Merge branch 'develop' into t/22937/distribute

sagemath · May 13, 2017 · b2b4a0f · b2b4a0f
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diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-SageMath version 8.0.beta5, Release Date: 2017-05-04
+SageMath version 8.0.beta6, Release Date: 2017-05-12
diff --git a/build/pkgs/configure/checksums.ini b/build/pkgs/configure/checksums.ini
@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=339f2474b789d33051dde8f69d047ae723a36379
-md5=9bb01c255b39648bb19f62a3fa24a80d
-cksum=2072910001
+sha1=6a2d4b05426a912b1589d9213760a6438105a502
+md5=4175d83db6c8a9a2a229bdbb383a923d
+cksum=2310778507
diff --git a/build/pkgs/configure/package-version.txt b/build/pkgs/configure/package-version.txt
@@ -1 +1 @@
-219
+220
diff --git a/build/pkgs/normaliz/checksums.ini b/build/pkgs/normaliz/checksums.ini
@@ -1,4 +1,4 @@
 tarball=normaliz-VERSION.tar.gz
-sha1=87bd2846a9132eb87ed6e9fa8cf875a0d6f5cc37
-md5=0eab32959e10b0c41b92c768ef562136
-cksum=1044635248
+sha1=81c89b5b2f8ff15d6939a3fd5822a288440f4d51
+md5=245b1c025ee45d0e2ffd3a77a585768e
+cksum=3791680398
diff --git a/build/pkgs/normaliz/package-version.txt b/build/pkgs/normaliz/package-version.txt
@@ -1 +1 @@
-3.1.4
+3.2.1
diff --git a/build/pkgs/normaliz/patches/22684_cone_reduce_memory_usage.patch b/build/pkgs/normaliz/patches/22684_cone_reduce_memory_usage.patch
@@ -0,0 +1,12 @@
+diff -druN src/source/libnormaliz/cone.cpp patches/source/libnormaliz/cone.cpp
+--- src/source/libnormaliz/cone.cpp	2017-02-22 17:59:08.000000000 +0100
++++ patches/source/libnormaliz/cone.cpp	2017-04-26 16:33:57.460366489 +0200
+@@ -3223,7 +3223,7 @@
+     Deg1Elements=Matrix<Integer>(0,dim);
+     ModuleGenerators=Matrix<Integer>(0,dim);
+
+-    Matrix<Integer> Raw=ApproxCone.getDeg1ElementsMatrix();
++    const Matrix<Integer>& Raw=ApproxCone.getDeg1ElementsMatrix();
+     Matrix<Integer> Result(0,dim);
+     Matrix<Integer> Eq=BasisChange.getEquations();
+     Matrix<Integer> Cong=BasisChange.getCongruences();
diff --git a/build/pkgs/normaliz/spkg-install b/build/pkgs/normaliz/spkg-install
@@ -14,6 +14,3 @@ cd src
 $MAKE || die "Error building normaliz"
 $MAKE install || die "Error installing normaliz"
 
-cd Singular || die "Normaliz distribution has no Singular subdirectory"
-cp -pf normaliz.lib "$SAGE_LOCAL/share/singular/" || die "Error installing normaliz.lib for Singular."
-
diff --git a/build/pkgs/pynormaliz/checksums.ini b/build/pkgs/pynormaliz/checksums.ini
@@ -1,4 +1,4 @@
 tarball=PyNormaliz-VERSION.tar.gz
-sha1=e69046012a18f73cc820cf072d43f7d852020d49
-md5=27a5f7d3fa0d96766d4f811495b0f5ce
-cksum=1643770354
+sha1=619d2b01d9ee20bfcf880cb25ea04b72cc2d2942
+md5=22eea4624caff219618640ed67003b9d
+cksum=4251733870
diff --git a/build/pkgs/pynormaliz/package-version.txt b/build/pkgs/pynormaliz/package-version.txt
@@ -1 +1 @@
-1.0
+1.5
diff --git a/build/pkgs/python3/patches/3.4.5-struct.patch b/build/pkgs/python3/patches/3.4.5-struct.patch
@@ -3,6 +3,15 @@ as been fixed upstream for Python 3.7; see https://bugs.python.org/issue21124
 diff -r b244bf74b638 Modules/_struct.c
 --- a/Modules/_struct.c	Sun Oct 02 13:49:05 2016 +0300
 +++ b/Modules/_struct.c	Sun Oct 02 19:54:56 2016 +0900
+@@ -1627,7 +1627,7 @@ unpackiter_iternext(unpackiterobject *self)
+ }
+
+ static PyTypeObject unpackiter_type = {
+-    PyVarObject_HEAD_INIT(&PyType_Type, 0)
++    PyVarObject_HEAD_INIT(NULL, 0)
+     "unpack_iterator",                          /* tp_name */
+     sizeof(unpackiterobject),                   /* tp_basicsize */
+     0,    
 @@ -2301,6 +2301,9 @@
      if (PyType_Ready(&PyStructType) < 0)
          return NULL;

