Merge branch 'develop' into public/ticket/15018

* develop: (467 commits)
  Updated Sage version to 6.1.beta5
  Don't use "missing"
  trac 15265: various changes, finishing review.
  allow disabling of maintainer mode
  trac 15265: Additional change to farey.cpp.
  trac 15265: Minor changes to farey_symbol.pyx
  trac 15265: Minor changes to sl2z.cpp and sl2z.hpp.
  trac 15265: Minor changes to farey.cpp and farey.hpp.
  Run "missing" using bash
  fix tarball url
  trac 15265: Add some further examples and one test to _acton_ of elements of arithmetic groups.
  Source sage-env inside configure
  Improved Karatsuba: more thorough tests
  bootstrap configure: small fixes
  make saving of the confball optional in bootstrap
  fix typos in SPKG.txt
  also commit changes to confball in sage-update-version
  add a SPKG.txt file
  rename to bootstrap, run during version bump
  trac 15265: correct mistakes done while converting to git branch.
  ...

.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

@@ -9,6 +9,7 @@
 
 PIPE = build/pipestatus
 
+
 all: start doc  # indirectly depends on build
 
 logs:
@@ -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 +152,16 @@ ptestoptional: ptestall # just an alias
 
 ptestoptionallong: ptestalllong # just an alias
 
+bootstrap:
+	$(MAKE) configure || \
+		bash -c 'source src/bin/sage-env; sage-download-file $$SAGE_UPSTREAM/configure/configure-`cat build/pkgs/configure/package-version.txt`.tar.gz | tar zxmf -'
+
+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
+	test -d config || mkdir config
+	aclocal -I m4
+	automake --add-missing --copy build/Makefile-auto
+	autoconf
 
 install:
 	echo "Experimental use only!"
@@ -160,8 +182,8 @@ install:
 	"$(DESTDIR)"/bin/sage -c # Run sage-location
 
 
-.PHONY: all build build-serial start install \
+.PHONY: all build build-serial start install micro_release bootstrap \
 	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.beta0, released 2013-12-19
+Sage version 6.1.beta5, released 2014-01-15

bootstrap

@@ -0,0 +1,79 @@
+#!/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
+########################################################################
+
+set -e
+
+# 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 () {
+    # Start cleanly
+    $MAKE bootstrap-clean
+
+    # Generate auto-generated files
+    $MAKE configure
+}
+
+
+save () {
+    # Create configure tarball
+    CONFBALL="upstream/configure-$CONFVERSION.tar.gz"
+    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
+    src/bin/sage-fix-pkg-checksums "$CONFBALL"
+}
+
+
+usage () {
+    echo >&2 "Usage: bootstrap [-i] [-s] [-h]"
+}
+
+
+# Parse options
+SAVE=
+while getopts "sih" OPTION
+do
+     case "$OPTION" in
+         s)
+             SAVE=yes
+             ;;
+         i)
+             CONFVERSION=$(( CONFVERSION + 1 ))
+             ;;
+         h)
+             usage
+             exit
+             ;;
+         ?)
+             usage
+             exit 2
+             ;;
+     esac
+done
+
+bootstrap
+if [ -n "$SAVE" ]; 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.

build/deps

@@ -80,7 +80,7 @@ all-sage: \
      $(INST)/$(PALP) \
      $(INST)/$(PARI) \
      $(INST)/$(PEXPECT) \
-     $(INST)/$(PIL) \
+     $(INST)/$(PILLOW) \
      $(INST)/$(POLYBORI) \
      $(INST)/$(POLYTOPES_DB) \
      $(INST)/$(PPL) \
@@ -109,10 +109,10 @@ all-sage: \
      $(INST)/$(NCURSES) \
      $(INST)/$(ZLIB) \
      $(INST)/$(ZNPOLY) \
-     scripts \
-     sage \
-     csage \
-     extcode
+     $(INST)/sage \
+     $(INST)/csage \
+     $(EXTCODE) \
+     $(SCRIPTS)
 
