Merge branch 'develop' into public/combinat/crystals/catalog-15882

* develop: (121 commits)
  Updated Sage version to 6.2.beta5
  in docstring: added ``
  OSX 10.4 build fix
  Only accepts fields as input for change_ring
  FiniteStateMachine.determine_alphabets: one more small correction in docstring
  add definition
  use pydoc.pager on _sage_doc_unformatted instead
  FiniteStateMachine.determine_alphabets: corrected description of parameter reset
  Trac #13174: sagedoc.help() didn't discriminate cachedfuncs from funcs
  trac #15951 correct one raise statement towards python3
  Added destruction of pool in parallel_iter
  separate absolute from local (implicit relative) imports
  microfixes
  Added global options to rigged configurations to improve printing.
  Trac 13609: fix symbolic expression auto evaluation when content is in GF(2^k)
  Trac 13048: fixed division without remainder for polynomials over QQbar
  allow Singular to build with recent versions of Xcode
  removed k from init
  remove the avoid section "Function" in the intial comment and implement a function are_mutually_orthogonal_latin_squares
  Do not forget to define ambient_field before computing its algebraic closure.
  ...

Conflicts:
	src/sage/combinat/crystals/affine_factorization.py

COPYING.txt

@@ -38,6 +38,7 @@ cliquer                     GPLv2+
 conway_polynomials          None (database)
 cvxopt                      GPLv2+
 cython                      Apache, version 2.0
+dateutil                    Simplified BSD
 docutils                    Modified BSD
 ecl                         LGPLv2+
 eclib                       GPLv2+
@@ -72,7 +73,7 @@ libm4rie                    GPLv2+
 libpng                      Custom, very similar to zlib
 linbox                      LGPLv2.1+
 lrcalc                      GPLv2+
-matplotlib                  Python License
+matplotlib                  Matplotlib License (BSD compatible, see below)
 maxima                      See below
 mercurial                   GPLv2+
 mpc                         LGPLv3+
@@ -96,6 +97,7 @@ ppl                         GPLv3+
 pycrypto                    Public domain & Python License
 pygments                    Modified BSD
 pynac                       GPLv2+
+pyparsing                   MIT License
 python                      Python License (see below)
 R                           GPLv2+
 ratpoints                   GPLv2+
@@ -113,6 +115,7 @@ scipy                       Modified BSD
 scons                       MIT License
 setuptools                  Python License
 singular                    GPLv2 or GPLv3 (see below)
+six                         MIT License
 sphinx                      Modified BSD
 sqlalchemy                  MIT License
 sqlite                      Public Domain (see below)
@@ -121,6 +124,7 @@ sympow                      Modified BSD
 sympy                       Modified BSD
 tachyon                     Modified BSD
 termcap                     GPLv2+
+tornado                     Apache License
 zlib                        Custom (Modified BSD)
 zn_poly                     GPLv2 or GPLv3 (no later versions, see below)
 
@@ -1010,6 +1014,17 @@ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 ================================================================================
 
+matplotlib:
+(from http://matplotlib.sourceforge.net/users/license.html)
+
+Matplotlib only uses BSD compatible code, and its license is based on
+the PSF license. See the Open Source Initiative licenses page for
+details on individual licenses. Non-BSD compatible licenses (eg LGPL)
+are acceptable in matplotlib toolkits. For a discussion of the
+motivations behind the licencing choice, see Licenses.
+
+================================================================================
+
 maxima:
 (from http://maxima.sourceforge.net/authorization-letter.html)
 

