Merge branch 'develop' into t/18329/ticket/18329

Conflicts:
	src/sage/combinat/root_system/cartan_matrix.py

COPYING.txt

@@ -96,6 +96,7 @@ pillow                      Apache License 2.0
 pip                         MIT License
 pkgconf                     ISC License (equivalent to Simplified BSD)
 pkgconfig                   MIT License
+planarity                   Modified BSD
 polybori                    GPLv2+
 polytopes_db                None (database)
 ppl                         GPLv3+

Makefile

@@ -18,7 +18,7 @@ logs:
 build: logs configure
 	+cd build && \
 	"../$(PIPE)" \
-		"env SAGE_PARALLEL_SPKG_BUILD='$(SAGE_PARALLEL_SPKG_BUILD)' ./install all 2>&1" \
+		"./install all 2>&1" \
 		"tee -a ../logs/install.log"
 	+./sage -b
 
@@ -36,9 +36,6 @@ download:
 ssl: all
 	./sage -i pyopenssl
 
-build-serial: SAGE_PARALLEL_SPKG_BUILD = no
-build-serial: build
-
 # Start Sage if the file local/etc/sage-started.txt does not exist
 # (i.e. when we just installed Sage for the first time).
 start: build
@@ -112,42 +109,33 @@ micro_release: bdist-clean lib-clean
 	@echo "Stripping binaries ..."
 	LC_ALL=C find local/lib local/bin -type f -exec strip '{}' ';' 2>&1 | grep -v "File format not recognized" |  grep -v "File truncated" || true
 
-TESTPRELIMS = local/bin/sage-starts
 TESTALL = ./sage -t --all
 PTESTALL = ./sage -t -p --all
 
-test: all # i.e. build and doc
-	$(TESTPRELIMS)
+test: all
 	$(TESTALL) --logfile=logs/test.log
 
 check: test
 
-testall: all # i.e. build and doc
-	$(TESTPRELIMS)
+testall: all
 	$(TESTALL) --optional=all --logfile=logs/testall.log
 
-testlong: all # i.e. build and doc
-	$(TESTPRELIMS)
+testlong: all
 	$(TESTALL) --long --logfile=logs/testlong.log
 
-testalllong: all # i.e. build and doc
-	$(TESTPRELIMS)
+testalllong: all
 	$(TESTALL) --long --optional=all --logfile=logs/testalllong.log
 
-ptest: all # i.e. build and doc
-	$(TESTPRELIMS)
+ptest: all
 	$(PTESTALL) --logfile=logs/ptest.log
 
-ptestall: all # i.e. build and doc
-	$(TESTPRELIMS)
+ptestall: all
 	$(PTESTALL) --optional=all --logfile=logs/ptestall.log
 
-ptestlong: all # i.e. build and doc
-	$(TESTPRELIMS)
+ptestlong: all
 	$(PTESTALL) --long --logfile=logs/ptestlong.log
 
-ptestalllong: all # i.e. build and doc
-	$(TESTPRELIMS)
+ptestalllong: all
 	$(PTESTALL) --long --optional=all --logfile=logs/ptestalllong.log
 
 
@@ -182,7 +170,7 @@ install:
 	"$(DESTDIR)"/bin/sage -c # Run sage-location
 
 
-.PHONY: all build build-serial start install micro_release \
+.PHONY: all build start install micro_release \
 	doc doc-html doc-html-jsmath doc-html-mathjax doc-pdf \
 	doc-clean clean lib-clean bdist-clean distclean bootstrap-clean maintainer-clean \
 	test check testoptional testall testlong testoptionallong testallong \

VERSION.txt

@@ -1 +1 @@
-Sage version 6.8.beta3, released 2015-06-04
+Sage version 6.8.beta6, released 2015-06-25

build/deps

@@ -25,6 +25,7 @@ all:
 # All targets except for the base packages
 all-sage: \
      $(STANDARD_PACKAGES) \
+     $(OPTIONAL_INSTALLED_PACKAGES) \
      $(INST)/$(SAGE_MP_LIBRARY) \
      $(INST)/sage \
      $(EXTCODE) \
@@ -49,7 +50,7 @@ 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 = $(SCRIPTS) $(INST)/sage $(INST)/$(IPYTHON)
+SAGERUNTIME = $(SCRIPTS) $(INST)/sage $(INST)/$(IPYTHON) $(INST)/$(PEXPECT)
 
 ###############################################################################
 # Building the base system
@@ -115,6 +116,7 @@ $(INST)/sage: \
 		 $(INST)/$(PYTHON) \
 		 $(INST)/$(RATPOINTS) \
 		 $(INST)/$(READLINE) \
+		 $(INST)/$(RW) \
 		 $(INST)/$(SINGULAR) \
 		 $(INST)/$(SIX) \
 		 $(INST)/$(SYMMETRICA) \
@@ -125,8 +127,19 @@ $(INST)/sage: \
 		touch $@; \
 	fi
 
