Merge branch 'develop' into t/16397/symbolic_cmp

* develop: (1874 commits)
  Updated Sage version to 6.4.beta2
  Trac 16886: fixed documentation, added one doctest.
  trac #16890 added doctest
  trac #16890 - Fixed wrong argument name in FreeQuadraticModule_submodule_with_basis_field
  Trac 16886: Added pari's idealchinese function.
  #16852: update eclib to 20140805
  trac #16739 reviewer patch, minor changes
  Remved unnecessary check for _freegroup_
  Trac #14684: make conversion between free groups aware of generator names
  Line wrap update.
  trac #16875: set the cache when we call difference_matrix
  trac #16875: move imports
  Fix incorrect help for reinstalling a package
  Change of code/doc to make it conform to layout conventions.
  Corrected indentation for seealso block.
  Updated docstrings to match ::/: indentation, added REFERENCE and SEEALSO.
  trac #16868: Mb was initialized twice
  trac #16881: fix documentation issue
  changelog update
  the obvious updates
  ...

.gitignore

@@ -37,6 +37,9 @@
 .idea
 .iml
 
+# XCode
+xcuserdata/
+
 # Eclipse
 *.pydevproject
 .project

VERSION.txt

@@ -1 +1 @@
-Sage version 6.3.beta2, released 2014-05-24
+Sage version 6.4.beta2, released 2014-08-28

build/deps

@@ -31,6 +31,7 @@ all-sage: \
      $(INST)/$(CDDLIB) \
      $(INST)/$(CEPHES) \
      $(INST)/$(CLIQUER) \
+     $(INST)/$(COMBINATORIAL_DESIGNS) \
      $(INST)/$(CONWAY) \
      $(INST)/$(CVXOPT) \
      $(INST)/$(CYTHON) \
@@ -163,12 +164,15 @@ $(INST)/prereq: ../configure
 	    fi; )
 	touch $@
 
+$(INST)/$(PATCH):
+	+$(PIPE) "$(SAGE_SPKG) $(PATCH) 2>&1" "tee -a $(SAGE_LOGS)/$(PATCH).log"
+
+$(INST)/$(PKGCONF): $(INST)/$(PATCH)
+	+$(PIPE) "$(SAGE_SPKG) $(PKGCONF) 2>&1" "tee -a $(SAGE_LOGS)/$(PKGCONF).log"
+
 $(INST)/$(BZIP2): $(INST)/prereq $(INST)/$(PKGCONF)
 	+$(PIPE) "$(SAGE_SPKG) $(BZIP2) 2>&1" "tee -a $(SAGE_LOGS)/$(BZIP2).log"
 
-$(INST)/$(PATCH): $(INST)/$(BZIP2)
-	+$(PIPE) "$(SAGE_SPKG) $(PATCH) 2>&1" "tee -a $(SAGE_LOGS)/$(PATCH).log"
-
 ###############################################################################
 # Building normal packages
 ###############################################################################
@@ -185,6 +189,9 @@ $(INST)/$(BOOST_CROPPED):
 $(INST)/$(CLIQUER):
 	+$(PIPE) "$(SAGE_SPKG) $(CLIQUER) 2>&1" "tee -a $(SAGE_LOGS)/$(CLIQUER).log"
 
+$(INST)/$(COMBINATORIAL_DESIGNS):
+	+$(PIPE) "$(SAGE_SPKG) $(COMBINATORIAL_DESIGNS) 2>&1" "tee -a $(SAGE_LOGS)/$(COMBINATORIAL_DESIGNS).log"
+
 $(INST)/$(NCURSES): $(INST)/$(PKGCONF)
 	+$(PIPE) "$(SAGE_SPKG) $(NCURSES) 2>&1" "tee -a $(SAGE_LOGS)/$(NCURSES).log"
 
@@ -336,7 +343,7 @@ $(INST)/$(SAGETEX): $(INST)/$(PYTHON) \
 $(INST)/$(SETUPTOOLS): $(INST)/$(PYTHON)
 	+$(PIPE) "$(SAGE_SPKG) $(SETUPTOOLS) 2>&1" "tee -a $(SAGE_LOGS)/$(SETUPTOOLS).log"
 
