Merge branch 'develop' into t/17400/17400-1

COPYING.txt

@@ -801,7 +801,7 @@ at the notice in config.guess or ltmain.sh.)
 
 The atomic_ops library contains some code that is covered by the GNU General
 Public License, but is not needed by, nor linked into the collector library.
-It is included here only becuase the atomic_ops distribution is, for
+It is included here only because the atomic_ops distribution is, for
 simplicity, included in its entirety.
 
 ================================================================================

VERSION.txt

@@ -1 +1 @@
-SageMath version 7.3.rc0, Release Date: 2016-07-28
+SageMath version 7.4.beta5, Release Date: 2016-09-16

bootstrap

@@ -26,6 +26,8 @@ MAKE="${MAKE:-make}"
 CONFVERSION=`cat $PKG/package-version.txt`
 
 bootstrap () {
+    # Get autotools from our own package into PATH (Trac #21214)
+    source src/bin/sage-env
     aclocal -I m4 && \
     automake --add-missing --copy build/make/Makefile-auto && \
     autoconf

build/make/deps

@@ -134,6 +134,7 @@ sagelib: \
 		$(inst_ntl) \
 		$(inst_numpy) \
 		$(inst_pari) \
+		$(inst_pip) \
 		$(inst_pkgconfig) \
 		$(inst_planarity) \
 		$(inst_ppl) \
@@ -192,7 +193,7 @@ 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_tachyon) $(inst_jmol) $(inst_thebe)
 
 doc: doc-html
 

build/pkgs/alabaster/spkg-install

@@ -1,3 +1,3 @@
 #!/usr/bin/env bash
 
-cd src && python setup.py install
+cd src && $PIP_INSTALL .

build/pkgs/appnope/SPKG.txt

@@ -0,0 +1,5 @@
+= appnope =
+
+== Description ==
+
+Disable App Nap on OS X 10.9

build/pkgs/appnope/checksums.ini

@@ -0,0 +1,4 @@
+tarball=appnope-VERSION.tar.gz
+sha1=838158bf881f3e8538b7bfeff4ad289a6623cdda
+md5=932fbaa73792c9b06754755a774dcac5
+cksum=4167491137

build/pkgs/appnope/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/appnope/package-version.txt

@@ -0,0 +1 @@
+0.1.0

build/pkgs/appnope/spkg-install

@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+
+cd src
+
+# Only install this package on OS X
+if python -c 'from sys import *; exit(0 if platform == "darwin" else 1)'; then
+    $PIP_INSTALL . || exit $?
+else
+    echo "Not OS X, skipping installation of package 'appnope'"
+fi

build/pkgs/appnope/type

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

build/pkgs/atlas/SPKG.txt

@@ -2,8 +2,7 @@
 
 == Description ==
 
-This spkg builds ATLAS for Sage. It is build per default on Linux and
-Solaris, but should also work on OSX and Cygwin.
+This spkg builds ATLAS for Sage.
 
 == License ==
 

build/pkgs/atlas/type

@@ -1 +1 @@
-standard
+optional

build/pkgs/autotools/Makefile.build

@@ -696,6 +696,7 @@ automake-all: $(SAGE_LOCAL)/automake-1.9 $(SAGE_LOCAL)/automake-1.9.1 $(SAGE_LOC
 libtool-1.5.20/.tarball-version: automake-1.14.1/.tarball-version
 	( cd $(SRC)/libtool && git archive --format=tar --prefix=libtool-1.5.20/ release-1-5-20 ) | tar xf -
 	echo 1.5.20 >libtool-1.5.20/.tarball-version
+	echo 1886 > libtool-1.5.20/.serial
 
