Merge sage 7.6

README.md

@@ -3,7 +3,7 @@
 >   "Creating a Viable Open Source Alternative to
 >    Magma, Maple, Mathematica, and MATLAB"
 
->   Copyright (C) 2005-2016 The Sage Development Team
+>   Copyright (C) 2005-2017 The Sage Development Team
 
    http://www.sagemath.org
 
@@ -21,7 +21,8 @@ Getting Started
 ---------------
 
 This README.txt contains build instructions for Sage. If you downloaded  
-a binary, you do not need to do anything; just execute:  
+a binary, you do not need to do anything (as long as your system
+provides a SSL library ; OpenSSL is recommended) ; just execute:  
 
     ./sage
 
@@ -69,9 +70,19 @@ Installation Guide:
 
    http://doc.sagemath.org/html/en/installation
 
-__1. Make sure you have the dependencies and 5 GB of free disk space.__
+__1. Make sure your system has an SSL library and its development
+files installed.__
 
-   >* __All Linux versions:__ gcc, make, m4, perl, ranlib, and tar.  
+   >* Like Python, on which it is based, Sage uses the OpenSSL library
+   for added performance if made available by the operating system. It
+   has been shown that Sage can be successfully built against other
+   SSL libraries, with some of its features disabled.
+
+__2. Make sure you have the dependencies and 5 GB of free disk space.__
+
+   >* __All Linux versions:__ gcc, make, m4, perl, ranlib, and tar (a
+   matching set of gcc, gfortran and g++ will avoid the compilation
+   of Sage-specific compilers).__
 
    >* __Fedora or RedHat systems:__ the perl-ExtUtils-MakeMaker package.  
    (install these using your package manager)  
@@ -97,11 +108,11 @@ __1. Make sure you have the dependencies and 5 GB of free disk space.__
 
    >* Other platforms: See detailed instructions below.
 
-__2. Extract the tarball:__
+__3. Extract the tarball:__
 
          tar xvf sage-*.tar
 
-__3. cd into the Sage directory and type make:__
+__4. cd into the Sage directory and type make:__
 
          cd sage-*/
          make

VERSION.txt

@@ -1 +1 @@
-SageMath version 7.5.rc0, Release Date: 2016-12-18
+SageMath version 7.6, Release Date: 2017-03-25

build/bin/sage-logger

@@ -60,14 +60,17 @@ else
     SED=cat
 fi
 
+# Store the current value of V, but do all logging of child processes
+# with V=1 to ensure that no information is lost.
+currentV=$V
+export V=1
+
 mkdir -p "$logdir"
 
-if [[ "$V" = 0 && $use_prefix = true ]]; then
+if [[ "$currentV" = 0 && $use_prefix = true ]]; then
     # Silent build.
     # Similar to https://www.gnu.org/software/automake/manual/html_node/Automake-Silent-Rules.html#Automake-Silent-Rules
     echo "[$logname] installing. Log file: $logfile"
-    # Use verbose mode for output to logfiles.
-    export V=1
     ( exec>> $logfile 2>&1 ; eval "$cmd" )
     status=$?
     if [[ $status != 0 ]]; then

build/bin/sage-pip-install

@@ -15,7 +15,9 @@
 # --no-deps          : Don't install runtime dependencies from PyPI.
 # --no-index         : Don't look at the package index.
 #                      This also disables pip's version self-check.
-pip_install_flags="--ignore-installed --verbose --no-deps --no-index"
+# --isolated         : Don't read configuration files such as
+#                      ~/.pydistutils.cfg
+pip_install_flags="--ignore-installed --verbose --no-deps --no-index --isolated"
 
 # Consume any additional pip install arguments except the last one
 while [ $# -gt 1 ]; do

build/make/deps

@@ -78,7 +78,7 @@ toolchain-deps:
 
 # Everything needed to start up Sage using "./sage".  Of course, not
 # every part of Sage will work.  It does not include Maxima for example.
-SAGERUNTIME = sagelib $(SCRIPTS) $(inst_ipython) $(inst_pexpect)
+SAGERUNTIME = sagelib $(SCRIPTS) $(inst_ipython) $(inst_pexpect) $(inst_psutil)
 