-# TODO: remove this once ccache is a new-style package
-CCACHE = ccache
-$(INST)/ccache: base $(INST)/$(ZLIB)
-	+$(PIPE) "$(SAGE_SPKG) ccache 2>&1" "tee -a $(SAGE_LOGS)/ccache.log"
-	touch $@
+
+###############################################################################
+# Building scripts and extcode
+###############################################################################
+
+# Don't just use "install" since we don't want to change permissions
+$(SAGE_LOCAL)/bin/%: $(SAGE_SRC)/bin/%
+	cp $< $@
+
+# Don't just use "install -D" since we don't want to change permissions.
+# cp won't correctly setup the SAGE_EXTCODE directory structure
+# (unlike install), so we need a mkdir here such that cp can copy into
+# an existing folder.
+$(SAGE_EXTCODE)/%: $(SAGE_SRC)/ext/%
+	@mkdir -p "$(@D)"
+	cp $< $@

build/install

@@ -268,15 +268,6 @@ EOF
 echo >&5 "SHELL = `command -v bash`"
 echo >&5
 
-# If the user (or the Makefile) has set SAGE_PARALLEL_SPKG_BUILD=no,
-# then turn off parallel building: disable just building multiple
-# packages at the same time.   Individual packages can still be built
-# in parallel by specifying '-j' in $MAKE.
-if [ "${SAGE_PARALLEL_SPKG_BUILD:-yes}" = no ]; then
-    echo ".NOTPARALLEL:" >&5
-    echo "" >&5
-fi
-
 # Usage: newest_version $pkg
 # Print version number of latest standard package $pkg
 newest_version() {
@@ -386,6 +377,18 @@ done
 echo >&5
 echo >&5
 
+echo >&5 '# All optional installed packages (triggers the auto-update)'
+echo >&5 'OPTIONAL_INSTALLED_PACKAGES = \'
+filtered_packages_list optional | while read PKG_NAME PKG_VERSION PKG_VAR; do
+    if [ "$PKG_NAME" = "gcc" ]; then
+        continue
+    fi
+    if [ -f $SAGE_SPKG_INST/$PKG_NAME-* ]; then
+        echo >&5 "    \$(INST)/\$($PKG_VAR) \\"
+    fi;
+done
+echo >&5
+echo >&5
 
 echo >&5 'SCRIPT_SOURCES = \'
 for file in "$SAGE_SRC/bin/"*; do
@@ -408,19 +411,6 @@ for file in `find "$SAGE_SRC"/ext -type f`; do
 done
 echo >&5
 
-cat >&5 <<EOF
-# don't just use \`install\` since we don't want to change permissions
-\$(SAGE_LOCAL)/bin/%: \$(SAGE_SRC)/bin/%
-	cp \$< \$@
-
-# don't just use \`install -D\` since we don't want to change permissions
-# cp won't correctly setup the SAGE_EXTCODE directory structure (unlike install)
-# so we need a mkdir here to cp can copy into an existing folder
-\$(SAGE_EXTCODE)/%: \$(SAGE_SRC)/ext/%
-	@mkdir -p "\$(@D)"
-	cp \$< \$@
-EOF
-
 # Copy build/deps
 cat >&5 <<EOF
 
@@ -445,8 +435,11 @@ EOF
 # Add a Makefile target corresponding to a given package
 filtered_packages_list all | while read PKG_NAME PKG_VERSION PKG_VAR; do
     DEP_FILE="$SAGE_ROOT/build/pkgs/$PKG_NAME/dependencies"
+    TYPE_FILE="$SAGE_ROOT/build/pkgs/$PKG_NAME/type"
     if [ -f "$DEP_FILE" ]; then
         DEPS=" $(head -n 1 $DEP_FILE)"
+    elif [ x`cat "$TYPE_FILE"` = xoptional ]; then
+        DEPS=' | $(STANDARD_PACKAGES)' # default for optional packages
     else
         DEPS=""
     fi

build/pkgs/arb/checksums.ini

@@ -1,4 +1,4 @@
 tarball=arb-VERSION.tar.gz
-sha1=ba51573e0c50250bbb16bfca027dc26531347f12
-md5=5b2c10b103cf64f33dc7d15c1fb2948f
-cksum=1391275088
+sha1=e8c367b9f617262b4a7e9956cf49b6acf5c0db24
+md5=683f4b9f975f8e546ca4481f803cd099
+cksum=444089473

build/pkgs/arb/package-version.txt

@@ -1,2 +1,2 @@
-2.5.0
+2.6.0
 

build/pkgs/autotools/version-list

@@ -1,5 +1,3 @@
-#!/bin/sh
-#
 # This file defines the versions installed by this spkg.  If you edit
 # this, re-create Makefile.build using
 #

build/pkgs/cbc/spkg-install

@@ -1,3 +1,5 @@
+#!/usr/bin/env bash
+
 if [ "$SAGE_LOCAL" = "" ]; then
    echo >&2 "SAGE_LOCAL undefined ... exiting";
    echo >&2 "Maybe run 'sage -sh'?"
@@ -19,4 +21,4 @@ cd src &&
 sed -i -e "s/clock\_gettime ()/Grrrrrrrrrrrr\ ()/g" Cbc/configure &&
 ./configure --prefix="$SAGE_LOCAL" "${args[@]}" --enable-cbc-parallel --enable-parallel --enable-gnu-packages --enable-static &&
 make &&
-make install
+make install