 $(SAGE_LOCAL)/libtool-1.5.20: libtool-1.5.20/.tarball-version $(SAGE_LOCAL)/bin/m4 $(SAGE_LOCAL)/bin/makeinfo $(SAGE_LOCAL)/autoconf-2.59 $(SAGE_LOCAL)/automake-1.9.6
 	export MAKE='$(MAKE) -j1' ; \
@@ -711,6 +712,7 @@ $(SAGE_LOCAL)/libtool-1.5.20: libtool-1.5.20/.tarball-version $(SAGE_LOCAL)/bin/
 libtool-1.5.22/.tarball-version: libtool-1.5.20/.tarball-version
 	( cd $(SRC)/libtool && git archive --format=tar --prefix=libtool-1.5.22/ release-1-5-22 ) | tar xf -
 	echo 1.5.22 >libtool-1.5.22/.tarball-version
+	echo 1965 > libtool-1.5.22/.serial
 
 $(SAGE_LOCAL)/libtool-1.5.22: libtool-1.5.22/.tarball-version $(SAGE_LOCAL)/bin/m4 $(SAGE_LOCAL)/bin/makeinfo $(SAGE_LOCAL)/autoconf-2.59 $(SAGE_LOCAL)/automake-1.9.6
 	export MAKE='$(MAKE) -j1' ; \
@@ -726,6 +728,7 @@ $(SAGE_LOCAL)/libtool-1.5.22: libtool-1.5.22/.tarball-version $(SAGE_LOCAL)/bin/
 libtool-1.5.24/.tarball-version: libtool-1.5.22/.tarball-version
 	( cd $(SRC)/libtool && git archive --format=tar --prefix=libtool-1.5.24/ release-1-5-24 ) | tar xf -
 	echo 1.5.24 >libtool-1.5.24/.tarball-version
+	echo 2056 > libtool-1.5.24/.serial
 
 $(SAGE_LOCAL)/libtool-1.5.24: libtool-1.5.24/.tarball-version $(SAGE_LOCAL)/bin/m4 $(SAGE_LOCAL)/bin/makeinfo $(SAGE_LOCAL)/autoconf-2.59 $(SAGE_LOCAL)/automake-1.9.6
 	export MAKE='$(MAKE) -j1' ; \
@@ -741,6 +744,7 @@ $(SAGE_LOCAL)/libtool-1.5.24: libtool-1.5.24/.tarball-version $(SAGE_LOCAL)/bin/
 libtool-1.5.26/.tarball-version: libtool-1.5.24/.tarball-version
 	( cd $(SRC)/libtool && git archive --format=tar --prefix=libtool-1.5.26/ release-1-5-26 ) | tar xf -
 	echo 1.5.26 >libtool-1.5.26/.tarball-version
+	echo 2093 > libtool-1.5.26/.serial
 
 $(SAGE_LOCAL)/libtool-1.5.26: libtool-1.5.26/.tarball-version $(SAGE_LOCAL)/bin/m4 $(SAGE_LOCAL)/bin/makeinfo $(SAGE_LOCAL)/autoconf-2.59 $(SAGE_LOCAL)/automake-1.9.6
 	export MAKE='$(MAKE) -j1' ; \
@@ -756,6 +760,7 @@ $(SAGE_LOCAL)/libtool-1.5.26: libtool-1.5.26/.tarball-version $(SAGE_LOCAL)/bin/
 libtool-2.2.4/.tarball-version: libtool-1.5.26/.tarball-version
 	( cd $(SRC)/libtool && git archive --format=tar --prefix=libtool-2.2.4/ v2.2.4 ) | tar xf -
 	echo 2.2.4 >libtool-2.2.4/.tarball-version
+	echo 3070 > libtool-2.2.4/.serial
 