-$(INST)/$(SINGULAR): $(INST)/$(MPIR) $(INST)/$(NTL) \
+$(INST)/$(SINGULAR): $(INST)/$(MPIR) $(INST)/$(NTL) $(INST)/$(FLINT) \
 		     $(INST)/$(READLINE) $(INST)/$(MPFR)
 	+$(PIPE) "$(SAGE_SPKG) $(SINGULAR) 2>&1" "tee -a $(SAGE_LOGS)/$(SINGULAR).log"
 
@@ -471,6 +478,7 @@ $(INST)/sage: \
 		 $(INST)/$(IML) \
 		 $(INST)/$(JINJA2) \
 		 $(INST)/$(LCALC) \
+		 $(INST)/$(LRCALC) \
 		 $(INST)/$(LIBGAP) \
 		 $(INST)/$(LIBPNG) \
 		 $(INST)/$(LINBOX) \
@@ -521,9 +529,6 @@ $(INST)/$(GCC): $(INST)/$(MPIR) $(INST)/$(MPFR) $(INST)/$(MPC) \
 $(INST)/$(PILLOW): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
 	+$(PIPE) "$(SAGE_SPKG) $(PILLOW) 2>&1" "tee -a $(SAGE_LOGS)/$(PILLOW).log"
 
-$(INST)/$(PKGCONF): 
-	+$(PIPE) "$(SAGE_SPKG) $(PKGCONF) 2>&1" "tee -a $(SAGE_LOGS)/$(PKGCONF).log"
-
 $(INST)/$(PKGCONFIG): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
 	+$(PIPE) "$(SAGE_SPKG) $(PKGCONFIG) 2>&1" "tee -a $(SAGE_LOGS)/$(PKGCONFIG).log"
 

build/install

@@ -324,6 +324,7 @@ BZIP2=`newest_version bzip2`
 CDDLIB=`newest_version cddlib`
 CEPHES=`newest_version cephes`
 CLIQUER=`newest_version cliquer`
+COMBINATORIAL_DESIGNS=`newest_version combinatorial_designs`
 CONWAY=`newest_version conway_polynomials`
 CVXOPT=`newest_version cvxopt`
 CYTHON=`newest_version cython`

build/pkgs/combinatorial_designs/SPKG.txt

@@ -0,0 +1,29 @@
+= Combinatorial Designs =
+
+== Description ==
+
+Data for Combinatorial Designs. Current content:
+
+- The table of MOLS (10 000 integers) from the Handbook of Combinatorial
+  Designs, 2ed.
+
+== SPKG Maintainers ==
+
+ * Nathann Cohen
+
+== License ==
+
+Public domain.
+
+== Upstream Contact ==
+
+ None
+
+== Dependencies ==
+
+N/A
+
+== Changelog ==
+
+== designs-20140630 (Nathann Cohen, 2014-06-30) ==
+ * #16541: Table of MOLS

build/pkgs/combinatorial_designs/checksums.ini

@@ -0,0 +1,4 @@
+tarball=combinatorial_designs-VERSION.tar.bz2
+sha1=353ba24217f9b7920890a784fd75dc59175f7196
+md5=f345a6918b1bcf34fcd71c2f26d10de0
+cksum=131472289

build/pkgs/combinatorial_designs/package-version.txt

@@ -0,0 +1 @@
+20140630

build/pkgs/combinatorial_designs/spkg-install

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+mkdir -p "$SAGE_SHARE"/combinatorial_designs
+mv src/* "$SAGE_SHARE"/combinatorial_designs

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=56399592db642ce25cd331edba8ceeecfa211393
-md5=030561c77e141c8e0c7c045b1c301964
-cksum=4180963490
+sha1=9f52b9a8917273a8b29a40c8e517ebb099cc0537
+md5=adfa272430f561682954687258364d5d
+cksum=3677976078

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-31
+46

build/pkgs/cvxopt/SPKG.txt

@@ -54,6 +54,9 @@ GNU Lesser General Public License, v2.1.  See src/LICENSE for more details.
 
