Merge branch 'develop' into public/combinat/rigged_configurations/met…

…hods-15560

* develop: (227 commits)
  Updated Sage version to 6.1.rc0
  only use CONFVERSION after it has been incremented
  note that the E6->A5 rule is now implemented
  document the glibc bug workaround patch
  Avoid scanf instead of just ignoring rest of file
  bump confball version
  fix for the m4_divert_push error
  sage-clone-source: allow downloading the configure tarball
  Require autoconf 2.64
  revised thematic tutorial regarding maximal_subgroup(s) method
  reference: branching_rules: minor fixup
  bump confball version
  removed bogus commits
  LinearMatroid.is_field_equivalent now tests if self is other before calling LinearMatroid._is_field_isomorphism.
  implemented maximal_subgroup(s) as a WeylCharacterRing method etc.
  Updated Sage version to 6.1.beta6
  Do not use the GNU extension chmod --recursive
  Workaround for glibc-2.18 scanf bug when building ATLAS
  Added  free_group and finitely_presented_group
  Made the repr sorted for the rules.
  ...

.gitignore

@@ -5,6 +5,18 @@
 /logs
 /upstream
 
+#############################
+# Autotools generated files #
+#############################
+/aclocal.m4
+/autom4te.cache/
+/config/
+/config.log
+/config.status
+/configure
+/build/Makefile-auto
+/build/Makefile-auto.in
+
 ###################
 # Temporary Files #
 ###################

Makefile

@@ -9,12 +9,13 @@
 
 PIPE = build/pipestatus
 
+
 all: start doc  # indirectly depends on build
 
 logs:
 	mkdir -p $@
 
-build: logs
+build: logs configure
 	cd build && \
 	"../$(PIPE)" \
 		"env SAGE_PARALLEL_SPKG_BUILD='$(SAGE_PARALLEL_SPKG_BUILD)' ./install all 2>&1" \
@@ -82,13 +83,24 @@ bdist-clean: clean
 	rm -rf logs
 	rm -rf dist
 	rm -rf tmp
-	rm -f build/Makefile
+	rm -f aclocal.m4 config.log config.status confcache
+	rm -rf autom4te.cache
+	rm -f build/Makefile build/Makefile-auto
 	rm -f .BUILDSTART
 
 distclean: clean doc-clean lib-clean bdist-clean
 	@echo "Deleting all remaining output from build system ..."
 	rm -rf local
 
+# Delete all auto-generated files which are distributed as part of the
+# source tarball
+bootstrap-clean:
+	rm -rf config configure build/Makefile-auto.in
+
+# Remove absolutely everything which isn't part of the git repo
+maintainer-clean: distclean bootstrap-clean
+	rm -rf upstream
+
 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
@@ -140,6 +152,9 @@ ptestoptional: ptestall # just an alias
 
 ptestoptionallong: ptestalllong # just an alias
 
+configure: configure.ac src/bin/sage-version.sh \
+        m4/ax_c_check_flag.m4 m4/ax_gcc_option.m4 m4/ax_gcc_version.m4 m4/ax_gxx_option.m4 m4/ax_gxx_version.m4 m4/ax_prog_perl_version.m4
+	./bootstrap -d
 
 install:
 	echo "Experimental use only!"
@@ -160,8 +175,8 @@ install:
 	"$(DESTDIR)"/bin/sage -c # Run sage-location
 
 
-.PHONY: all build build-serial start install \
+.PHONY: all build build-serial start install micro_release \
 	doc doc-html doc-html-jsmath doc-html-mathjax doc-pdf \
-	doc-clean clean lib-clean bdist-clean distclean micro_release \
+	doc-clean clean lib-clean bdist-clean distclean bootstrap-clean maintainer-clean \
 	test check testoptional testall testlong testoptionallong testallong \
 	ptest ptestoptional ptestall ptestlong ptestoptionallong ptestallong