 $(SAGE_LOCAL)/libtool-2.2.4: libtool-2.2.4/.tarball-version $(SAGE_LOCAL)/bin/m4 $(SAGE_LOCAL)/bin/makeinfo $(SAGE_LOCAL)/autoconf-2.59 $(SAGE_LOCAL)/automake-1.9.6
 	export MAKE='$(MAKE) -j1' ; \
@@ -771,6 +776,7 @@ $(SAGE_LOCAL)/libtool-2.2.4: libtool-2.2.4/.tarball-version $(SAGE_LOCAL)/bin/m4
 libtool-2.2.6/.tarball-version: libtool-2.2.4/.tarball-version
 	( cd $(SRC)/libtool && git archive --format=tar --prefix=libtool-2.2.6/ v2.2.6 ) | tar xf -
 	echo 2.2.6 >libtool-2.2.6/.tarball-version
+	echo 3117 > libtool-2.2.6/.serial
 
 $(SAGE_LOCAL)/libtool-2.2.6: libtool-2.2.6/.tarball-version $(SAGE_LOCAL)/bin/m4 $(SAGE_LOCAL)/bin/makeinfo $(SAGE_LOCAL)/autoconf-2.60 $(SAGE_LOCAL)/automake-1.10.1
 	export MAKE='$(MAKE) -j1' ; \
@@ -786,6 +792,7 @@ $(SAGE_LOCAL)/libtool-2.2.6: libtool-2.2.6/.tarball-version $(SAGE_LOCAL)/bin/m4
 libtool-2.2.6b/.tarball-version: libtool-2.2.6/.tarball-version
 	( cd $(SRC)/libtool && git archive --format=tar --prefix=libtool-2.2.6b/ v2.2.6b ) | tar xf -
 	echo 2.2.6b >libtool-2.2.6b/.tarball-version
+	echo 3123 > libtool-2.2.6b/.serial
 
 $(SAGE_LOCAL)/libtool-2.2.6b: libtool-2.2.6b/.tarball-version $(SAGE_LOCAL)/bin/m4 $(SAGE_LOCAL)/bin/makeinfo $(SAGE_LOCAL)/autoconf-2.60 $(SAGE_LOCAL)/automake-1.10.1
 	export MAKE='$(MAKE) -j1' ; \
@@ -801,6 +808,7 @@ $(SAGE_LOCAL)/libtool-2.2.6b: libtool-2.2.6b/.tarball-version $(SAGE_LOCAL)/bin/
 libtool-2.2.8/.tarball-version: libtool-2.2.6b/.tarball-version
 	( cd $(SRC)/libtool && git archive --format=tar --prefix=libtool-2.2.8/ v2.2.8 ) | tar xf -
 	echo 2.2.8 >libtool-2.2.8/.tarball-version
+	echo 3328 > libtool-2.2.8/.serial
 
 $(SAGE_LOCAL)/libtool-2.2.8: libtool-2.2.8/.tarball-version $(SAGE_LOCAL)/bin/m4 $(SAGE_LOCAL)/bin/makeinfo $(SAGE_LOCAL)/bin/help2man $(SAGE_LOCAL)/autoconf-2.62 $(SAGE_LOCAL)/automake-1.10.1
 	export MAKE='$(MAKE) -j1' ; \
@@ -816,6 +824,7 @@ $(SAGE_LOCAL)/libtool-2.2.8: libtool-2.2.8/.tarball-version $(SAGE_LOCAL)/bin/m4
 libtool-2.2.10/.tarball-version: libtool-2.2.8/.tarball-version
 	( cd $(SRC)/libtool && git archive --format=tar --prefix=libtool-2.2.10/ v2.2.10 ) | tar xf -
 	echo 2.2.10 >libtool-2.2.10/.tarball-version
+	echo 3349 > libtool-2.2.10/.serial
 
