Merge branch 'develop' into public/combinat/rigged_configurations/met…

…hods-15560

.gitignore

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

VERSION.txt

@@ -1 +1 @@
-Sage version 6.3.beta4, released 2014-06-19
+Sage version 6.3.beta5, released 2014-07-01

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=100d46c2358df82a93feb63bc339620f413caa1b
-md5=d10af4cfec628f992109225444e68ba3
-cksum=553182482
+sha1=4d10c539769b8aa53c2bd97f9d9ae6b8a139d356
+md5=b9ea7956de216fc5e5965e17b14bab3f
+cksum=2387138201

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-34
+35

build/pkgs/libgap/checksums.ini

@@ -1,4 +1,4 @@
 tarball=libgap-VERSION.tar.gz
-sha1=4ae83174267adbe615be9cab0d1f4a3c53bddb5e
-md5=e69513efa609ac1fa095db981b6c7c2b
-cksum=2720542483
+sha1=6880c1c36a59051a1e94f4866848a37f4d79cb7c
+md5=f797ca3b8d3232cb24b5fe3be704a08a
+cksum=1046627126

build/pkgs/libgap/package-version.txt

@@ -1 +1 @@
-4.7.5
+4.7.5.1

build/pkgs/lrcalc/SPKG.txt

@@ -29,42 +29,3 @@ Anders S. Buch ([email protected])
    spkg-src and the patch patches/build.diff. So, whenever you update
    the sources, you should use/modify the spkg-src script.
 
-== Changelog ==
-
-=== lrcalc-1.1.6.p0 (Jeroen Demeyer, 8 May 2013)  ===
- * Trac #14487: fix various build and packaging issues, add spkg-src
-   and patches/build.diff (to be applied at packaging time).
-
-=== lrcalc-1.1.6 (Jean-Pierre Flori, December 2012 - February 2013)  ===
-
- * Trac #13839:
-  * Updated to lrcalc-sage-1.1.6: let lrcalc build a shared library on Cygwin.
-  * Stop tracking the src directory which is now tracked upstream.
-
-=== lrcalc-1.1.6beta1 (Nicolas M. Thiéry, June 2012)  ===
-
- * Updated to lrcalc-1.1.6beta1:
-   * Fixed segmentation fault on Open Solaris (name conflict with hash_insert)
-   * Added quantum and fusion calculations in the README and testsuite
- * Don't install the lrcalc binaries, only the libraries and headers
-
-=== lrcalc-1.1.6beta.p0 (Nicolas M. Thiéry, June 2012)  ===
-
- * Fixed make -> $MAKE
-
-=== lrcalc-1.1.6beta (Nicolas M. Thiéry, January 2012)  ===
-
- * Upgrade to lrcalc 1.1.6beta which combines:
-   * lrcalc-1.1.5.tar.gz
-   * schmult-1.1.5.tar.gz
-   * an autotools build system
-
- * First release as optional spkg (see #10333)
-
-=== lrcalc-1.1.5b (Nicolas M. Thiéry, May 2011) ===
-
- * An alpha prerelease of 1.1.6beta
-
-=== lrcalc-1.1.4 (Mike Hansen, May 2010) ===
-
- * Initial version

build/pkgs/lrcalc/checksums.ini

@@ -1,4 +1,4 @@
-tarball=lrcalc-VERSION.tar.bz2
-sha1=b36a8bdfab9f8ca0cfc7f922b4f4b0064d364464
-md5=e41f12d2f1f04e868c5d651951f9b0ff
-cksum=3021882451
+tarball=lrcalc-VERSION.tar.gz
+sha1=8149a4c676f4b21ce9dc23145b272a061a04240a
+md5=a1d85113d9c915b41ba38fcf1741e637
+cksum=4041239855

