Merge branch 'develop' into t/15692/ticket/15692

VERSION.txt

@@ -1 +1 @@
-SageMath version 7.3.beta5, Release Date: 2016-06-24
+SageMath version 7.3.beta6, Release Date: 2016-06-30

build/pkgs/cddlib/package-version.txt

@@ -1 +1 @@
-094g.p0
+094g.p1

build/pkgs/cddlib/patches/lib-src-gmp_Makefile.am.patch

@@ -1,7 +1,7 @@
-diff --git a/src.bak/lib-src-gmp/Makefile.am b/src/lib-src-gmp/Makefile.am
+diff --git a/lib-src-gmp/Makefile.am b/lib-src-gmp/Makefile.am
 index b3ab11a..a9673b8 100644
---- a/src.bak/lib-src-gmp/Makefile.am
-+++ b/src/lib-src-gmp/Makefile.am
+--- a/lib-src-gmp/Makefile.am
++++ b/lib-src-gmp/Makefile.am
 @@ -13,7 +13,8 @@ cddmp_f.c \
  cddio_f.c \
  cddlib_f.c \

build/pkgs/cddlib/patches/lib-src-gmp_Makefile.in.patch

@@ -1,7 +1,7 @@
-diff --git a/src.bak/lib-src-gmp/Makefile.in b/src/lib-src-gmp/Makefile.in
+diff --git a/lib-src-gmp/Makefile.in b/lib-src-gmp/Makefile.in
 index 4ab9342..93ff335 100644
---- a/src.bak/lib-src-gmp/Makefile.in
-+++ b/src/lib-src-gmp/Makefile.in
+--- a/lib-src-gmp/Makefile.in
++++ b/lib-src-gmp/Makefile.in
 @@ -54,7 +54,7 @@
  libcddgmp_la_LIBADD =
  am_libcddgmp_la_OBJECTS = cddcore.lo cddlp.lo cddmp.lo cddio.lo \

build/pkgs/cddlib/patches/lib-src_Makefile.am.patch

@@ -1,7 +1,7 @@
-diff --git a/src.bak/lib-src/Makefile.am b/src/lib-src/Makefile.am
+diff --git a/lib-src/Makefile.am b/lib-src/Makefile.am
 index fe08dc3..5b964c6 100644
---- a/src.bak/lib-src/Makefile.am
-+++ b/src/lib-src/Makefile.am
+--- a/lib-src/Makefile.am
++++ b/lib-src/Makefile.am
 @@ -7,7 +7,8 @@ cddmp.c \
  cddio.c \
  cddlib.c \

build/pkgs/cddlib/patches/lib-src_Makefile.in.patch

@@ -1,7 +1,7 @@
-diff --git a/src.bak/lib-src/Makefile.in b/src/lib-src/Makefile.in
+diff --git a/lib-src/Makefile.in b/lib-src/Makefile.in
 index bd3c2b5..ccf4a6c 100644
---- a/src.bak/lib-src/Makefile.in
-+++ b/src/lib-src/Makefile.in
+--- a/lib-src/Makefile.in
++++ b/lib-src/Makefile.in
 @@ -53,7 +53,7 @@ libLTLIBRARIES_INSTALL = $(INSTALL)
  LTLIBRARIES = $(lib_LTLIBRARIES)
  libcdd_la_LIBADD =

build/pkgs/cddlib/patches/lib-src_cddcore.c.patch

@@ -1,7 +1,7 @@
-diff --git a/src.bak/lib-src/cddcore.c b/src/lib-src/cddcore.c
+diff --git a/lib-src/cddcore.c b/lib-src/cddcore.c
 index 9644788..a029bc3 100644
---- a/src.bak/lib-src/cddcore.c
-+++ b/src/lib-src/cddcore.c
+--- a/lib-src/cddcore.c
++++ b/lib-src/cddcore.c
 @@ -17,6 +17,7 @@
  #include <time.h>
  #include <math.h>

build/pkgs/cddlib/patches/lib-src_cddlp.c.patch

@@ -1,7 +1,7 @@
-diff --git a/src.bak/lib-src/cddlp.c b/src/lib-src/cddlp.c
+diff --git a/lib-src/cddlp.c b/lib-src/cddlp.c
 index 855b197..dd1268b 100644
---- a/src.bak/lib-src/cddlp.c
-+++ b/src/lib-src/cddlp.c
+--- a/lib-src/cddlp.c
++++ b/lib-src/cddlp.c
 @@ -13,6 +13,7 @@
 