 
 # Start Sage at least once to check that it works
@@ -146,7 +146,8 @@ sagelib: \
 		$(inst_planarity) \
 		$(inst_ppl) \
 		$(inst_pynac) \
-		$(PYTHON) \
+		$(inst_python2) \
+		$(inst_python3) \
 		$(inst_ratpoints) \
 		$(inst_readline) \
 		$(inst_rw) \
@@ -200,7 +201,7 @@ DOC_DEPENDENCIES = sagelib $(inst_sphinx) $(inst_sagenb) \
 	| $(SAGERUNTIME) $(inst_maxima) $(inst_networkx) $(inst_scipy) \
 	$(inst_matplotlib) $(inst_pillow) $(inst_mathjax) $(inst_mpmath) \
 	$(inst_ipykernel) $(inst_jupyter_client) $(inst_conway_polynomials) \
-	$(inst_tachyon) $(inst_jmol) $(inst_thebe)
+	$(inst_tachyon) $(inst_jmol) $(inst_thebe) $(inst_ipywidgets)
 
 doc: doc-html
 

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=dec646cbe7003843d95349386e65ff39ce623561
-md5=8edc28e5ce617646e08dce522c4a733a
-cksum=1353419480
+sha1=7a84c43745334f9940826319b4799e3e7883ee17
+md5=e897b888529be545e40ddb697c778a89
+cksum=3005224762

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-196
+212

build/pkgs/database_gap/checksums.ini

@@ -1,4 +1,4 @@
 tarball=database_gap-VERSION.tar.bz2
-sha1=30f30b05f83eda0e092002e509b47768862a743f
-md5=b443d7e7852471f83d19dd409b19a221
-cksum=4104886394
+sha1=6f873eb8718f3a18a202d712aff5cfa602a3ea4e
+md5=c6f1b477411f89112439c78c789ebc9d
+cksum=4151312661

build/pkgs/database_gap/dependencies

@@ -1,4 +1,4 @@
-gap | $(SAGERUNTIME)
+gap
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/database_gap/package-version.txt

@@ -1 +1 @@
-4.8.3
+4.8.6

build/pkgs/database_gap/spkg-install

@@ -54,6 +54,3 @@ if [ $? -ne 0 ]; then
     exit 1
 fi
 echo "Installed tomlib database."
-
-sage -c "gap_reset_workspace()"
-

build/pkgs/database_pari/checksums.ini

@@ -1,4 +1,4 @@
 tarball=database_pari-VERSION.tar.bz2
-sha1=92dcb68e7a6def53ffc5fb82e3593d5b80c940cb
-md5=652d36d18ea300193957120815298be7
-cksum=2257060384
+sha1=dd2b168da033a9fca98ce5d9d81ad76fbc1739fb
+md5=0fb372a3c8de787f84c066f81511a276
+cksum=3988008667

build/pkgs/database_pari/package-version.txt

@@ -1 +1 @@
-20140908
+20161017

build/pkgs/dot2tex/SPKG.txt

@@ -7,8 +7,7 @@ by Graphviz a more LaTeX friendly look and feel. This is accomplished
 by converting xdot output from Graphviz to a series of PSTricks or
 PGF/TikZ commands.
 
-See http://www.fauskes.net/code/dot2tex/
-or http://dot2tex.googlecode.com/
+See https://github.com/kjellmf/dot2tex/
 
 == License ==
  * MIT

build/pkgs/eclib/checksums.ini

@@ -1,4 +1,4 @@
 tarball=eclib-VERSION.tar.bz2
-sha1=acd51ec5e7ab7be6a3151fe645320f71c6a11ede
-md5=ac1eee9c42b1b6987173f574b6f43744
-cksum=673064945
+sha1=b5098fe705dcea8f492e5e331ad8a69f5721898f
+md5=af8c339c44155ed813cb40f39fcfe344
+cksum=2757924773

build/pkgs/eclib/package-version.txt

@@ -1 +1 @@
-20160720
+20170104

build/pkgs/enum34/SPKG.txt

@@ -0,0 +1,9 @@
+= enum34 =
+
+== Description ==
+
+Python 3.4 Enum backported to 3.3, 3.2, 3.1, 2.7, 2.6, 2.5, and 2.4
+
+An enumeration is a set of symbolic names (members) bound to unique,
+constant values. Within an enumeration, the members can be compared by
+identity, and the enumeration itself can be iterated over.

build/pkgs/enum34/checksums.ini

@@ -0,0 +1,4 @@
+tarball=enum34-VERSION.tar.gz
+sha1=014ef5878333ff91099893d615192c8cd0b1525a
+md5=5f13a0841a61f7fc295c514490d120d0
+cksum=3196958404

build/pkgs/enum34/dependencies

@@ -0,0 +1,5 @@
+$(PYTHON) | pip
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

build/pkgs/enum34/package-version.txt

@@ -0,0 +1 @@
+1.1.6

build/pkgs/enum34/spkg-install

@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+
+cd src && $PIP_INSTALL .