diff --git a/src/bin/sage-banner b/src/bin/sage-banner
@@ -1,5 +1,5 @@
 ┌────────────────────────────────────────────────────────────────────┐
-│ SageMath version 8.0.beta5, Release Date: 2017-05-04               │
+│ SageMath version 8.0.beta6, Release Date: 2017-05-12               │
 │ Type "notebook()" for the browser-based notebook interface.        │
 │ Type "help()" for help.                                            │
 └────────────────────────────────────────────────────────────────────┘

diff --git a/src/bin/sage-version.sh b/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='8.0.beta5'
-SAGE_RELEASE_DATE='2017-05-04'
+SAGE_VERSION='8.0.beta6'
+SAGE_RELEASE_DATE='2017-05-12'
diff --git a/src/doc/en/a_tour_of_sage/index.rst b/src/doc/en/a_tour_of_sage/index.rst
@@ -1,3 +1,5 @@
+.. _a-tour-of-sage:
+
 ==============
 A Tour of Sage
 ==============

diff --git a/src/doc/en/constructions/index.rst b/src/doc/en/constructions/index.rst
@@ -2,6 +2,8 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
+.. _constructions:
+
 Welcome to the Sage Constructions documentation!
 ================================================
 

diff --git a/src/doc/en/developer/index.rst b/src/doc/en/developer/index.rst
@@ -1,3 +1,5 @@
+.. _developers-guide:
+
 ======================================
 Welcome to the Sage Developer's Guide!
 ======================================

diff --git a/src/doc/en/faq/index.rst b/src/doc/en/faq/index.rst
@@ -3,6 +3,8 @@
 .. your liking, but it should at least contain the root `toctree`
 .. directive.
 
+.. _faq:
+
 Welcome to the Sage FAQ!
 ========================
 

diff --git a/src/doc/en/installation/index.rst b/src/doc/en/installation/index.rst
@@ -1,3 +1,5 @@
+.. _installation-guide:
+
 Welcome to the Sage Installation Guide
 ======================================
 

diff --git a/src/doc/en/prep/Advanced-2DPlotting.rst b/src/doc/en/prep/Advanced-2DPlotting.rst
@@ -2,6 +2,8 @@
 
 .. linkall
 
+.. _prep-advanced-2dplotting:
+
 Tutorial for Advanced 2d Plotting
 =================================
 

diff --git a/src/doc/en/prep/Calculus.rst b/src/doc/en/prep/Calculus.rst
@@ -2,6 +2,8 @@
 
 .. linkall
 
+.. _prep-calculus:
+
 Tutorial for Calculus
 =====================
 

diff --git a/src/doc/en/prep/Intro-Tutorial.rst b/src/doc/en/prep/Intro-Tutorial.rst
@@ -2,6 +2,8 @@
 
 .. linkall
 
+.. _prep-intro-tutorial:
+
 Introductory Sage Tutorial
 ==========================
 

diff --git a/src/doc/en/prep/Logging-On.rst b/src/doc/en/prep/Logging-On.rst
@@ -2,6 +2,7 @@
 
 .. linkall
 
+.. _prep-logging-on:
 .. _logging-on:
 
 Logging on to a Sage Server and Creating a Worksheet

diff --git a/src/doc/en/prep/Programming.rst b/src/doc/en/prep/Programming.rst
@@ -2,6 +2,8 @@
 
 .. linkall
 
+.. _prep-programming:
+
 Sage Introductory Programming Tutorial
 ======================================
 

diff --git a/src/doc/en/prep/Quickstarts/Abstract-Algebra.rst b/src/doc/en/prep/Quickstarts/Abstract-Algebra.rst
@@ -2,6 +2,8 @@
 
 .. linkall
 
+.. _prep-quickstart-abstract-algebra:
+
 Sage Quickstart for Abstract Algebra
 ====================================
 

diff --git a/src/doc/en/prep/Quickstarts/Differential-Equations.rst b/src/doc/en/prep/Quickstarts/Differential-Equations.rst
@@ -2,6 +2,8 @@
 
 .. linkall
 
+.. _prep-quickstart-differential-equations:
+
 Sage Quickstart for Differential Equations
 ==========================================
 

diff --git a/src/doc/en/prep/Quickstarts/Graphs-and-Discrete.rst b/src/doc/en/prep/Quickstarts/Graphs-and-Discrete.rst
@@ -2,6 +2,8 @@
 