build/pkgs/lrcalc/package-version.txt

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

build/pkgs/lrcalc/patches/lrcalc-1.1.7-jump.patch

@@ -0,0 +1,138 @@
+diff -Naur lrcalc-sage-1.1.7-orig/lrcoef/coprod.c lrcalc-sage-1.1.7/lrcoef/coprod.c
+--- lrcalc-sage-1.1.7-orig/lrcoef/coprod.c	2013-06-09 16:12:42.000000000 +1200
++++ lrcalc-sage-1.1.7/lrcoef/coprod.c	2014-06-29 09:51:37.000000000 +1200
+@@ -11,7 +11,7 @@
+ #include <vectarg.h>
+
+ #include "symfcn.h"
+-
++#include "lrcalc_jump.h"
+
+ void print_usage()
+ {
+diff -Naur lrcalc-sage-1.1.7-orig/lrcoef/lrcalc.c lrcalc-sage-1.1.7/lrcoef/lrcalc.c
+--- lrcalc-sage-1.1.7-orig/lrcoef/lrcalc.c	2013-06-09 16:12:42.000000000 +1200
++++ lrcalc-sage-1.1.7/lrcoef/lrcalc.c	2014-06-29 09:52:25.000000000 +1200
+@@ -12,7 +12,7 @@
+
+ #include "symfcn.h"
+ #include "maple.h"
+-
++#include "lrcalc_jump.h"
+
+ #define MULT_USAGE \
+ "lrcalc mult [-mz] [-r rows] [-q rows,cols] [-f rows,level] part1 - part2\n"
+diff -Naur lrcalc-sage-1.1.7-orig/lrcoef/lrcoef.c lrcalc-sage-1.1.7/lrcoef/lrcoef.c
+--- lrcalc-sage-1.1.7-orig/lrcoef/lrcoef.c	2013-06-09 16:12:42.000000000 +1200
++++ lrcalc-sage-1.1.7/lrcoef/lrcoef.c	2014-06-29 09:52:50.000000000 +1200
+@@ -14,7 +14,7 @@
+
+ #include "symfcn.h"
+ #include "maple.h"
+-
++#include "lrcalc_jump.h"
+
+ void print_usage()
+ {
+diff -Naur lrcalc-sage-1.1.7-orig/lrcoef/lrskew.c lrcalc-sage-1.1.7/lrcoef/lrskew.c
+--- lrcalc-sage-1.1.7-orig/lrcoef/lrskew.c	2013-06-09 16:12:42.000000000 +1200
++++ lrcalc-sage-1.1.7/lrcoef/lrskew.c	2014-06-29 09:53:16.000000000 +1200
+@@ -11,7 +11,7 @@
+ #include <vectarg.h>
+
+ #include "symfcn.h"
+-
++#include "lrcalc_jump.h"
+
+ void print_usage()
+ {
+diff -Naur lrcalc-sage-1.1.7-orig/lrcoef/mult.c lrcalc-sage-1.1.7/lrcoef/mult.c
+--- lrcalc-sage-1.1.7-orig/lrcoef/mult.c	2013-06-09 16:12:42.000000000 +1200
++++ lrcalc-sage-1.1.7/lrcoef/mult.c	2014-06-29 09:53:45.000000000 +1200
+@@ -12,7 +12,7 @@
+
+ #include "symfcn.h"
+ #include "maple.h"
+-
++#include "lrcalc_jump.h"
+
+ void print_usage()
+ {
+diff -Naur lrcalc-sage-1.1.7-orig/lrcoef/sat.c lrcalc-sage-1.1.7/lrcoef/sat.c
+--- lrcalc-sage-1.1.7-orig/lrcoef/sat.c	2013-06-09 16:12:42.000000000 +1200
++++ lrcalc-sage-1.1.7/lrcoef/sat.c	2014-06-29 09:54:08.000000000 +1200
+@@ -10,7 +10,7 @@
+ #include <vector.h>
+
+ #include "symfcn.h"
+-
++#include "lrcalc_jump.h"
+