 $(SAGE_LOCAL)/libtool-2.2.10: libtool-2.2.10/.tarball-version $(SAGE_LOCAL)/bin/m4 $(SAGE_LOCAL)/bin/makeinfo $(SAGE_LOCAL)/bin/help2man $(SAGE_LOCAL)/autoconf-2.62 $(SAGE_LOCAL)/automake-1.10.1
 	export MAKE='$(MAKE) -j1' ; \
@@ -831,6 +840,7 @@ $(SAGE_LOCAL)/libtool-2.2.10: libtool-2.2.10/.tarball-version $(SAGE_LOCAL)/bin/
 libtool-2.4/.tarball-version: libtool-2.2.10/.tarball-version
 	( cd $(SRC)/libtool && git archive --format=tar --prefix=libtool-2.4/ v2.4 ) | tar xf -
 	echo 2.4 >libtool-2.4/.tarball-version
+	echo 3560 > libtool-2.4/.serial
 
 $(SAGE_LOCAL)/libtool-2.4: libtool-2.4/.tarball-version $(SAGE_LOCAL)/bin/m4 $(SAGE_LOCAL)/bin/makeinfo $(SAGE_LOCAL)/bin/help2man $(SAGE_LOCAL)/autoconf-2.62 $(SAGE_LOCAL)/automake-1.11.1
 	export MAKE='$(MAKE) -j1' ; \
@@ -846,6 +856,7 @@ $(SAGE_LOCAL)/libtool-2.4: libtool-2.4/.tarball-version $(SAGE_LOCAL)/bin/m4 $(S
 libtool-2.4.2/.tarball-version: libtool-2.4/.tarball-version
 	( cd $(SRC)/libtool && git archive --format=tar --prefix=libtool-2.4.2/ v2.4.2 ) | tar xf -
 	echo 2.4.2 >libtool-2.4.2/.tarball-version
+	echo 3620 > libtool-2.4.2/.serial
 
 $(SAGE_LOCAL)/libtool-2.4.2: libtool-2.4.2/.tarball-version $(SAGE_LOCAL)/bin/m4 $(SAGE_LOCAL)/bin/makeinfo $(SAGE_LOCAL)/bin/help2man $(SAGE_LOCAL)/autoconf-2.62 $(SAGE_LOCAL)/automake-1.11.1
 	export MAKE='$(MAKE) -j1' ; \
@@ -861,6 +872,7 @@ $(SAGE_LOCAL)/libtool-2.4.2: libtool-2.4.2/.tarball-version $(SAGE_LOCAL)/bin/m4
 libtool-2.4.3/.tarball-version: libtool-2.4.2/.tarball-version
 	( cd $(SRC)/libtool && git archive --format=tar --prefix=libtool-2.4.3/ v2.4.3 ) | tar xf -
 	echo 2.4.3 >libtool-2.4.3/.tarball-version
+	echo 4105 > libtool-2.4.3/.serial
 
 $(SAGE_LOCAL)/libtool-2.4.3: libtool-2.4.3/.tarball-version $(SAGE_LOCAL)/bin/m4 $(SAGE_LOCAL)/bin/makeinfo $(SAGE_LOCAL)/bin/help2man $(SAGE_LOCAL)/autoconf-2.62 $(SAGE_LOCAL)/automake-1.11.1
 	export MAKE='$(MAKE) -j1' ; \

build/pkgs/autotools/dependencies

@@ -1,4 +1,4 @@
-ncurses git
+ncurses git xz 
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/autotools/spkg-install

@@ -23,6 +23,14 @@ git init
 SRC=`pwd`/src
 BUILD=`pwd`/build
 
+# Mac OS X 10.11.5 installs GNU m4 1.4.6 as both "m4" and "gm4".
+# This is too old to bootstrap libtool 1.4.3.
+# The configure script prefers "gm4" to "m4" and thus does not
+# find the m4 from SageMath.
+# The following environment variable makes sure we use the m4 from
+# SageMath.  See trac #21047.
+export M4="$SAGE_LOCAL/bin/m4"
+
 ########################################################################
 # Apply patch(es)
 ########################################################################
@@ -105,3 +113,10 @@ cd "$BUILD"
 ) >Makefile
 