 # TOOLCHAIN consists of dependencies determined by build/install,
 # including for example the GCC package.
@@ -133,7 +133,7 @@ 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 sage $(INST)/$(SAGENB) $(INST)/$(IPYTHON) $(INST)/$(GAP)
+SAGERUNTIME = $(SCRIPTS) $(INST)/sage $(INST)/$(SAGENB) $(INST)/$(IPYTHON)
 
 ###############################################################################
 # Building the base system
@@ -143,12 +143,13 @@ SAGERUNTIME = scripts sage $(INST)/$(SAGENB) $(INST)/$(IPYTHON) $(INST)/$(GAP)
 # an update of these packages will not trigger a rebuild of every other
 # package during an upgrade, see #13415.
 ###############################################################################
-base: $(INST)/$(PREREQ) $(INST)/$(BZIP2) $(INST)/$(PATCH)
+base: $(INST)/prereq $(INST)/$(BZIP2) $(INST)/$(PATCH)
 
-$(INST)/$(PREREQ):
-	$(PIPE) "base/$(PREREQ)-install 2>&1" "tee -a $(SAGE_LOGS)/$(PREREQ).log"
+$(INST)/prereq: prereq.sh
+	$(PIPE) "./prereq.sh 2>&1" "tee -a $(SAGE_LOGS)/prereq.log"
+	touch $@
 
-$(INST)/$(BZIP2): $(INST)/$(PREREQ)
+$(INST)/$(BZIP2): $(INST)/prereq
 	+$(PIPE) "$(SAGE_SPKG) $(BZIP2) 2>&1" "tee -a $(SAGE_LOGS)/$(BZIP2).log"
 
 $(INST)/$(PATCH): $(INST)/$(BZIP2)
@@ -308,10 +309,10 @@ $(INST)/$(SQLITE): $(INST)/$(READLINE)
 	+$(PIPE) "$(SAGE_SPKG) $(SQLITE) 2>&1" "tee -a $(SAGE_LOGS)/$(SQLITE).log"
 
 # To build SageTeX, you just need Python, but to test (SAGE_CHECK=yes)
-# SageTeX, you actually need to run sage, produce plots,...
+# SageTeX, you actually need to run Sage, produce plots,...
 $(INST)/$(SAGETEX): $(INST)/$(PYTHON) \
                     $(SAGERUNTIME) $(INST)/$(MAXIMA) $(INST)/$(SCIPY) \
-                    $(INST)/$(MATPLOTLIB) $(INST)/$(PIL) $(INST)/$(TACHYON)
+                    $(INST)/$(MATPLOTLIB) $(INST)/$(PILLOW) $(INST)/$(TACHYON)
 	+$(PIPE) "$(SAGE_SPKG) $(SAGETEX) 2>&1" "tee -a $(SAGE_LOGS)/$(SAGETEX).log"
 
 $(INST)/$(SETUPTOOLS): $(INST)/$(PYTHON)
@@ -336,7 +337,7 @@ $(INST)/$(ZLIB):
 $(INST)/$(JMOL): $(INST)/$(SAGENB)
 	+$(PIPE) "$(SAGE_SPKG) $(JMOL) 2>&1" "tee -a $(SAGE_LOGS)/$(JMOL).log"
 
-$(INST)/$(FREETYPE):
+$(INST)/$(FREETYPE): $(INST)/$(LIBPNG)
 	+$(PIPE) "$(SAGE_SPKG) $(FREETYPE) 2>&1" "tee -a $(SAGE_LOGS)/$(FREETYPE).log"
 