VERSION.txt

@@ -1 +1 @@
-Sage version 6.2.beta4, released 2014-03-11
+Sage version 6.2.beta5, released 2014-03-23

build/deps

@@ -34,6 +34,7 @@ all-sage: \
      $(INST)/$(CONWAY) \
      $(INST)/$(CVXOPT) \
      $(INST)/$(CYTHON) \
+     $(INST)/$(DATEUTIL) \
      $(INST)/$(DOCUTILS) \
      $(INST)/$(ECL) \
      $(INST)/$(ECLIB) \
@@ -89,6 +90,7 @@ all-sage: \
      $(INST)/$(PYCRYPTO) \
      $(INST)/$(PYGMENTS) \
      $(INST)/$(PYNAC) \
+     $(INST)/$(PYPARSING) \
      $(INST)/$(PYTHON) \
      $(INST)/$(RATPOINTS) \
      $(INST)/$(R) \
@@ -101,13 +103,15 @@ all-sage: \
      $(INST)/$(SCONS) \
      $(INST)/$(SETUPTOOLS) \
      $(INST)/$(SINGULAR) \
+     $(INST)/$(SIX) \
      $(INST)/$(SPHINX) \
      $(INST)/$(SQLALCHEMY) \
      $(INST)/$(SQLITE) \
      $(INST)/$(SYMMETRICA) \
      $(INST)/$(SYMPOW) \
      $(INST)/$(SYMPY) \
      $(INST)/$(TACHYON) \
+     $(INST)/$(TORNADO) \
      $(INST)/$(NCURSES) \
      $(INST)/$(ZLIB) \
      $(INST)/$(ZNPOLY) \
@@ -357,9 +361,23 @@ $(INST)/$(FREETYPE): $(INST)/$(LIBPNG)
 $(INST)/$(LIBPNG): $(INST)/$(ZLIB)
 	+$(PIPE) "$(SAGE_SPKG) $(LIBPNG) 2>&1" "tee -a $(SAGE_LOGS)/$(LIBPNG).log"
 
+$(INST)/$(SIX): $(INST)/$(PYTHON)
+	+$(PIPE) "$(SAGE_SPKG) $(SIX) 2>&1" "tee -a $(SAGE_LOGS)/$(SIX).log"
+
+$(INST)/$(DATEUTIL): $(INST)/$(PYTHON) $(INST)/$(SIX)
+	+$(PIPE) "$(SAGE_SPKG) $(DATEUTIL) 2>&1" "tee -a $(SAGE_LOGS)/$(DATEUTIL).log"
+
+$(INST)/$(PYPARSING): $(INST)/$(PYTHON)
+	+$(PIPE) "$(SAGE_SPKG) $(PYPARSING) 2>&1" "tee -a $(SAGE_LOGS)/$(PYPARSING).log"
+
+$(INST)/$(TORNADO): $(INST)/$(PYTHON)
+	+$(PIPE) "$(SAGE_SPKG) $(TORNADO) 2>&1" "tee -a $(SAGE_LOGS)/$(TORNADO).log"
+
 $(INST)/$(MATPLOTLIB): $(INST)/$(PYTHON) $(INST)/$(NUMPY) \
 		       $(INST)/$(FREETYPE) $(INST)/$(LIBPNG) \
-		       $(INST)/$(GDMODULE)
+		       $(INST)/$(GDMODULE) $(INST)/$(DATEUTIL) \
+		       $(INST)/$(PKGCONFIG) $(INST)/$(PYPARSING) \
+                       $(INST)/$(SETUPTOOLS)
 	+$(PIPE) "$(SAGE_SPKG) $(MATPLOTLIB) 2>&1" "tee -a $(SAGE_LOGS)/$(MATPLOTLIB).log"
 
 $(INST)/$(CDDLIB): $(INST)/$(MPIR)