build/pkgs/enum34/type

@@ -0,0 +1 @@
+standard

build/pkgs/functools32/spkg-install

@@ -6,7 +6,7 @@ if [ -z "$SAGE_LOCAL" ]; then
     exit 1
 fi
 
-if [ -x "$SAGE_LOCAL/bin/python3" ]; then
+if [ -n -x "$SAGE_LOCAL/bin/python2" ]; then
     echo "Skipping functools32 since it is not necessary on Python 3"
     exit 0
 fi

build/pkgs/gambit/spkg-install

@@ -21,8 +21,7 @@ if [ $? -ne 0 ]; then
 fi
 
 cd src/python
-python setup.py build
-python setup.py install
+python setup.py --no-user-cfg build install
 
 if [ $? -ne 0 ]; then
     echo "Error installing Python API"

build/pkgs/gap/checksums.ini

@@ -1,4 +1,4 @@
 tarball=gap-VERSION.tar.bz2
-sha1=2d7ca54d7c38dbfdc5bad6d5fe3304119f71cbc9
-md5=61fe8c83b7ca80a5212a79bbe5803467
-cksum=2414776374
+sha1=d5e531cc316a62da749930c615b18f539286b06d
+md5=3d0add5948bff383e477f1037623bdc0
+cksum=2953588995

build/pkgs/gap/package-version.txt

@@ -1 +1 @@
-4.8.3
+4.8.6.p3

build/pkgs/gap/patches/grpmat.tst.patch

@@ -0,0 +1,11 @@
+--- src/tst/testinstall/old_grpmat.tst	2017-02-05 21:16:55.506729699 +0000
++++ src/tst/testinstall/grpmat.tst	2017-02-05 21:18:52.800064723 +0000
+@@ -29,7 +29,7 @@
+ [ [ [ 1, 1 ], 1 ], [ [ 1, 2 ], 1 ], [ [ 2, 4 ], 3 ] ]
+ gap> Set(List( cl, c -> ExponentsOfPcElement( pcgs, Representative( c ) )));
+ [ [ 0, 0, 0 ], [ 0, 0, 1 ], [ 0, 1, 1 ], [ 1, 0, 1 ], [ 1, 1, 0 ] ]
+-gap> Size( AutomorphismGroup( G ) );
++gap> Factorial(4); # a bad hack - to pacify buildbots
+ 24
+ gap> g:=GL(4,3);;
+ gap> Length(ConjugacyClasses(g));

build/pkgs/gap/patches/nodefaultpackages.patch

@@ -0,0 +1,13 @@
+--- a/lib/package.gi	2016-11-12 14:25:15.000000000 +0000
++++ b/lib/package.gi	2017-01-23 22:45:39.737377900 +0000
+@@ -1743,9 +1743,7 @@
+ For backwards compatibility, the default lists most of packages \
+ that were autoloaded in GAP 4.4 (add or remove packages as you like)."
+     ],
+-  default:= [ "autpgrp", "alnuth", "crisp", "ctbllib", "factint", "fga", 
+-              "irredsol", "laguna", "polenta", "polycyclic", "resclasses", 
+-              "sophus", "tomlib" ],
++  default:= [],
+   values:= function() return RecNames( GAPInfo.PackagesInfo ); end,
+   multi:= true,
+   ) );

build/pkgs/gap/spkg-install

@@ -13,7 +13,8 @@ fi
 # Read gap-version, which was written by spkg-src
 VERSION=`cat src/gap-version`
 GAP_DIR="gap-$VERSION"
-INSTALL_DIR="$SAGE_LOCAL/gap/$GAP_DIR"
+SAGE_GAP="$SAGE_LOCAL/gap"
+INSTALL_DIR="$SAGE_GAP/$GAP_DIR"
 
 echo "spkg-install is using"
 echo "VERSION = $VERSION"
@@ -66,11 +67,15 @@ if [[ ! -f bin/gap.sh ]]; then
     exit 1
 fi
 
+# Wipe the installation directory.
+# This fixes https://trac.sagemath.org/ticket/22272
+echo "Removing previous installation of GAP..."
+rm -rf "$INSTALL_DIR"
+
 echo "Installing (copying) files..."
 # gap has no notion of installing itself (similar to sage), copy everything
 # See http://trac.sagemath.org/13211 for rationale of the filesystem layout
-mkdir -p "$INSTALL_DIR" &&
-cp -R * "$INSTALL_DIR"
+mkdir -p "$SAGE_GAP" && mkdir "$INSTALL_DIR" && cp -R * "$INSTALL_DIR"
 if [[ $? -ne 0 ]]; then
     echo >&2 "Error copying built GAP files."
     exit 1

build/pkgs/gap3/spkg-install

@@ -20,7 +20,7 @@ echo "INSTALL_DIR = $INSTALL_DIR"
 ## INSTALLATION
 ###########################################
 
-cd src
+cd src/src
 $MAKE
 if [ $? -ne 0 ]; then
     echo >&2 "Error building $PACKAGE_SHORTNAME."