VERSION.txt

@@ -1 +1 @@
-Sage version 6.1.beta4, released 2014-01-05
+Sage version 6.1.rc0, released 2014-01-25

bootstrap

@@ -0,0 +1,133 @@
+#!/usr/bin/env bash
+
+########################################################################
+# Regenerate auto-generated files (e.g. configure)
+#
+# If the -s option is given, save the autogenerated scripts in
+# $SAGE_ROOT/upstream/configure-$CONFVERSION.tar.gz where CONFVERSION
+# is the version number stored in
+# build/pkgs/configure/package-version.txt
+#
+# If optional argument -i is given, then automatically increment the
+# version number.
+#
+# If optional argument -d is given and bootstrapping failed, instead
+# extract the files from a local configure tarball, downloading it if
+# needed. If -D is given, don't try to bootstrap and always extract or
+# donwload.
+########################################################################
+
+# Either run this script from SAGE_ROOT or make sure that SAGE_ROOT
+# is set
+test -z "$SAGE_ROOT" || cd "$SAGE_ROOT"
+
+PKG=build/pkgs/configure
+MAKE="${MAKE:-make}"
+CONFVERSION=`cat $PKG/package-version.txt`
+
+bootstrap () {
+    aclocal -I m4 && \
+    automake --add-missing --copy build/Makefile-auto && \
+    autoconf
+
+    st=$?
+    case $st in
+        0) true;; # Success
+
+        63|127)  # Autotools not installed or version too old
+            if [ $DOWNLOAD = yes ]; then
+                echo >&2 "Bootstrap failed, downloading required files instead."
+                bootstrap-download || exit $?
+            else
+                if [ $st -eq 127 ]; then
+                    verb="install"
+                else
+                    verb="upgrade"
+                fi
+                echo >&2 "Bootstrap failed. Either $verb autotools or run bootstrap with"
+                echo >&2 "the -d option to download the auto-generated files instead."
+                exit $st
+            fi;;
+
+        *) exit $st;; # Failure
+    esac
+}
+
+# Bootstrap by downloading the auto-generated files
+bootstrap-download () {
+    source src/bin/sage-env
+
+    mkdir upstream 2>/dev/null
+    if [ ! -f $CONFBALL ]; then
+        sage-download-file $SAGE_UPSTREAM/configure/configure-$CONFVERSION.tar.gz >$CONFBALL
+        if [ $? -ne 0 ]; then
+            rm -f "$CONFBALL"
+            echo >&2 "Error: downloading configure-$CONFVERSION.tar.gz failed"
+            exit 1
+        fi
+    fi
+
+    # The "m" option to tar ensures that timestamps are set to the
+    # current time, not taken from the tarball.
+    # We need these files to be more recent than the input files
+    # like configure.ac, otherwise "make" gets confused.
+    tar xzmf $CONFBALL || exit $?
+}
+
+save () {
+    set -e
+
+    # Create configure tarball
+    echo "Creating $CONFBALL..."
+    mkdir -p upstream
+    tar zcf "$CONFBALL" configure config/* build/Makefile-auto.in
+
+    # Update version number
+    echo "$CONFVERSION" >$PKG/package-version.txt
+
+    # Compute checksum
+    SAGE_ROOT=. src/bin/sage-fix-pkg-checksums "$CONFBALL"
+}
+
+
+usage () {
+    echo >&2 "Usage: $0 [-d|-D|-s] [-i] [-h]"
+}
+
+
+# Parse options
+SAVE=no
+DOWNLOAD=no
+ALWAYSDOWNLOAD=no
+while getopts "Ddsih" OPTION
+do
+     case "$OPTION" in
+         D) ALWAYSDOWNLOAD=yes; DOWNLOAD=yes;;
+         d) DOWNLOAD=yes;;
+         s) SAVE=yes;;
+         i) CONFVERSION=$(( CONFVERSION + 1 ));;
+         h) usage; exit 0;;
+         ?) usage; exit 2;;
+     esac
+done
+CONFBALL="upstream/configure-$CONFVERSION.tar.gz"
+
+if [ $DOWNLOAD$SAVE = yesyes ]; then
+    echo >&2 "$0: refusing to download and save."
+    usage
+    exit 2
+fi
+
+# Start cleanly (it's not a problem if this fails)
+$MAKE bootstrap-clean 2>/dev/null
+mkdir config 2>/dev/null
+
+if [ $ALWAYSDOWNLOAD = yes ]; then
+    bootstrap-download || exit $?
+else
+    bootstrap
+fi
+
+if [ $SAVE = yes ]; then
+    save
+fi

build/Makefile-auto.am

@@ -0,0 +1,2 @@
+# Currently, this file is unused. However, it needs to exist to coerce
+# automake into thinking that this is an Automake project.