 .. linkall
 
+.. _prep-quickstart-graphs-and-discrete:
+
 Sage Quickstart for Graph Theory and Discrete Mathematics
 =========================================================
 

diff --git a/src/doc/en/prep/Quickstarts/Interact.rst b/src/doc/en/prep/Quickstarts/Interact.rst
@@ -2,6 +2,8 @@
 
 .. linkall
 
+.. _prep-quickstart-interact:
+
 Sage Interact Quickstart
 ========================
 

diff --git a/src/doc/en/prep/Quickstarts/Linear-Algebra.rst b/src/doc/en/prep/Quickstarts/Linear-Algebra.rst
@@ -2,6 +2,8 @@
 
 .. linkall
 
+.. _prep-quickstart-linear-algebra:
+
 Sage Quickstart for Linear Algebra
 ==================================
 

diff --git a/src/doc/en/prep/Quickstarts/Multivariable-Calculus.rst b/src/doc/en/prep/Quickstarts/Multivariable-Calculus.rst
@@ -2,6 +2,8 @@
 
 .. linkall
 
+.. _prep-quickstart-multivariate-calculus:
+
 Sage Quickstart for Multivariable Calculus
 ==========================================
 

diff --git a/src/doc/en/prep/Quickstarts/NumAnalysis.rst b/src/doc/en/prep/Quickstarts/NumAnalysis.rst
@@ -2,6 +2,8 @@
 
 .. linkall
 
+.. _prep-quickstart-numerical-analysis:
+
 Sage Quickstart for Numerical Analysis
 ======================================
 

diff --git a/src/doc/en/prep/Quickstarts/Number-Theory.rst b/src/doc/en/prep/Quickstarts/Number-Theory.rst
@@ -2,6 +2,8 @@
 
 .. linkall
 
+.. _prep-quickstart-number-theory:
+
 Sage Quickstart for Number Theory
 =================================
 

diff --git a/src/doc/en/prep/Quickstarts/Statistics-and-Distributions.rst b/src/doc/en/prep/Quickstarts/Statistics-and-Distributions.rst
@@ -2,6 +2,8 @@
 
 .. linkall
 
+.. _prep-quickstart-statistics-and-distributions:
+
 Sage Quickstart for Statistics
 ==============================
 

diff --git a/src/doc/en/prep/Symbolics-and-Basic-Plotting.rst b/src/doc/en/prep/Symbolics-and-Basic-Plotting.rst
@@ -2,6 +2,8 @@
 
 .. linkall
 
+.. _prep-symbolics-and-basic-plotting:
+
 Tutorial for Symbolics and Plotting
 ===================================
 
@@ -486,6 +488,6 @@ We close this tutorial with a cool plot that we define *implicitly* as a
     Graphics3d Object
 
 The next tutorial will use all that you have learned about Sage basics,
-symbolics, and plotting in a specific mathematical venue \- the calculus
-sequence!
+symbolics, and plotting in a specific mathematical venue \- the
+:ref:`calculus sequence <prep-calculus>`!
 
diff --git a/src/doc/en/prep/index.rst b/src/doc/en/prep/index.rst
@@ -3,6 +3,8 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
+.. _prep-tutorials:
+
 PREP Tutorials
 ==============
 

diff --git a/src/doc/en/prep/quickstart.rst b/src/doc/en/prep/quickstart.rst
@@ -3,6 +3,8 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
+.. _prep-quickstart-tutorials:
+
 PREP Quickstart Tutorials
 =========================
 

diff --git a/src/doc/en/reference/categories/index.rst b/src/doc/en/reference/categories/index.rst
@@ -125,6 +125,7 @@ Individual Categories
    sage/categories/lie_algebras
    sage/categories/lie_algebras_with_basis
    sage/categories/lie_groups
+   sage/categories/loop_crystals
    sage/categories/l_trivial_semigroups
    sage/categories/magmas
    sage/categories/magmas_and_additive_magmas

diff --git a/src/doc/en/reference/combinat/module_list.rst b/src/doc/en/reference/combinat/module_list.rst
@@ -65,13 +65,16 @@ Comprehensive Module list
     sage/combinat/crystals/highest_weight_crystals
     sage/combinat/crystals/induced_structure
     sage/combinat/crystals/infinity_crystals
-    sage/combinat/crystals/polyhedral_realization
     sage/combinat/crystals/kirillov_reshetikhin
     sage/combinat/crystals/kyoto_path_model
     sage/combinat/crystals/letters
     sage/combinat/crystals/littelmann_path
     sage/combinat/crystals/monomial_crystals
     sage/combinat/crystals/multisegments
+    sage/combinat/crystals/mv_polytopes
+    sage/combinat/crystals/pbw_crystal
+    sage/combinat/crystals/pbw_datum
+    sage/combinat/crystals/polyhedral_realization
     sage/combinat/crystals/spins
     sage/combinat/crystals/star_crystal
     sage/combinat/crystals/tensor_product
@@ -213,6 +216,7 @@ Comprehensive Module list
     sage/combinat/root_system/all
     sage/combinat/root_system/ambient_space
     sage/combinat/root_system/associahedron
+    sage/combinat/root_system/braid_move_calculator
     sage/combinat/root_system/branching_rules
     sage/combinat/root_system/cartan_matrix
     sage/combinat/root_system/cartan_type