 $MAKE
+
+# Install symlinks bin/aclocal-AM_API_VERSION and bin/automake-AM_API_VERSION.
+# (am__api_version).  These are required for autoreconf to work (Trac #21047).
+cd "$SAGE_LOCAL"/bin
+for x in $automake_versions; do
+    ln -sf ../automake-$x/bin/automake-* ../automake-$x/bin/aclocal-* .
+done

build/pkgs/autotools/spkg-write-makefile

@@ -141,6 +141,11 @@ write_make_rules() {
                 ac_ver=`( echo 2.59; autoconf --trace='AC_PREREQ:$1' configure.ac ) | latest_version`
             fi
 
+	    # Automake 1.10 thinks it only needs autoconf 2.59, when in fact it needs 2.60.  Fix it up.
+	    if [ $p = automake ] && [ $v = 1.10 ]; then
+		ac_ver=2.60
+	    fi
+
             # Minimum required version of libtool.
             # Empty by default.
             lt_ver=`( autoconf --trace='LT_PREREQ:$1' configure.ac ) | latest_version`
@@ -178,20 +183,29 @@ write_make_rules() {
         echo "$p-$v/.tarball-version: $prevextract"
         echo -e "\t( cd \$(SRC)/$p && git archive --format=tar --prefix=$p-$v/ $tag ) | tar xf -"
         echo -e "\techo $v >$p-$v/.tarball-version"
+	if [ $p = libtool -a ! -f .serial ] ; then
+	    # The file .serial would be generated at "make dist" time.  It is used in ltversion.m4.
+	    # If .serial is missing, ltmversion.m4 will be malformed, causing the following warning
+	    # when the user uses autoreconf.
+	    #   m4/ltversion.m4:12: warning: ill-formed serial number 'ltversion.m4',
+	    #                                expecting a version string with only digits and dots
+	    # See Trac #21047.
+	    # Since we don't do "make dist" but rather build from a repository check-out, we have to
+	    # supply the .serial file ourselves.  The following recipe is from libtool's Makefile.am.
+	    echo -e "\techo $( git log --pretty=oneline | wc -l | sed 's|[\t ]||g ' ) > $p-$v/.serial"
+	fi
         echo
 
         echo "\$(SAGE_LOCAL)/$p-$v: $p-$v/.tarball-version $deps"
         echo -e "\texport MAKE='\$(MAKE) -j1' ; \\\\"
         [ -z "$lt_ver" ] || echo -e "\texport LIBTOOL_VERSION=$lt_ver ; \\\\"
         [ -z "$ac_ver" ] || echo -e "\texport AUTOCONF_VERSION=$ac_ver ; \\\\"
         [ -z "$am_ver" ] || echo -e "\texport AUTOMAKE_VERSION=$am_ver ; \\\\"
-sed 's/^/\t/;' <<EOF
-cd $p-$v && ${bootstrap}\\
-    ./configure --prefix="\$(SAGE_LOCAL)/$p-$v" && \\
-    \$\$MAKE && \$\$MAKE install
-# Remove all files except for the .* files
-[ "\$\$SAGE_KEEP_BUILT_SPKGS" = yes ] || rm -rf $p-$v/*
-EOF
+	echo -e "\tcd $p-$v && ${bootstrap}\\\\"
+	echo -e "\t    ./configure --prefix=\"\$(SAGE_LOCAL)/$p-$v\" && \\\\"
+	echo -e "\t    \$\$MAKE && \$\$MAKE install"
+	echo -e "\t# Remove all files except for the .* files"
+	echo -e "\t[ \"\$\$SAGE_KEEP_BUILT_SPKGS\" = yes ] || rm -rf $p-$v/*"
         echo
 
         prevextract="$p-$v/.tarball-version"

build/pkgs/babel/spkg-install

@@ -1,3 +1,3 @@
 #!/usr/bin/env bash
 
-cd src && python setup.py install
+cd src && $PIP_INSTALL .

