Merge branch 'develop' into t/17953/inconsistency_in_returned_type_of…

…_builtinfunction_result

* develop: (129 commits)
  Updated Sage version to 6.6.beta6
  Fix doctest because of new doc category.
  adds SageMathCloud files to .gitignore
  Convert database_pari to new-style package and update
  17305: Two more coeffs()
  17977: adds some non-symmetric tests
  17305: Another coeffs and fix ambiguous citation
  17305: React to deprecation from 17518
  17305: Remove whitespaces
  17305: Typos and replace some $-signs.
  fill out BackendIPython.display_immediately
  trac #17976 typo correction
  corrected code and incorrect example
  Fixed 2 broken doctests
  17975: use the occasion to do further rephrasing
  17975: typo fixes
  Fixed 4 broken doctests
  Fixed 2 broken doctests
  Replaced call to deprecation by the method deprecation_function_alias Minor change to the docstirng of parity_check_matrix.
  Replaced check_mat method by parity_check_matrix
  ...

.gitignore

@@ -70,3 +70,10 @@ $RECYCLE.BIN/
 
 # SublimeText
 *.sublime-workspace
+
+#################
+# SageMathCloud #
+#################
+*.sage-chat
+*.sage-history
+*.syncdoc*

COPYING.txt

@@ -76,6 +76,7 @@ linbox                      LGPLv2.1+
 lrcalc                      GPLv2+
 m4ri                        GPLv2+
 m4rie                       GPLv2+
+markupsafe                  Simplified BSD
 mathjax                     Apache License 2.0
 matplotlib                  Matplotlib License (BSD compatible, see below)
 maxima                      See below

VERSION.txt

@@ -1 +1 @@
-Sage version 6.6.beta5, released 2015-03-13
+Sage version 6.6.beta6, released 2015-03-19

build/deps

@@ -68,6 +68,7 @@ all-sage: \
      $(INST)/$(LINBOX) \
      $(INST)/$(M4RI) \
      $(INST)/$(M4RIE) \
+     $(INST)/$(MARKUPSAFE) \
      $(INST)/$(MATHJAX) \
      $(INST)/$(MATPLOTLIB) \
      $(INST)/$(MAXIMA) \
@@ -467,7 +468,10 @@ $(INST)/$(SPHINX): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS) $(INST)/$(DOCUTILS) \
                    $(INST)/$(JINJA2) $(INST)/$(PYGMENTS)
 	+$(PIPE) "$(SAGE_SPKG) $(SPHINX) 2>&1" "tee -a $(SAGE_LOGS)/$(SPHINX).log"
 
-$(INST)/$(JINJA2): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS) $(INST)/$(DOCUTILS)
+$(INST)/$(MARKUPSAFE): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
+	+$(PIPE) "$(SAGE_SPKG) $(MARKUPSAFE) 2>&1" "tee -a $(SAGE_LOGS)/$(MARKUPSAFE).log"
+
+$(INST)/$(JINJA2): $(INST)/$(MARKUPSAFE) $(INST)/$(SPHINX)
 	+$(PIPE) "$(SAGE_SPKG) $(JINJA2) 2>&1" "tee -a $(SAGE_LOGS)/$(JINJA2).log"
 
 $(INST)/$(PYGMENTS): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)

build/install

@@ -343,6 +343,7 @@ LIBPNG=`newest_version libpng`
 LINBOX=`newest_version linbox`
 M4RI=`newest_version m4ri`
 M4RIE=`newest_version m4rie`
+MARKUPSAFE=`newest_version markupsafe`
 MATHJAX=`newest_version mathjax`
 MATPLOTLIB=`newest_version matplotlib`
 MAXIMA=`newest_version maxima`

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=12e8d35579711c8bf8beddb890aaebd6b2c51db1
-md5=dbb592c16e66f4f2e3345071fb115abf
-cksum=693230472
+sha1=89ece2f5d378cda9468a3437854b10809d1e57c3
+md5=6bf787d800c20ead4a74e5ff00b1c9c8
+cksum=913450101