  #include "setoper.h"  /* set operation library header (Ver. May 18, 2000 or later) */

build/pkgs/cddlib/patches/src-gmp_Makefile.am.patch

@@ -1,7 +1,7 @@
-diff --git a/src.bak/src-gmp/Makefile.am b/src/src-gmp/Makefile.am
+diff --git a/src-gmp/Makefile.am b/src-gmp/Makefile.am
 index e4dbb86..e579d71 100644
---- a/src.bak/src-gmp/Makefile.am
-+++ b/src/src-gmp/Makefile.am
+--- a/src-gmp/Makefile.am
++++ b/src-gmp/Makefile.am
 @@ -11,7 +11,8 @@
  testcdd2_gmp \
  testlp1_gmp \

build/pkgs/cddlib/patches/src-gmp_Makefile.in.patch

@@ -1,7 +1,7 @@
-diff --git a/src.bak/src-gmp/Makefile.in b/src/src-gmp/Makefile.in
+diff --git a/src-gmp/Makefile.in b/src-gmp/Makefile.in
 index f88c83f..3470dc9 100644
---- a/src.bak/src-gmp/Makefile.in
-+++ b/src/src-gmp/Makefile.in
+--- a/src-gmp/Makefile.in
++++ b/src-gmp/Makefile.in
 @@ -37,7 +37,8 @@
  	projection_gmp$(EXEEXT) adjacency_gmp$(EXEEXT) \
  	allfaces_gmp$(EXEEXT) testshoot_gmp$(EXEEXT) \

build/pkgs/cddlib/patches/src_Makefile.am.patch

@@ -1,7 +1,7 @@
-diff --git a/src.bak/src/Makefile.am b/src/src/Makefile.am
+diff --git a/src/Makefile.am b/src/Makefile.am
 index 17f8625..ad50af2 100644
---- a/src.bak/src/Makefile.am
-+++ b/src/src/Makefile.am
+--- a/src/Makefile.am
++++ b/src/Makefile.am
 @@ -11,7 +11,8 @@ testshoot \
  testcdd2 \
  testlp1 \

build/pkgs/cddlib/patches/src_Makefile.in.patch

@@ -1,7 +1,7 @@
-diff --git a/src.bak/src/Makefile.in b/src/src/Makefile.in
+diff --git a/src/Makefile.in b/src/Makefile.in
 index 8385e4d..b9f6a26 100644
---- a/src.bak/src/Makefile.in
-+++ b/src/src/Makefile.in
+--- a/src/Makefile.in
++++ b/src/Makefile.in
 @@ -36,7 +36,7 @@ bin_PROGRAMS = scdd$(EXEEXT) lcdd$(EXEEXT) redcheck$(EXEEXT) \
  	fourier$(EXEEXT) projection$(EXEEXT) adjacency$(EXEEXT) \
  	allfaces$(EXEEXT) testcdd1$(EXEEXT) testshoot$(EXEEXT) \

build/pkgs/cddlib/spkg-install

@@ -38,7 +38,7 @@ for patch in ../patches/*.patch; do
     if echo "$patch" | grep 'Makefile.am.patch$' > /dev/null; then
         continue
     fi
-    patch -p2 < "$patch" ||
+    patch -p1 < "$patch" ||
       die "Error patching cddlib"
 done
 

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=387750b93152bd04031fc79fefbedf67a81d2570
-md5=168ddf3b69c6a1d16126b247dbb266a4
-cksum=1400068458
+sha1=7ff2fae8aa57607ba55ede02162d35c6a65dc0ce
+md5=406cc1b178d03e1045bd0a9678a88b77
+cksum=2873788725