+ #define NUM_PRIMES	50
+
+diff -Naur lrcalc-sage-1.1.7-orig/lrcoef/skew.c lrcalc-sage-1.1.7/lrcoef/skew.c
+--- lrcalc-sage-1.1.7-orig/lrcoef/skew.c	2013-06-09 16:12:42.000000000 +1200
++++ lrcalc-sage-1.1.7/lrcoef/skew.c	2014-06-29 09:54:40.000000000 +1200
+@@ -13,7 +13,7 @@
+
+ #include "symfcn.h"
+ #include "maple.h"
+-
++#include "lrcalc_jump.h"
+
+ void print_usage()
+ {
+diff -Naur lrcalc-sage-1.1.7-orig/mathlib/alloc.c lrcalc-sage-1.1.7/mathlib/alloc.c
+--- lrcalc-sage-1.1.7-orig/mathlib/alloc.c	2013-06-09 16:12:17.000000000 +1200
++++ lrcalc-sage-1.1.7/mathlib/alloc.c	2014-06-29 09:55:08.000000000 +1200
+@@ -8,6 +8,7 @@
+ #include <string.h>
+
+ #include "alloc.h"
++#include "lrcalc_jump.h"
+
+ #if 0
+ #define DEBUG_MEMORY_PRINT
+diff -Naur lrcalc-sage-1.1.7-orig/mathlib/alloc.h lrcalc-sage-1.1.7/mathlib/alloc.h
+--- lrcalc-sage-1.1.7-orig/mathlib/alloc.h	2013-06-09 16:12:17.000000000 +1200
++++ lrcalc-sage-1.1.7/mathlib/alloc.h	2014-06-29 09:50:13.000000000 +1200
+@@ -2,13 +2,6 @@
+ #define _ALLOC_H
+
+ #include <stdlib.h>
+-#include <setjmp.h>
+-
+-/*  Programs using the lrcalc library should set lrcalc_panic_frame
+- *  with setjmp(lrcalc_panic_frame).  The lrcalc library will call
+- *  longjmp(lrcalc_panic_frame, 1) if an "out of memory" event occurs.
+- */
+-jmp_buf lrcalc_panic_frame;
+
+ void *amalloc(size_t size);
+ void *acalloc(size_t num, size_t size);
+diff -Naur lrcalc-sage-1.1.7-orig/mathlib/lrcalc_jump.h lrcalc-sage-1.1.7/mathlib/lrcalc_jump.h
+--- lrcalc-sage-1.1.7-orig/mathlib/lrcalc_jump.h	1970-01-01 12:00:00.000000000 +1200
++++ lrcalc-sage-1.1.7/mathlib/lrcalc_jump.h	2014-06-29 09:49:42.000000000 +1200
+@@ -0,0 +1,11 @@
++#ifndef _JUMP_H
++
++#include <setjmp.h>
++
++/*  Programs using the lrcalc library should set lrcalc_panic_frame
++ *  with setjmp(lrcalc_panic_frame).  The lrcalc library will call
++ *  longjmp(lrcalc_panic_frame, 1) if an "out of memory" event occurs.
++ */
++jmp_buf lrcalc_panic_frame;
++
++#endif
+diff -Naur lrcalc-sage-1.1.7-orig/mathlib/salloc.c lrcalc-sage-1.1.7/mathlib/salloc.c
+--- lrcalc-sage-1.1.7-orig/mathlib/salloc.c	2013-06-09 16:12:17.000000000 +1200
++++ lrcalc-sage-1.1.7/mathlib/salloc.c	2014-06-29 09:55:34.000000000 +1200
+@@ -13,6 +13,7 @@
+ #include <string.h>
+
+ #include "alloc.h"
++#include "lrcalc_jump.h"
+
+ typedef struct mlink {
+   struct mlink *next;