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-75
+76

build/pkgs/database_pari/SPKG.txt

@@ -0,0 +1,29 @@
+= database_pari =
+
+== Description ==
+
+The collection of optional PARI packages elldata, seadata, galpol,
+nftables (galdata is included in the standard PARI spkg).
+See http://pari.math.u-bordeaux.fr/packages.html
+
+== License ==
+
+GNU General Public License (GPL version 2 or any later version).
+
+== SPKG Maintainers ==
+
+* Jeroen Demeyer
+
+== Upstream Contact ==
+
+http://pari.math.u-bordeaux.fr/
+
+== Dependencies ==
+
+* Installation: None
+* Runtime: PARI/GP
+
+== Special Update/Build Instructions ==
+
+Download the four mentioned tarballs and extract them, then move them
+out of the top-level directory data.

build/pkgs/database_pari/checksums.ini

@@ -0,0 +1,4 @@
+tarball=database_pari-VERSION.tar.bz2
+sha1=92dcb68e7a6def53ffc5fb82e3593d5b80c940cb
+md5=652d36d18ea300193957120815298be7
+cksum=2257060384

build/pkgs/database_pari/package-version.txt

@@ -0,0 +1 @@
+20140908

build/pkgs/database_pari/spkg-check

@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+
+if [ -z "$SAGE_SRC" ]; then
+    echo >&2 "SAGE_SRC undefined ... exiting"
+    echo >&2 "Maybe run 'sage --sh'?"
+    exit 1
+fi
+
+sage -tp --long --optional=database_pari,sage "$SAGE_SRC/sage/tests/parigp.py" "$SAGE_SRC/sage/libs/pari"

build/pkgs/database_pari/spkg-install

@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+
+if [ -z "$GP_DATA_DIR" ]; then
+    echo >&2 "GP_DATA_DIR undefined ... exiting"
+    echo >&2 "Maybe run 'sage --sh'?"
+    exit 1
+fi
+
+cd src
+cp -pR elldata galpol nftables seadata "$GP_DATA_DIR"

build/pkgs/eclib/checksums.ini

@@ -1,4 +1,4 @@
 tarball=eclib-VERSION.tar.bz2
-sha1=b8a8b5232caf2332e650d8b6b8ec009979312974
-md5=da8b822c6bbef913bcef6d7491c8c999
-cksum=3800001876
+sha1=208567933690c8805eec313cfdedf7f9b9475ddb
+md5=2ebc69ef8d99750e91178b8eb8f26c9d
+cksum=3283693850

build/pkgs/eclib/package-version.txt

@@ -1 +1 @@
-20140921
+20150228

build/pkgs/jinja2/checksums.ini

@@ -1,4 +1,4 @@
-tarball=jinja2-VERSION.tar.bz2
-sha1=e9e13b4f573effd35e03b1ecd978c684342d549c
-md5=3ca3504c27a147d38f4d32214a3f3004
-cksum=1443664485
+tarball=jinja2-VERSION.tar.gz
+sha1=25ab3881f0c1adfcf79053b58de829c5ae65d3ac
+md5=b9dffd2f3b43d673802fe857c8445b1a
+cksum=3563905877

build/pkgs/jinja2/package-version.txt

@@ -1 +1 @@
-2.5.5
+2.7.3

build/pkgs/latte_int/checksums.ini

@@ -1,4 +1,4 @@
-tarball=latte_int-VERSION.tar.gz
-sha1=165c9173b13f4bc9cb825ef63c06d6fb20dc41b5
-md5=57b151f7bb49fe5154a5697b70d359f9
-cksum=1072837189
+tarball=latte_int-VERSION.tar.bz2
+sha1=1a1b475d69697c45218b133df9b0519894ebce28
+md5=3a862e6a5d1b2e10b0bee342fc0f27a9
+cksum=3434585848