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-170
+171

build/pkgs/ecl/package-version.txt

@@ -1 +1 @@
-16.1.2.p0
+16.1.2.p1

build/pkgs/ecl/patches/16.1.2-getcwd.patch

@@ -0,0 +1,14 @@
+Backport of fix in master ecl repo. See trac 20845.
+diff --git a/src/c/unixfsys.d b/src/c/unixfsys.d
+index d3dd4d1..287eded 100644
+--- a/src/c/unixfsys.d
++++ b/src/c/unixfsys.d
+@@ -158,7 +158,7 @@ current_dir(void) {
+                 output = ecl_alloc_adjustable_base_string(size);
+                 ecl_disable_interrupts();
+                 ok = getcwd((char*)output->base_string.self, size);
+-                if (ok == NULL && errno != ENAMETOOLONG) {
++                if (ok == NULL && errno != ERANGE) {
+                         perror("ext::getcwd error");
+                         ecl_internal_error("Can't work without CWD");
+                 }

build/pkgs/gfan/package-version.txt

@@ -1 +1 @@
-0.5.p0
+0.5.p1

build/pkgs/gfan/patches/Makefile.patch

@@ -1,5 +1,5 @@
---- Makefile.orig	2012-07-11 11:50:44.733022911 +1200
-+++ Makefile	2012-07-11 12:20:02.644997882 +1200
+--- a/Makefile.orig	2012-07-11 11:50:44.733022911 +1200
++++ b/Makefile	2012-07-11 12:20:02.644997882 +1200
 @@ -75,18 +75,10 @@
  MKDIR=mkdir -p
 

build/pkgs/gfan/patches/app_minkowski.cpp.patch

@@ -1,5 +1,5 @@
---- app_minkowski.cpp.orig	2011-01-24 06:21:47.000000000 +1300
-+++ app_minkowski.cpp	2012-07-23 11:43:29.172776129 +1200
+--- a/app_minkowski.cpp.orig	2011-01-24 06:21:47.000000000 +1300
++++ b/app_minkowski.cpp	2012-07-23 11:43:29.172776129 +1200
 @@ -64,9 +64,9 @@
      registerOptions();
      optionPartOne.hide();

build/pkgs/gfan/spkg-install

@@ -33,14 +33,14 @@ cd src
 
 # Patch the Makefile so it can build in Sage:
 echo "Copying a revised Makefile, to improve portability..."
-patch -p0 <../patches/Makefile.patch
+patch -p1 <../patches/Makefile.patch
 if [[ $? -ne 0 ]]; then
     echo >&2 "Error: Patch to improve portability did not copy correctly."
     exit 1
 fi
 
 echo "Copying patched file to fix an issue with GCC 4.7.0..."
-patch -p0 <../patches/app_minkowski.cpp.patch
+patch -p1 <../patches/app_minkowski.cpp.patch
 if [[ $? -ne 0 ]]; then
     echo >&2 "Error: Patch to fix GCC 4.7.0 issue did not copy correctly."
     exit 1

build/pkgs/git_trac/checksums.ini

@@ -1,4 +1,4 @@
 tarball=git_trac-VERSION.tar.bz2
-sha1=90c1e2c279fcac22b050c62253cfb53c8fe9c9c1
-md5=1f6e913132aa16b19cb5c99ee921f3f5
-cksum=774035580
+sha1=137c70eb041c62de31e543e5b76fb6d30d044a58
+md5=7783a2da02dbb9156ccb0ff5b7cff9bc
+cksum=2994355167

build/pkgs/git_trac/package-version.txt

@@ -1 +1 @@
-20150522
+20160625

build/pkgs/pygments/package-version.txt

@@ -1 +1 @@
-2.1.3
+2.1.3.p0

build/pkgs/pygments/spkg-install

@@ -9,19 +9,19 @@ fi
 #Remove old version
 rm -rf "$SAGE_LOCAL"/lib/python/site-packages/Pygments-*
 
+#Install new version
+cd src
+
 # Apply patches
 echo "Patching Pygments..."
-for p in patches/*.patch; do
-    patch -p0 <$p
+for p in ../patches/*.patch; do
+    patch -p1 <$p
     if [ $? -ne 0 ]; then
         echo "Error applying patch $p"
         exit 1
     fi
 done
 
-#Install new version
-cd src
-
 python setup.py install
 if [ $? -ne 0 ]; then
    echo "Error installing Pygments."