build/install

@@ -328,6 +328,7 @@ CLIQUER=`newest_version cliquer`
 CONWAY=`newest_version conway_polynomials`
 CVXOPT=`newest_version cvxopt`
 CYTHON=`newest_version cython`
+DATEUTIL=`newest_version dateutil`
 DOCUTILS=`newest_version docutils`
 ECL=`newest_version ecl`
 ECLIB=`newest_version eclib`
@@ -387,6 +388,7 @@ PPL=`newest_version ppl`
 PYCRYPTO=`newest_version pycrypto`
 PYGMENTS=`newest_version pygments`
 PYNAC=`newest_version pynac`
+PYPARSING=`newest_version pyparsing`
 PYTHON=`newest_version python`
 R=`newest_version r`
 RPY=`newest_version rpy2`
@@ -399,13 +401,15 @@ SCIPY=`newest_version scipy`
 SCONS=`newest_version scons`
 SETUPTOOLS=`newest_version setuptools`
 SINGULAR=`newest_version singular`
+SIX=`newest_version six`
 SPHINX=`newest_version sphinx`
 SQLALCHEMY=`newest_version sqlalchemy`
 SQLITE=`newest_version sqlite`
 SYMMETRICA=`newest_version symmetrica`
 SYMPOW=`newest_version sympow`
 SYMPY=`newest_version sympy`
 TACHYON=`newest_version tachyon`
+TORNADO=`newest_version tornado`
 NCURSES=`newest_version ncurses`
 ZLIB=`newest_version zlib`
 ZNPOLY=`newest_version zn_poly`

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=e2547006cb57f11981c7d8f28d9c23a23cf4ec72
-md5=4698d0aa23f7e03548f43eaa33e7d663
-cksum=551574147
+sha1=e4f7a8b1595adc80b90d3118c35d3f8568588b8e
+md5=fb4ca501460d44ab117694de80be374c
+cksum=474790094

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-16
+18

build/pkgs/dateutil/SPKG.txt

@@ -0,0 +1,31 @@
+= dateutil =
+
+== Description ==
+
+The dateutil module provides powerful extensions to the standard
+datetime module.
+
+== License ==
+
+Simplified BSD License
+
+== SPKG Maintainers ==
+
+John H. Palmieri
+
+== Upstream Contact ==
+
+Author: Gustavo Niemeyer <[email protected]>
+Home page: http://labix.org/python-dateutil
+
+== Dependencies ==
+
+* Python
+* Six
+
+== Changelog ==
+
+=== dateutil-2.2 (John H. Palmieri, 20 December 2013) ===
+
+ * Trac #14993: initial release.
+

build/pkgs/dateutil/checksums.ini

@@ -0,0 +1,4 @@
+tarball=dateutil-VERSION.tar.gz
+sha1=51bdee8ba3817707fcb22767da0d2d039c5ab921
+md5=2d5bcc656d801e9dd3c1e658f4db50cf
+cksum=3142219490

build/pkgs/dateutil/package-version.txt

@@ -0,0 +1 @@
+2.2

build/pkgs/dateutil/spkg-install

@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+
+if [ "$SAGE_LOCAL" = "" ]; then
+   echo "SAGE_LOCAL undefined ... exiting";
+   echo "Maybe run 'sage -sh'?"
+   exit 1
+fi
+
+cd src
+
+python setup.py install
+if [ $? -ne 0 ]; then
+    echo "Error installing dateutil ... exiting"
+    exit 1
+fi

build/pkgs/flint/checksums.ini

@@ -1,4 +1,4 @@
 tarball=flint-VERSION.tar.gz
-sha1=b506c3870a3d976796ec0b6224659e9c82dcceae
-md5=3b9bc754ef9e974ad4d0cf808d9809df
-cksum=1290600232
+sha1=cf73447b181d7fcfe968146f5464e56213a6a6af
+md5=0ac731aa9593034481671c949278f41d
+cksum=63954925

build/pkgs/flint/package-version.txt

@@ -1 +1 @@
-2.4.1.p0
+2.4.2

build/pkgs/flint/spkg-install

@@ -41,7 +41,7 @@ for patch in ../patches/*.patch; do
 done
 
 echo "Configuring FLINT."
-./configure --prefix="$SAGE_LOCAL" --with-mpir="$SAGE_LOCAL" \
+./configure --prefix="$SAGE_LOCAL" --with-gmp="$SAGE_LOCAL" \
     --with-mpfr="$SAGE_LOCAL" --with-ntl="$SAGE_LOCAL" $FLINT_CONFIGURE
 if [ $? -ne 0 ]; then
     echo >&2 "Error: Failed to configure FLINT."

build/pkgs/gap/SPKG.txt

@@ -57,3 +57,4 @@ update GAP, please also update and use the spkg-src script.
 