build/pkgs/markupsafe/SPKG.txt

@@ -0,0 +1,19 @@
+= markupsafe =
+
+== Description ==
+
+Implements a XML/HTML/XHTML Markup safe string for Python
+
+== License ==
+
+Simplified BSD
+
+== Upstream Contact ==
+
+Home page: http://github.com/mitsuhiko/markupsafe
+
+== Dependencies ==
+
+Python, setuptools
+
+

build/pkgs/markupsafe/checksums.ini

@@ -0,0 +1,4 @@
+tarball=markupsafe-VERSION.tar.gz
+sha1=cd5c22acf6dd69046d6cb6a3920d84ea66bdf62a
+md5=f5ab3deee4c37cd6a922fb81e730da6e
+cksum=586757310

build/pkgs/markupsafe/package-version.txt

@@ -0,0 +1 @@
+0.23

build/pkgs/markupsafe/spkg-install

@@ -0,0 +1,15 @@
+#!/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
+
+python setup.py install
+if [ $? -ne 0 ]; then
+    echo "Error installing markupsafe ... exiting"
+    exit 1
+fi

build/pkgs/modular_decomposition/SPKG.txt

@@ -0,0 +1,29 @@
+= modular decomposition =
+
+== Description ==
+
+This is an implementation of a modular decomposition algorithm.
+
+http://www.liafa.jussieu.fr/~fm/ (in french)
+
+== License ==
+
+GPL
+
+== SPKG Maintainers ==
+
+Nathann Cohen  (nathann.cohen@gmail.com)
+
+== Upstream Contact ==
+
+Fabien de Montgolfier
+
+http://www.liafa.jussieu.fr/~fm/
+
+== Dependencies ==
+
+None
+
+== Patches ==
+
+None

build/pkgs/modular_decomposition/checksums.ini

@@ -0,0 +1,4 @@
+tarball=modular_decomposition-VERSION.tar.bz2
+sha1=b0ce6d839d1cd2e93d806e70b13bc40bcdbaf9e9
+md5=9bc5245c5fab9df4f45c8e10c27cf3b8
+cksum=2034006428

build/pkgs/modular_decomposition/package-version.txt

@@ -0,0 +1 @@
+20100607

build/pkgs/modular_decomposition/spkg-install

@@ -0,0 +1,17 @@
+#!/usr/bin/env bash
+
+if [ "$SAGE_LOCAL" = "" ]; then
+   echo "SAGE_LOCAL undefined ... exiting";
+   echo "Maybe run 'sage -sh'?"
+   exit 1
+fi
+
+cd "src"
+
+gcc -o "$SAGE_LOCAL/lib/libmodulardecomposition.so" dm.c random.c -fPIC --shared &&
+mv dm_english.h "$SAGE_LOCAL/include/modular_decomposition.h"
+
+if [ $? -ne 0 ]; then
+    echo "An error occurred whilst building modular_decomposition"
+    exit 1
+fi

build/pkgs/pari/checksums.ini

@@ -1,4 +1,4 @@
 tarball=pari-VERSION.tar.gz
-sha1=c11c4452abfaf1a8f1498e4d0ae83995d2cc1f6e
-md5=7bb2efb14829832627bc81735bc50db5
-cksum=2193237587
+sha1=7617f60af26582d4a77e5af413b26fde32bd4f1a
+md5=2ae5684a10d557016fc1b6ad10b8bf80
+cksum=4177496658

build/pkgs/pari/package-version.txt

@@ -1 +1 @@
-2.8-1315-g031c9d6
+2.8-1369-g0e48e9b

build/pkgs/pari/spkg-install

@@ -17,7 +17,9 @@ TOP=`pwd`
 #######################################################################
 cd src
 for patch in ../patches/*.patch; do
-    patch -p1 <"$patch"
+    # Use --no-backup-if-mismatch to prevent .orig files (these confuse
+    # PARI's Perl script which creates pari.desc).
+    patch --no-backup-if-mismatch -p1 <"$patch"
     if [ $? -ne 0 ]; then
         echo >&2 "Error applying '$patch'"
         exit 1

build/pkgs/sagenb/spkg-install

@@ -46,3 +46,12 @@ PKG=$(ls -1 src | GREP_OPTIONS= grep sagenb-)
 