src/bin/sage-banner

@@ -1,5 +1,5 @@
 ┌────────────────────────────────────────────────────────────────────┐
-│ SageMath version 7.3.beta5, Release Date: 2016-06-24               │
+│ SageMath version 7.3.beta6, Release Date: 2016-06-30               │
 │ 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='7.3.beta5'
-SAGE_RELEASE_DATE='2016-06-24'
+SAGE_VERSION='7.3.beta6'
+SAGE_RELEASE_DATE='2016-06-30'

src/doc/de/tutorial/afterword.rst

@@ -101,7 +101,7 @@ sein, also verhält sich Sage an manchen Stellen anders als Python.
        '3^2'
 
 -  **Integerdivision:** Der Pythonaudruck ``2/3`` verhält sich nicht
-   so, wie es Mathematiker erwarten würden. In Python wird, falls ``m`` und
+   so, wie es Mathematiker erwarten würden. In Python 2 wird, falls ``m`` und
    ``n`` Integer sind, auch ``m/n`` als Integer behandelt, es ist
    nämlich der Quotient von ``m`` geteilt durch ``n``. Daher ist
    ``2/3=0``.  Es wurde in der Pythoncommunity darüber geredet, ob in
@@ -121,7 +121,7 @@ sein, also verhält sich Sage an manchen Stellen anders als Python.
        Rational Field
        sage: 2//3
        0
-       sage: int(2)/int(3)
+       sage: int(2)/int(3)    # optional - python2
        0
 
 -  **Große ganze Zahlen:** Python besitzt von Hause aus Unterstützung

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

@@ -37,6 +37,7 @@ Linear codes and related constructions
    sage/coding/sd_codes
    sage/coding/guava
    sage/coding/binary_code
+   sage/coding/reed_muller_code
 
 Bounds on codes
 ---------------

src/doc/en/thematic_tutorials/structures_in_coding_theory.rst

@@ -252,6 +252,15 @@ To do that, just add the following line at the end of your file::
 
    BinaryRepetitionCode._registered_encoders["RepetitionGeneratorMatrixEncoder"] = BinaryRepetitionCodeGeneratorMatrixEncoder
 
+.. NOTE::
+
+    In case you are implementing a generic encoder (an encoder which works
+    with any family of linear codes), please add the following statement in
+    ``AbstractLinearCode``'s constructor instead:
+    ``self._registered_encoders["EncName"] = MyGenericEncoder``.
+    This will make it immediately available to any code
+    class which inherits from `AbstractLinearCode`.
+
 Summary of the implementation for encoders
 ------------------------------------------
 
@@ -375,6 +384,16 @@ Also put this line to set ``decoder_type``::
 
    BinaryRepetitionCode._decoder_type = {"hard-decision", "unique"}
 
+
+.. NOTE::
+
+    In case you are implementing a generic decoder (a decoder which works
+    with any family of linear codes), please add the following statement in
+    ``AbstractLinearCode``'s constructor instead:
+    ``self._registered_decoders["DecName"] = MyGenericDecoder``.
+    This will make it immediately available to any code
+    class which inherits from `AbstractLinearCode`.
+
 Summary of the implementation for decoders
 ------------------------------------------
 

src/doc/en/tutorial/programming.rst

@@ -684,7 +684,7 @@ the Python int ``1`` is unique, but the Sage Integer ``1`` is not:
 
     sage: 1 is 2/2
     False
-    sage: int(1) is int(2)/int(2)
+    sage: int(1) is int(2)/int(2)   # optional - python2
     True
     sage: 1 is 1
     False

src/doc/fr/tutorial/afterword.rst

@@ -113,12 +113,11 @@ Aussi, Sage se comporte différemment de Python à plusieurs égards.
         10
 
 -  **Division entière :** L'expression Python ``2/3`` ne se comporte pas
-   de la manière à laquelle s'attendraient des mathématiciens. En Python, si
+   de la manière à laquelle s'attendraient des mathématiciens. En Python 2, si
    ``m`` et ``n`` sont de type int, alors ``m/n`` est aussi de type int, c'est
-   le quotient entier de ``m`` par ``n``. Par conséquent, ``2/3=0``. Il
-   y a eu dans la communauté Python des débats sur une éventuelle
-   modification du langage de sorte que ``2/3`` renvoie un flottant
-   ``0.6666...`` et que ce soit ``2//3`` qui renvoie ``0``.
+   le quotient entier de ``m`` par ``n``. Par conséquent, ``2/3=0``. Ce
+   comportement est différent en Python 3, où ``2/3`` renvoie un flottant
+   ``0.6666...`` et c'est ``2//3`` qui renvoie ``0``.
 