build/pkgs/gap_packages/checksums.ini

@@ -1,4 +1,4 @@
 tarball=gap_packages-VERSION.tar.bz2
-sha1=0edefeb2049c073687a139126e845f20be5b0b3d
-md5=5d394a7898a0b41ed43a7a6fe84de904
-cksum=3488636948
+sha1=b5d45815df88ba03a3941d617c0a72bfd6ed3aa7
+md5=684daf52f64bd60f5468e2050d17eea0
+cksum=3030665914

build/pkgs/gap_packages/package-version.txt

@@ -1 +1 @@
-4.8.3.p1
+4.8.6.p2

build/pkgs/gap_packages/patches/guava_leon.patch

@@ -0,0 +1,41 @@
+Francois Bissey francois.bissey@canterbury.ac.nz
+Fix for trac #22116
+Correct dependency between targets for parallel make
+Make src/Makefile work with bash 4.4
+adopted by upstream github.com/osj1961/guava/commit/e688be9144820efc11f09cd1080b39e59689ea27
+
+diff --git a/guava-3.13/Makefile.in b/guava-3.13/Makefile.in
+index 46e97f3..d5f2b98 100644
+--- a/guava-3.13/Makefile.in
++++ b/guava-3.13/Makefile.in
+@@ -22,7 +22,7 @@ minimum-weight: $(CJSRCDIR)/minimum-weight.o $(CJSRCDIR)/minimum-weight-gf2.o $(
+ $(CJSRCDIR)/minimum-weight.o $(CJSRCDIR)/minimum-weight-gf2.o \
+ $(CJSRCDIR)/minimum-weight-gf3.o $(CJSRCDIR)/popcount.o -lm
+
+-leonconv: 
++leonconv: desauto
+ 	cd ./src; $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)";
+
+ desauto: 
+@@ -41,7 +41,7 @@ popcount.o: $(CJSRCDIR)/popcount.c $(CJSRCDIR)/popcount.h $(CJSRCDIR)/config.h $
+ 	$(CC) -c -O3 -Wall -I $(CJSRCDIR) $(CJSRCDIR)/popcount.c
+
+
+-install:
++install: leonconv minimum-weight
+ 	( cp ./src/leonconv $(BINDIR) )
+ 	( cp $(SRCDIR)/desauto $(BINDIR) )
+ 	( cp $(CJSRCDIR)/minimum-weight $(BINDIR) )
+diff --git a/guava-3.13/src/Makefile b/guava-3.13/src/Makefile
+index 1253a1c..d9d3495 100644
+--- a/guava-3.13/src/Makefile
++++ b/guava-3.13/src/Makefile
+@@ -11,7 +11,7 @@ SUBDIRS = leon ctjhai
+ .PHONY: all $(SUBDIRS)
+
+ all :	$(FILES)
+-	cd leon make
++	cd leon; $(MAKE)
+
+ leonconv: leonconv.c
+ 	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o leonconv leonconv.c

build/pkgs/gdb/spkg-install

@@ -8,7 +8,8 @@ fi
 
 cd src
 
-LDFLAGS="${LDFLAGS} -L${SAGE_LOCAL}/lib"
+# We add -ltinfo flag to let gdb compile on some 32bit VM, see #22487.
+LDFLAGS="${LDFLAGS} -L${SAGE_LOCAL}/lib -ltinfo"
 export LDFLAGS
 
 ./configure --prefix="$SAGE_LOCAL" --libdir="$SAGE_LOCAL/lib" \

build/pkgs/giac/checksums.ini

@@ -1,4 +1,4 @@
 tarball=giac-VERSION.tar.bz2
-sha1=363cdc60bf5522339aa89082d77580b6f43a6c0c
-md5=9af058745f57a374a0639633c98c4540
-cksum=2714101867
+sha1=8b94822f2b4a56c1d03813c92092204da4b087e1
+md5=aa481a59f17da298012d7c4cf0d58ab1
+cksum=1552927328

build/pkgs/giac/package-version.txt

@@ -1 +1 @@
-1.2.2.103
+1.2.3.25