build/pkgs/ccache/SPKG.txt

@@ -0,0 +1,17 @@
+= ccache =
+
+== Description ==
+
+ccache is a compiler cache. It speeds up recompilation by caching
+previous compilations and detecting when the same compilation is being
+done again.
+Supported languages are C, C++, Objective-C and Objective-C++.
+
+== License ==
+
+GNU General Public License version 3 or later
+
+== Upstream Contact ==
+
+ * Author: Andrew Tridgell
+ * Website: http://ccache.samba.org/

build/pkgs/ccache/ccache.conf

@@ -0,0 +1,2 @@
+compression = true
+max_size = 4G

build/pkgs/ccache/checksums.ini

@@ -0,0 +1,4 @@
+tarball=ccache-VERSION.tar.bz2
+sha1=1f0d9d5786b15fbb1e50de16896d71bbfa0e4e6c
+md5=0823f62b5b44f7b4b0fa5205416be74a
+cksum=1085040985

build/pkgs/ccache/dependencies

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

build/pkgs/ccache/package-version.txt

@@ -0,0 +1 @@
+3.2.2

build/pkgs/ccache/spkg-check

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+cd src
+
+$MAKE check

build/pkgs/ccache/spkg-install

@@ -0,0 +1,34 @@
+#!/usr/bin/env bash
+
+die () {
+    echo >&2 "$@"
+    exit 1
+}
+
+[ -n "$SAGE_LOCAL" ] || die "SAGE_LOCAL undefined, maybe run \`sage -sh\`?"
+
+cd src
+
+export LDFLAGS="-L$SAGE_LOCAL/lib $LDFLAGS"
+export CPPFLAGS="-I$SAGE_LOCAL/include $CPPFLAGS"
+./configure --prefix="$SAGE_LOCAL" ||
+    die "configuring ccache failed"
+
+$MAKE || die "building ccache failed"
+
+$MAKE install || die "installing ccache failed"
+
+
+set -e
+
+mkdir -p "$SAGE_LOCAL/libexec/ccache"
+ln -sf ../../bin/ccache "$SAGE_LOCAL/libexec/ccache/cc"
+ln -sf ../../bin/ccache "$SAGE_LOCAL/libexec/ccache/c++"
+ln -sf ../../bin/ccache "$SAGE_LOCAL/libexec/ccache/gcc"
+ln -sf ../../bin/ccache "$SAGE_LOCAL/libexec/ccache/g++"
+ln -sf ../../bin/ccache "$SAGE_LOCAL/libexec/ccache/clang"
+ln -sf ../../bin/ccache "$SAGE_LOCAL/libexec/ccache/clang++"
+
+# Copy a reasonable default configuration for Sage
+# (cache size of 4G and compression enabled)
+cp -p ../ccache.conf "$SAGE_LOCAL/etc"

build/pkgs/ccache/type

@@ -0,0 +1 @@
+optional

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=ba70d13aace4a7894ceec5d6e56f29b39756ab30
-md5=b2e6ae57f6f348b3f5bf9baaa2b7049f
-cksum=2993700783
+sha1=6e078846812390c4eea0142800d782397d05d09a
+md5=e5a3122e7cde1825c1c793d0ccf274d4
+cksum=3099888041

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-97
+100

build/pkgs/conway_polynomials/spkg-install

@@ -2,15 +2,15 @@
 
 import os
 from sage.all import save
-from sage.misc.misc import SAGE_SHARE
+from sage.env import SAGE_SHARE
 
 install_root = os.path.join(SAGE_SHARE, 'conway_polynomials')
 
 def create_db():
     db = {}
     from src import conway_polynomials
     for p,n,v in conway_polynomials:
-        if not db.has_key(p):
+        if not p in db:
             db[p] = {}
         db[p][n] = v
     if not os.path.exists(install_root):

build/pkgs/dot2tex/SPKG.txt

@@ -26,6 +26,12 @@ example via the graphviz spkg).
 
 preview, a LaTeX package for extracting parts of a document.
 
+== Patches ==
+
+ * remove_test_semicolon.patch:
+   Remove the failing semicolon test for the open dot2tex
+   issue #5 - https://github.com/kjellmf/dot2tex/issues/5
+
 == Special Update/Build Instructions ==
 
 Make sure corresponding optional doctests still pass:

build/pkgs/dot2tex/checksums.ini

@@ -1,4 +1,4 @@
-tarball=dot2tex-VERSION.tar.bz2
-sha1=514771c38869014d8af36cc942bef2653187ae7c
-md5=9713baa89479c775a2d400932df93832
-cksum=2176770381
+tarball=dot2tex-VERSION.tar.gz
+sha1=03f502c0922c2dc87b5dd38456021a6774e4c8be
+md5=2dbaeac905424d0410751235bde4b8b2
+cksum=1572429696

build/pkgs/dot2tex/package-version.txt

@@ -1 +1 @@
-20120520
+2.9.0.p0