 $(INST)/$(LIBPNG): $(INST)/$(ZLIB)
@@ -418,7 +419,7 @@ $(INST)/$(PYGMENTS): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
 # on the one hand, programs needed for the build/install process of the
 # Sage library (e.g. JINJA2), and on the
 # other hand all dependencies for Cython files (e.g. PARI, NTL, MPIR).
-sage: \
+$(INST)/sage: \
 		 $(INST)/$(ATLAS) \
 		 $(INST)/$(CEPHES) \
 		 $(INST)/$(CLIQUER) \
@@ -456,21 +457,25 @@ sage: \
 		 $(INST)/$(SINGULAR) \
 		 $(INST)/$(SYMMETRICA) \
 		 $(INST)/$(ZNPOLY) \
-		 csage
-	$(PIPE) '{ if [ -z "$(SAGE_INSTALL_FETCH_ONLY)" ]; then cd $(SAGE_SRC) && . ./bin/sage-env && time python setup.py install; fi; } 2>&1' 'tee -a $(SAGE_LOGS)/sage-$(SAGE_VERSION).log'
-
-scripts: $(SCRIPT_TARGETS)
-
-extcode: $(EXTCODE_TARGETS)
-
-csage: $(INST)/$(SCONS) \
+		 $(INST)/csage
+	if [ -z "$$SAGE_INSTALL_FETCH_ONLY" ]; then \
+		cd $(SAGE_SRC) && source bin/sage-env && \
+		$(PIPE) 'time python setup.py install 2>&1' 'tee -a $(SAGE_LOGS)/sage-$(SAGE_VERSION).log' && \
+		touch $@; \
+	fi
+
+$(INST)/csage: $(INST)/$(SCONS) \
        $(INST)/$(MPIR) \
        $(INST)/$(NTL) \
        $(INST)/$(PARI) \
        $(INST)/$(POLYBORI) \
        $(INST)/$(PYNAC) \
        $(INST)/$(PYTHON)
-	$(PIPE) '{ if [ -z "$(SAGE_INSTALL_FETCH_ONLY)" ]; then cd $(SAGE_SRC)/c_lib && . ../bin/sage-env && time scons -Q install; fi; } 2>&1' 'tee -a $(SAGE_LOGS)/csage-$(SAGE_VERSION).log'
+	if [ -z "$$SAGE_INSTALL_FETCH_ONLY" ]; then \
+		cd $(SAGE_SRC) && source bin/sage-env && cd c_lib && \
+		$(PIPE) 'time scons -Q install 2>&1' 'tee -a $(SAGE_LOGS)/csage-$(SAGE_VERSION).log' && \
+		touch $@; \
+	fi
 
 $(INST)/ccache: $(BASE) $(INST)/$(ZLIB)
 	+$(PIPE) "$(SAGE_SPKG) ccache 2>&1" "tee -a $(SAGE_LOGS)/ccache.log"
@@ -480,8 +485,8 @@ $(INST)/$(GCC): $(INST)/$(MPIR) $(INST)/$(MPFR) $(INST)/$(MPC) \
                 $(INST)/$(ZLIB)
 	+$(PIPE) "$(SAGE_SPKG) $(GCC) 2>&1" "tee -a $(SAGE_LOGS)/$(GCC).log"
 
-$(INST)/$(PIL): $(INST)/$(PYTHON)
-	+$(PIPE) "$(SAGE_SPKG) $(PIL) 2>&1" "tee -a $(SAGE_LOGS)/$(PIL).log"
+$(INST)/$(PILLOW): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
+	+$(PIPE) "$(SAGE_SPKG) $(PILLOW) 2>&1" "tee -a $(SAGE_LOGS)/$(PILLOW).log"
 
 $(INST)/$(NUMPY): $(INST)/$(PYTHON) $(INST)/$(ATLAS)
 	+$(PIPE) "$(SAGE_SPKG) $(NUMPY) 2>&1" "tee -a $(SAGE_LOGS)/$(NUMPY).log"
@@ -503,6 +508,7 @@ $(INST)/$(CEPHES):
 # setuptools forgets to update easy-install.pth during parallel
 # builds, so we build the relevant packages serially.
 
+$(INST)/$(SQLALCHEMY): $(INST)/$(PILLOW)
 $(INST)/$(PYGMENTS): $(INST)/$(SQLALCHEMY)
 $(INST)/$(JINJA2): $(INST)/$(PYGMENTS)
 $(INST)/$(SPHINX): $(INST)/$(JINJA2)