────────────────────────────────────────┘

src/bin/sage-rst2sws

@@ -129,7 +129,7 @@ worksheet_txt = translator.process_doc_html(html)
 
 # create a Notebook object
 from sagenb.notebook.notebook import Notebook
-from sage.misc.misc import tmp_dir
+from sage.misc.all import tmp_dir
 nb = Notebook(tmp_dir()+'.sagenb')
 nb.user_manager().create_default_users('password')
 

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='6.6.beta0'
+SAGE_RELEASE_DATE='2015-02-18'