diff --git a/src/doc/en/reference/index.rst b/src/doc/en/reference/index.rst
@@ -1,14 +1,13 @@
-********
-Contents
-********
+.. _reference-manual:
 
-Welcome to Sage's Reference Manual!
+************************************
+Welcome to the Sage Reference Manual
+************************************
 
-This manual is a thematic index of all of `Sage's <http://www.sagemath.org/>`_
-features. It also contains many examples that illustrate their use, all of them
-systematically tested with each release.
-
-Enjoy Sage!
+This manual contains documentation for (almost) all of `Sage's
+<http://www.sagemath.org/>`_ features, each illustrated with examples
+that are systematically tested with each release. A thematic index is
+available below.
 
 User Interface
 ==============

diff --git a/src/doc/en/reference/references/index.rst b/src/doc/en/reference/references/index.rst
@@ -322,6 +322,11 @@ REFERENCES:
             complexes and posets. I*. Trans. of
             Amer. Math. Soc. **348** No. 4. (1996)
 
+.. [BZ01] \A. Berenstein, A. Zelevinsky
+          *Tensor product multiplicities, canonical bases
+          and totally positive varieties*
+          Invent. Math. **143** No. 1. (2002), 77-128.
+
 .. _ref-C:
 
 **C**
@@ -668,6 +673,10 @@ REFERENCES:
             curves". LMS Journal of Computation and Mathematics
             (2014), volume 17, issue 01, pp. 1-23.
 
+.. [FOS2010] \G. Fourier, M. Okado, A. Schilling. *Perfectness of
+             Kirillov-Reshetikhin crystals for nonexceptional types*.
+             Contemp. Math. 506 (2010) 127-143 ( :arxiv:`0811.1604` )
+
 .. [FP1996] Komei Fukuda, Alain Prodon: Double Description Method
             Revisited, Combinatorics and Computer Science, volume 1120
             of Lecture Notes in Computer Science, page
@@ -940,6 +949,13 @@ REFERENCES:
 .. [Kal1980] \T. Kaliath, "Linear Systems", Prentice-Hall, 1980,
              383--386.
 
+.. [Kam2007] Joel Kamnitzer,
+             *The crystal structure on the set of Mirković-Vilonen polytopes*,
+             Adv. Math. **215** (2007), 66-93.
+
+.. [Kam2010] Joel Kamnitzer, *Mirković-Vilonen cycles and polytopes*,
+             Ann. Math. (2) **171** (2010), 731-777.
+
 .. [Kan1958] \D. M. Kan, *A combinatorial definition of homotopy
              groups*, Ann. Math. (2) 67 (1958), 282-312.
 
@@ -959,6 +975,10 @@ REFERENCES:
             \M. Grötschel, \L Lovász, *Handbook of combinatorics*,
             Vol. 1, Chapter 18, 1995
 
+.. [KKMMNN1992] S-J. Kang, M. Kashiwara, K. C. Misra, T. Miwa, T. Nakashima,
+                and A. Nakayashiki. *Affine crystals and vertex models*.
+                Int. J. Mod. Phys. A, **7** (suppl. 1A), (1992) pp. 449-484.
+
 .. [KL2008] Chris Kurth and Ling Long, "Computations with finite index
             subgroups of `{\rm PSL}_2(\ZZ)` using Farey symbols",
             Advances in algebra and combinatorics, 225--242, World
@@ -1500,6 +1520,11 @@ REFERENCES:
             manifolds and complexes into a cubic lattice", *Uspekhi
             Mat. Nauk* 47 (1992), 219-220.
 
+.. [ST2011] \A. Schilling, P. Tingley. *Demazure crystals,
+            Kirillov-Reshetikhin crystals, and the energy function*.
+            Electronic Journal of Combinatorics. **19(2)**. 2012.
+            :arXiv:`1104.2359`
+
 .. [Sta2007] Stanley, Richard: *Hyperplane Arrangements*, Geometric
              Combinatorics (E. Miller, V. Reiner, and B. Sturmfels,
              eds.), IAS/Park City Mathematics Series, vol. 13,