  * sparc_segfault.patch: fix alignment issue on SPARC
 
+ * osx_10_4.patch: OSX 10.4 build fix taken from https://bitbucket.org/gap-system/gap/

build/pkgs/gap/patches/osx_10_4.patch

@@ -0,0 +1,36 @@
+# HG changeset patch
+# User Max Horn <[email protected]>
+# Date 1395263557 -3600
+# Branch stable-4.7
+# Node ID 070b4a964402c4396625dbf81e8f1a4e830259da
+# Parent  388dbf0c64b27825cf19ea9b4f9865a94bb7d561
+build: do not use -no_pie linker option on older OS X versions
+
+diff --git a/cnf/aclocal.m4 b/cnf/aclocal.m4
+--- a/cnf/aclocal.m4
++++ b/cnf/aclocal.m4
+@@ -158,7 +158,9 @@
+ AC_DEFUN(GP_LDFLAGS,
+ [AC_CACHE_CHECK(Linker default flags, gp_cv_ldflags,
+  [ case "$host-$CC" in
+-    *-apple-* )
++    *-darwin[[6-9]].* | *-darwin10.* )
++        gp_cv_ldflags="-g ${ABI_CFLAGS}";;
++    *-darwin* )
+         gp_cv_ldflags="-g -Wl,-no_pie ${ABI_CFLAGS}";;
+     *-gcc* | *-egcs )
+         gp_cv_ldflags="-g ${ABI_CFLAGS}";;
+diff --git a/cnf/configure.out b/cnf/configure.out
+--- a/cnf/configure.out
++++ b/cnf/configure.out
+@@ -4435,7 +4435,9 @@
+   $as_echo_n "(cached) " >&6
+ else
+    case "$host-$CC" in
+-    *-apple-* )
++    *-darwin[6-9].* | *-darwin10.* )
++        gp_cv_ldflags="-g ${ABI_CFLAGS}";;
++    *-darwin* )
+         gp_cv_ldflags="-g -Wl,-no_pie ${ABI_CFLAGS}";;
+     *-gcc* | *-egcs )
+         gp_cv_ldflags="-g ${ABI_CFLAGS}";;

build/pkgs/gmp/SPKG.txt

@@ -0,0 +1,15 @@
+= GMP =
+
+== Description ==
+
+GMP is a free library for arbitrary precision arithmetic, operating on signed
+integers, rational numbers, and floating-point numbers.
+There is no practical limit to the precision except the ones implied by the available memory in the machine GMP runs on.
+GMP has a rich set of functions, and the functions have a regular interface.
+
+== License ==
+ * LGPL V3
+
+== Upstream Contact ==
+ * http://gmplib.org
+

build/pkgs/gmp/checksums.ini

@@ -0,0 +1,4 @@
+tarball=gmp-VERSION.tar.bz2
+sha1=b35928e2927b272711fdfbf71b7cfd5f86a6b165
+md5=a082867cbca5e898371a97bb27b31fea
+cksum=2362548932

build/pkgs/gmp/package-version.txt

@@ -0,0 +1 @@
+5.1.3

build/pkgs/gmp/spkg-check

@@ -0,0 +1,21 @@
+#!/usr/bin/env bash
+
+if [ -z "$SAGE_LOCAL" ]; then
+    echo >&2 "Error: SAGE_LOCAL undefined - exiting..."
+    echo >&2 "Maybe run 'sage -sh'?"
+    exit 1
+fi
+
+cd src
+
+# We don't have to set up any environment variables here since the
+# Makefiles already have them from 'configure'.
+
+echo "Now building and running GMP's test suite..."
+$MAKE check
+if [ $? -ne 0 ]; then
+    echo >&2 "Error: The GMP test suite failed."
+    exit 1
+fi
+
+echo "The GMP test suite passed successfully."