build/pkgs/lrcalc/spkg-install

@@ -8,6 +8,15 @@ fi
 
 cd src
 
+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
+
 ./configure --prefix="$SAGE_LOCAL"
 if [ $? -ne 0 ]; then
    echo "Error configuring lrcalc."

src/bin/sage-banner

@@ -1,5 +1,5 @@
 ┌────────────────────────────────────────────────────────────────────┐
-│ Sage Version 6.3.beta4, Release Date: 2014-06-19                   │
+│ Sage Version 6.3.beta5, Release Date: 2014-07-01                   │
 │ 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='6.3.beta4'
-SAGE_RELEASE_DATE='2014-06-19'
+SAGE_VERSION='6.3.beta5'
+SAGE_RELEASE_DATE='2014-07-01'

src/doc/common/conf.py

@@ -1,5 +1,6 @@
 import sys, os, sphinx
 from sage.env import SAGE_DOC
+from datetime import date
 
 def get_doc_abspath(path):
     """
@@ -37,7 +38,7 @@ def get_doc_abspath(path):
 
 # General information about the project.
 project = u""
-copyright = u'2005--2011, The Sage Development Team'
+copyright = u"2005--{}, The Sage Development Team".format(date.today().year)
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

src/doc/en/reference/combinat/designs.rst

@@ -20,6 +20,7 @@ Constructions
    ../sage/combinat/designs/steiner_quadruple_systems
    ../sage/combinat/designs/latin_squares
    ../sage/combinat/designs/orthogonal_arrays
+   ../sage/combinat/designs/orthogonal_arrays_recursive
    ../sage/combinat/designs/difference_family
    ../sage/combinat/designs/database
 

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

@@ -26,6 +26,7 @@ Combinatorics
    sage/combinat/alternating_sign_matrix
    sage/combinat/composition
    sage/combinat/core
+   designs
    sage/combinat/knutson_tao_puzzles
    sage/combinat/gelfand_tsetlin_patterns
    sage/combinat/necklace
@@ -190,7 +191,6 @@ Combinatorics
    root_systems
    crystals
    rigged_configurations
-   designs
    species
 
 **Developer Tools**

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

@@ -8,6 +8,7 @@ Numerical Optimization
    sage/numerical/mip
    sage/numerical/linear_functions
    sage/numerical/optimize
+   sage/numerical/interactive_simplex_method
 
 LP Solver backends
 ------------------

src/doc/en/thematic_tutorials/lie/affine_finite_crystals.rst

@@ -120,7 +120,7 @@ In Sage this can be obtained via::
 
     sage: K = crystals.KirillovReshetikhin(['A',2,1],1,1)
     sage: G = K.digraph()
-    sage: view(G, pdflatex=True, tightpage=True) # optional - dot2tex graphviz
+    sage: view(G, tightpage=True) # optional - dot2tex graphviz
 
 
 Types `D_n^{(1)}`, `B_n^{(1)}`, `A_{2n-1}^{(2)}`
@@ -168,7 +168,8 @@ only holds in the ranges `1\le r\le n-2` for type `D_n^{(1)}`, and
 
     sage: K = crystals.KirillovReshetikhin(['D',6,1],4,2)
     sage: K.classical_decomposition()
-    The crystal of tableaux of type ['D', 6] and shape(s) [[], [1, 1], [1, 1, 1, 1], [2, 2], [2, 2, 1, 1], [2, 2, 2, 2]]
+    The crystal of tableaux of type ['D', 6] and shape(s)
+     [[], [1, 1], [1, 1, 1, 1], [2, 2], [2, 2, 1, 1], [2, 2, 2, 2]]
 
 For type `B_n^{(1)}` and `r=n`, one needs to be aware that `\omega_n`
 is a spin weight and hence corresponds in the partition language to a
@@ -471,6 +472,32 @@ crystal are labelled by tuples which specify their nonzero `\phi_i(b)` and
    :align: center
 
 
+Single column KR crystals
+-------------------------
+
+A single column KR crystal is `B^{r,1}` for any `r \in I_0`.
+
+In [LNSSS14I]_ and [LNSSS14II]_, it was shown that single column KR
+crystals can be constructed by projecting level 0 crystals of LS paths onto
+the classical weight lattice. We first verify that we do get an isomorphic
+crystal for `B^{1,1}` in type `E_6^{(1)}`::
+
+    sage: K = crystals.KirillovReshetikhin(['E',6,1], 1,1)
+    sage: K2 = crystals.kirillov_reshetikhin.LSPaths(['E',6,1], 1,1)
+    sage: K.digraph().is_isomorphic(K2.digraph(), edge_labels=True)
+    True
+
+Here is an example in `E_8^{(1)}` and we calculate its
+classical decomposition::
+
+    sage: K = crystals.kirillov_reshetikhin.LSPaths(['E',8,1], 8,1)
+    sage: K.cardinality()
+    249
+    sage: L = [x for x in K if x.is_highest_weight([1,2,3,4,5,6,7,8])]
+    sage: map(lambda x: x.weight(), L)
+    [-2*Lambda[0] + Lambda[8], 0]
+
+
 Applications
 ------------