build/pkgs/backports_abc/dependencies

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

build/pkgs/backports_abc/spkg-install

@@ -8,7 +8,8 @@ fi
 
 cd src
 
-python setup.py install
+$PIP_INSTALL .
+
 if [ $? -ne 0 ]; then
     echo "Error installing backports_abc ... exiting"
     exit 1

build/pkgs/backports_shutil_get_terminal_size/dependencies

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

build/pkgs/backports_shutil_get_terminal_size/spkg-install

@@ -11,4 +11,4 @@ for patch in ../patches/*.patch; do
     fi
 done
 
-python setup.py install
+$PIP_INSTALL .

build/pkgs/backports_ssl_match_hostname/dependencies

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

build/pkgs/backports_ssl_match_hostname/spkg-install

@@ -8,7 +8,8 @@ fi
 
 cd src
 
-python setup.py install
+$PIP_INSTALL .
+
 if [ $? -ne 0 ]; then
     echo "Error installing backports.ssl_match_hostname ... exiting"
     exit 1

build/pkgs/bliss/SPKG.txt

@@ -1,4 +1,4 @@
-= bliss 0.72 =
+= bliss 0.73+debian-1 =
 
 == Description ==
 
@@ -15,13 +15,12 @@ Bliss is currently being maintained by Tommi Junttila and Petteri Kaski.
 
 http://www.tcs.tkk.fi/Software/bliss/index.html
 
+We apply patches generated from https://github.com/mkoeppe/bliss
+(branch apply_debian_patches) as our upstream.  This tracks the
+patches from the Debian package, adding an autotools build system
+and adjusting the include file locations.
+
 == Dependencies ==
 
 None
 
-== Patches ==
-
-There is one patch to be applied that affects the code for computing
-automorphism groups of Digraphs. See http://trac.sagemath.org/ticket/17464#comment:33
-
-The patch will be removed once the author of bliss makes a new release.

build/pkgs/bliss/checksums.ini

@@ -1,4 +1,4 @@
-tarball=bliss-VERSION.zip
-sha1=ca86a10c674a5b3ec9fa163edf6ffde002699628
-md5=72f2e310786923b5c398ba0fc40b42ce
-cksum=1722393284
+tarball=bliss-VERSION.tar.gz
+sha1=1da8f098046824fbfff4c64c337e28b2a082f74f
+md5=452aea8737d3c4ad0d8ff39180be8004
+cksum=2193930007

build/pkgs/bliss/dependencies

@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+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/bliss/package-version.txt

@@ -1 +1 @@
-0.73
+0.73+debian-1+sage-2016-08-02

build/pkgs/bliss/spkg-install

@@ -17,8 +17,7 @@ for patch in ../patches/*.patch; do
     fi
 done
 
-
-$MAKE && cp libbliss.a "$SAGE_LOCAL/lib" && cp *.hh "$SAGE_LOCAL/include"
+./configure --prefix="$SAGE_LOCAL" --disable-gmp && $MAKE && $MAKE install
 
 if [ $? -ne 0 ]; then
     echo "An error occurred whilst building bliss"

build/pkgs/bliss/spkg-src

@@ -0,0 +1,28 @@
+#!/bin/sh
+#
+# creates the tarball in the current dir, to be moved to ../../../upstream
+#
+# adapted from cliquer/spkg-src
+
+die () {
+    echo >&2 "$@"
+    exit 1
+}
+
+rm -rf bliss/
+git clone -b sage_package https://github.com/mkoeppe/bliss.git  || die "Failed to git clone"
+cd bliss/ 
+
+VERSION=`autoconf --trace='AC_INIT:$2'`
+libtoolize || die "Failed to autoreconf"
+autoreconf -fi || die "Failed to autoreconf"
+automake --add-missing --copy || die "automake failed"
+./configure || die "configure failed"
+
+rm -f bliss-$VERSION.tar.gz
+make dist || die "make dist failed"
+mv bliss-$VERSION.tar.gz ../
+cd ..
+rm -rf bliss/ 
+
+