    Dans l'interpréteur Sage, nous réglons cela en encapsulant
    automatiquement les entiers litéraux par ``Integer( )`` et en faisant
@@ -133,7 +132,7 @@ Aussi, Sage se comporte différemment de Python à plusieurs égards.
        Rational Field
        sage: 2//3
        0
-       sage: int(2)/int(3)
+       sage: int(2)/int(3)   # optional - python2
        0
 
 -  **Entiers longs :** Python possède nativement un support pour les entiers de

src/doc/ja/tutorial/afterword.rst

@@ -96,7 +96,7 @@ Pythonの数学機能には混乱を招きがちな面があり，SageにはPyth
        Rational Field
        sage: 2//3
        0
-       sage: int(2)/int(3)
+       sage: int(2)/int(3)   # optional - python2
        0
 
 -  **長整数:** Python本体は，C言語由来のint型だけではなく任意精度整数をサポートしている．

src/doc/ja/tutorial/programming.rst

@@ -661,7 +661,7 @@ Sageにおける異種オブジェクト間の比較演算では，まず対象
 
     sage: 1 is 2/2
     False
-    sage: int(1) is int(2)/int(2)
+    sage: int(1) is int(2)/int(2)  # optional - python2
     True
     sage: 1 is 1
     False

src/doc/pt/tutorial/afterword.rst

@@ -94,7 +94,7 @@ se comporta diferentemente do Python em diversas situações.
        '3^2'
 
 -  **Divisão por inteiros:** A expressão em Python ``2/3`` não se
-   comporta da forma que um matemático esperaria. Em Python, se ``m``
+   comporta da forma que um matemático esperaria. Em Python 2, se ``m``
    e ``n`` são inteiros (int), então ``m/n`` também é um inteiro
    (int), a saber, o quociente de ``m`` dividido por ``n``. Portanto
    ``2/3=0``. Tem havido discussões na comunidade do Python para
@@ -113,7 +113,7 @@ se comporta diferentemente do Python em diversas situações.
        Rational Field
        sage: 2//3
        0
-       sage: int(2)/int(3)
+       sage: int(2)/int(3)   # optional - python2
        0
 
 -  **Inteiros longos:** O Python possui suporte nativo para inteiros

src/doc/pt/tutorial/programming.rst

@@ -705,7 +705,7 @@ o int ``1`` do Python é único, mas o Inteiro ``1`` do Sage não é.
 
     sage: 1 is 2/2
     False
-    sage: int(1) is int(2)/int(2)
+    sage: int(1) is int(2)/int(2)  # optional - python2
     True
     sage: 1 is 1
     False

src/doc/ru/tutorial/afterword.rst

@@ -89,7 +89,7 @@ Sage ведет себя немного другим образом.
        '3^2'
 
 -  **Деление целых чисел:** Выражение ``2/3`` в Python означает не то, чего
-   ожидает математик. В Python, если ``m`` и ``n`` - целые числа, то ``m/n``
+   ожидает математик. В Python 2, если ``m`` и ``n`` - целые числа, то ``m/n``
    также целое число, если быть точнее, то целая часть от деления ``m`` на
    ``n``. Следовательно ``2/3=0``. В сообществе Python обсуждается вариант
    изменения оператора так, чтобы ``2/3`` возвращало число с плавающей точкой
@@ -106,7 +106,7 @@ Sage ведет себя немного другим образом.
        Rational Field
        sage: 2//3
        0
-       sage: int(2)/int(3)
+       sage: int(2)/int(3)   # optional - python2
        0
 
 -  **Большие целые числа:** Python имеет встроенную поддержку целых чисел