 # Install sagenb into site-packages
 easy_install -H None "src/$PKG" || die "Error installing sagenb !"
+
+# let sagenb use mathjax spkg
+SAGENB_VERSION=$(cat ${SAGE_ROOT}/build/pkgs/sagenb/package-version.txt)
+PYTHON_MAJOR_VERSION=$(cat ${SAGE_ROOT}/build/pkgs/python/package-version.txt | sed 's/\.[^.]*$//g')
+cd ${SAGE_LOCAL}/lib/python/site-packages/sagenb-${SAGENB_VERSION}-py${PYTHON_MAJOR_VERSION}.egg/sagenb/data
+# the following line can be removed once sagenb does not ship mathjax anymore.
+rm -rf mathjax
+ln -s ../../../../../../share/mathjax/
+

src/bin/sage-CSI

@@ -1,5 +1,7 @@
 #!/usr/bin/env python
 
+from __future__ import print_function
+
 description = """
     Attach the debugger to a Python process (given by its pid) and
     extract as much information about its internal state as possible
@@ -12,8 +14,6 @@ description = """
 # set) are automatically deleted, but with a negative value they are
 # never deleted.
 
-from __future__ import print_function
-
 import sys
 import os
 import subprocess

src/bin/sage-banner

@@ -1,5 +1,5 @@
 ┌────────────────────────────────────────────────────────────────────┐
-│ Sage Version 6.6.beta5, Release Date: 2015-03-13                   │
+│ Sage Version 6.6.beta6, Release Date: 2015-03-19                   │
 │ 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='6.6.beta5'
-SAGE_RELEASE_DATE='2015-03-13'
+SAGE_VERSION='6.6.beta6'
+SAGE_RELEASE_DATE='2015-03-19'

src/c_lib/SConstruct

@@ -128,13 +128,11 @@ env['PYV']=platform.python_version().rsplit('.', 1)[0]
 # whitespace without the syntax clutter of lists of strings.
 includes = ['$SAGE_LOCAL/include/', '$SAGE_LOCAL/include/python$PYV/',
             '$SAGE_LOCAL/include/NTL/', 'include']
-cFiles = Split( "interrupt.c  mpn_pylong.c  mpz_pylong.c") + \
-         Split( "mpz_longlong.c stdsage.c" )
+cFiles = Split( "interrupt.c")
 cppFiles = Split( "ntl_wrap.cpp" )
 srcFiles = cFiles + cppFiles
-incFiles = Split( "ccobject.h" ) + \
-           Split( "interrupt.h  mpn_pylong.h  mpz_longlong.h" ) + \
-           Split( "mpz_pylong.h  ntl_wrap.h  parisage.h  stdsage.h" )
+incFiles = Split( "interrupt.h" ) + \
+           Split( "ntl_wrap.h" )
 
 lib = env.SharedLibrary( "csage", [ "src/" + x for x in srcFiles ],
                          LIBS=['ntl', 'pari', 'gmp', 'python$PYV'],

src/c_lib/include/interrupt.h

@@ -18,8 +18,8 @@ redirects stdin from /dev/null, to cause interactive sessions to exit.
 These are critical because they cannot be ignored.  If they happen
 outside of sig_on(), we can only exit Sage with the dreaded
 "unhandled SIG..." message.  Inside of sig_on(), they can be handled
-and raise various exceptions (see sage/ext/c_lib.pyx).  SIGQUIT will
-never be handled and always causes Sage to exit.
+and raise various exceptions (see sage/ext/interrupt.pyx).  SIGQUIT
+will never be handled and always causes Sage to exit.
 
 
 AUTHORS:
@@ -108,9 +108,6 @@ void sage_signal_handler(int sig);
 
 /*
  * Setup the signal handlers. It is safe to call this more than once.
- *
- * We do not handle SIGALRM since there is code to deal with
- * alarms in sage/misc/misc.py
  */
 void setup_sage_signal_handler(void);