 == Changelog ==
 
+=== cvxopt-1.1.7 (Dima Pasechnik, 24 Aug 2014) ===
+ * #16874: upgrade to version 1.1.7.
+
 === cvxopt-1.1.6.p0 (Volker Braun, Jeroen Demeyer, 15 May 2013) ===
  * #12832: upgrade to version 1.1.6.
  * Remove undocumented patch changing int_t to int.

build/pkgs/cvxopt/checksums.ini

@@ -1,4 +1,4 @@
-tarball=cvxopt-VERSION.tar.bz2
-sha1=ded19c9acfa3c256e6cbd738fbaf5a155c7dbc96
-md5=7114b6952d0428da51d237b974ab64bd
-cksum=2074500616
+tarball=cvxopt-VERSION.tar.gz
+sha1=199ae22f7175be8e46b277993eea7c39e30da1f1
+md5=3073a5da23cb5a77d3bc143edde1e4f1
+cksum=708245817

build/pkgs/cvxopt/package-version.txt

@@ -1 +1 @@
-1.1.6.p0
+1.1.7

build/pkgs/cvxopt/patches/setup.py.patch

@@ -1,8 +1,9 @@
-diff -ru src/setup.py b/setup.py
---- src/setup.py	2013-04-22 08:44:28.000000000 +0200
-+++ b/setup.py	2013-05-15 10:43:21.332392968 +0200
-@@ -2,26 +2,38 @@
- from glob import glob
+diff --git a/setup.py b/setup.py
+index 20670f7..62e82c5 100644
+--- a/setup.py
++++ b/setup.py
+@@ -7,26 +7,38 @@ from glob import glob
+ import os
 
  # Modifiy this if BLAS and LAPACK libraries are not in /usr/lib.
 -BLAS_LIB_DIR = '/usr/lib'
@@ -45,7 +46,7 @@ diff -ru src/setup.py b/setup.py
 
  # Set to 1 if you are installing the fftw module.
  BUILD_FFTW = 0 
-@@ -33,13 +45,13 @@
+@@ -38,13 +50,13 @@ FFTW_LIB_DIR = '/usr/lib'
  FFTW_INC_DIR = '/usr/include'
 
  # Set to 1 if you are installing the glpk module.
@@ -62,7 +63,7 @@ diff -ru src/setup.py b/setup.py
 
  # Set to 1 if you are installing the DSDP module.
  BUILD_DSDP = 0
-@@ -77,7 +89,7 @@
+@@ -103,7 +115,7 @@ if BUILD_FFTW:
      extmods += [fftw];
 
  if BUILD_GLPK:

build/pkgs/d3js/SPKG.txt

@@ -0,0 +1,33 @@
+= d3js =
+
+== Description ==
+
+D3.js is a JavaScript library for manipulating documents based on data.
+The file d3.min.js will be placed into the ${SAGE_SHARE}/d3js/ directory.
+
+== License ==
+
+BSD 3-Clause License
+
+== SPKG Maintainers ==
+
+* Thierry Monteil
+
+== Upstream Contact ==
+
+Author: Mike Bostock (http://bost.ocks.org/mike/)
+Home page: http://d3js.org/
+
+== Dependencies ==
+
+None.
+
+== Special Update/Build Instructions ==
+
+Two kind of archives can be downloaded from d3.js website: one with all source
+code and tests that weights 2,9M (both in zip and tar.gz formats) and one with
+the final javascript scripts which weights 121K (zip format only). Since
+testing requires node.js that is not shipped with Sage, we currenlty ship the
+final js only. Hence we have to transform it from zip to tar.gz format.
+Running sage-src should do all the repackaging job.
+

build/pkgs/d3js/checksums.ini

@@ -0,0 +1,4 @@
+tarball=d3js-VERSION.tar.gz
+sha1=2fd4da34ca9e645cf81bf914d289c21c7bb8c166
+md5=d859a120f1eaebb8b563f4598868c564
+cksum=527881311

build/pkgs/d3js/package-version.txt

@@ -0,0 +1 @@
+3.4.8

build/pkgs/d3js/spkg-install

@@ -0,0 +1,15 @@
+#!/bin/sh
+
+if [ -z "$SAGE_SHARE" ]; then
+    echo >&2 "SAGE_SHARE undefined ... exiting"
+    echo >&2 "Maybe run 'sage --sh'?"
+    exit 1
+fi
+
+TARGET="${SAGE_SHARE}/d3js"
+if [ ! -d "${TARGET}" ]; then
+   mkdir "${TARGET}"
+fi
+
+cp 'src/d3.min.js' "${TARGET}/"
+

build/pkgs/d3js/spkg-src

@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+
+set -e
+
+[ -n "${SAGE_ROOT}" ] || SAGE_ROOT="$(pwd)/../../../"
+
+
+# prepare a clean directory.
+[ -d "work" ] && rm -rf "work"
+mkdir "work"
+cd "work"
+
+
+# determine latest version.
+wget 'https://raw.githubusercontent.com/mbostock/d3/master/package.json'
+GIT_VERSION="$(grep '"version":' 'package.json' | sed 's/.*: "\(.*\)",/\1/g')"
+
+
+# fetch source and check version.
+wget "https://github.com/mbostock/d3/releases/download/v${GIT_VERSION}/d3.zip"
+unzip 'd3.zip'
+ZIP_VERSION="$(grep 'version:' 'd3.js' | sed 's/.*: "\(.*\)"/\1/g')"
+if [ ! "${GIT_VERSION}" = "${ZIP_VERSION}" ] ; then
+    echo "Version mismatch: ${GIT_VERSION} vs ${ZIP_VERSION}."
+    exit 1
+fi
+
+
+# build and move tarball
+mkdir "d3js-${ZIP_VERSION}"
+mv 'd3.min.js' 'LICENSE' "d3js-${ZIP_VERSION}"
+tar czvf "d3js-${ZIP_VERSION}.tar.gz" "d3js-${ZIP_VERSION}"
+mv "d3js-${ZIP_VERSION}.tar.gz" "${SAGE_ROOT}/upstream/"
+
+
+# update package info
+cd ..
+echo "${ZIP_VERSION}" > 'package-version.txt'
+sage -sh 'sage-fix-pkg-checksums'
+
+

build/pkgs/database_cremona_ellcurve/checksums.ini

@@ -1,4 +1,4 @@
 tarball=database_cremona_ellcurve-VERSION.tar.bz2
-sha1=25f256d78bf5c4454d85bb9a22df2d396e4962ba
-md5=14de1b11227fdd66e1a87e8101940988
-cksum=2753267872
+sha1=ab96f509574419c03d9f1c8820c4d96042a17a04
+md5=56956829063534142f9f12bc1274c01c
+cksum=2400753722

build/pkgs/database_cremona_ellcurve/package-version.txt

@@ -1 +1 @@
-20140325
+20140512

build/pkgs/database_gap/checksums.ini

@@ -1,4 +1,4 @@
 tarball=database_gap-VERSION.tar.bz2
-sha1=6e5f63df55881a509076c4ecbd02c7afc8f81ef9
-md5=6f9d4632f6d2f4a7000c22cff5d15406
-cksum=1275532986
+sha1=0e81cd017dc0542fc5faf923324eb1fffb61cdeb
+md5=879fc85f53fa9ff9f12dc7ebd621a528
+cksum=3437971482

build/pkgs/database_gap/package-version.txt

@@ -1 +1 @@
-4.7.4
+4.7.5

build/pkgs/eclib/checksums.ini

@@ -1,4 +1,4 @@
 tarball=eclib-VERSION.tar.bz2
-sha1=1210d69f679f6d70c378cb78231980f28e18a0af
-md5=87773eb30baaa7f413afa01a5c251265
-cksum=4230857238
+sha1=d868342a9d763787dfecd7d07ffacead8d04be73
+md5=5ee8cc313b5383dc463ed13f4b147edc
+cksum=420082920

build/pkgs/eclib/package-version.txt

@@ -1 +1 @@
-20140128
+20140805

build/pkgs/gap/SPKG.txt

@@ -54,7 +54,3 @@ update GAP, please also update and use the spkg-src script.
 
  * writeandcheck.patch: fix infinite loop in writeandcheck() when
    writing an error message fails.
-
- * 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/checksums.ini

@@ -1,4 +1,4 @@
 tarball=gap-VERSION.tar.bz2
-sha1=e61699cedf56b3b1668dec7387437eeb08fba3e7
-md5=3d3c1a40185d05863afbfd59956eecd9
-cksum=2711033242
+sha1=8a2437546c374652457da6d4d9749e94f39d83e7
+md5=348a75094d3320303e8179bd6962d560
+cksum=2730509972

build/pkgs/gap/package-version.txt

@@ -1 +1 @@
-4.7.4
+4.7.5