Merge branch 'develop' into t/12962/implement_multi_function_plotting…

…_options_in_plot__

* develop: (282 commits)
  Updated Sage version to 6.8.rc0
  Fix remaining occurence of old path in sage-spkg
  Trac #18907: mention sage -pip in sage -advanced
  18896: add logic for given domain; fix failing doctests
  Add change to linking options on OS X so that using g++ instead of ld doesn't turn libsingular.dylib into an executable but still generate a library.
  18896: handle relations of algebraic expressions
  Fix PARI with Perl 5.22
  Move sage-spkg to build/bin
  Fix paths in documentation and comments
  Move README inside sage_bootstrap directory
  needs CXXFLAGS="-DNTL_STD_CXX ..." now
  Reorganize /build
  add Singular patch
  trac 18891: fix a typo in build/deps
  giacpy 0.5.1 (remove __init__.py in build dir + clean in setup.py)
  giacpy 0.5.0p1 fix in setup.py
  trac 18748: add URL for tox to sage_bootstrap/README
  Fix Python 2.6 test error
  Make package.tarball a Tarball instance
  Convert public attributes to properties and document
  ...

.gitignore

@@ -15,8 +15,6 @@
 /config.log
 /config.status
 /configure
-/build/Makefile-auto
-/build/Makefile-auto.in
 
 ###################
 # Temporary Files #

Makefile

@@ -11,12 +11,12 @@ default: all
 
 build: all-build
 
-# Defer unknown targets to build/Makefile
+# Defer unknown targets to build/make/Makefile
 %::
 	$(MAKE) configure logs
-	+cd build && ./pipestatus \
+	+cd build/make && ./pipestatus \
 		"./install '$@' 2>&1" \
-		"tee -a ../logs/install.log"
+		"tee -a ../../logs/install.log"
 
 logs:
 	mkdir -p $@
@@ -42,7 +42,7 @@ misc-clean:
 	rm -rf tmp
 	rm -f aclocal.m4 config.log config.status confcache
 	rm -rf autom4te.cache
-	rm -f build/Makefile build/Makefile-auto
+	rm -f build/make/Makefile build/make/Makefile-auto
 	rm -f .BUILDSTART
 
 bdist-clean: clean
@@ -56,7 +56,7 @@ distclean: build-clean
 # Delete all auto-generated files which are distributed as part of the
 # source tarball
 bootstrap-clean:
-	rm -rf config configure build/Makefile-auto.in
+	rm -rf config configure build/make/Makefile-auto.in
 
 # Remove absolutely everything which isn't part of the git repo
 maintainer-clean: distclean bootstrap-clean

VERSION.txt

@@ -1 +1 @@
-Sage version 6.8.beta7, released 2015-07-02
+Sage version 6.8.rc0, released 2015-07-15

bootstrap

@@ -27,7 +27,7 @@ CONFVERSION=`cat $PKG/package-version.txt`
 
 bootstrap () {
     aclocal -I m4 && \
-    automake --add-missing --copy build/Makefile-auto && \
+    automake --add-missing --copy build/make/Makefile-auto && \
     autoconf
 
     st=$?
@@ -75,7 +75,7 @@ save () {
     # Create configure tarball
     echo "Creating $CONFBALL..."
     mkdir -p upstream
-    tar zcf "$CONFBALL" configure config/* build/Makefile-auto.in
+    tar zcf "$CONFBALL" configure config/* build/make/Makefile-auto.in
 
     # Update version number
     echo "$CONFVERSION" >$PKG/package-version.txt

build/.gitignore

@@ -1 +1,2 @@
-/Makefile
+/.tox
+/MANIFEST

build/bin/sage-download-file

@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+
+# USAGE:
+#
+#     sage-download-file --print-fastest-mirror
+#
+# Print out the fastest mirror. All further arguments are ignored in
+# that case.
+#
+#     sage-download-file [--quiet] url-or-tarball [destination]
+#
+# The single mandatory argument can be a http:// url or a tarball
+# filename. In the latter case, the tarball is downloaded from the
+# mirror network and its checksum is verified.
+#
+# If the destination is not specified:
+# * a url will be downloaded and the content written to stdout
+# * a tarball will be saved under {SAGE_DISTFILES}
+
+try:
+    import sage_bootstrap
+except ImportError:
+    import os, sys
+    sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
+    import sage_bootstrap
+
+from sage_bootstrap.cmdline import SageDownloadFileApplication
+SageDownloadFileApplication().run()

build/bin/sage-package

@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+
+# Script to manage third-party tarballs.
+#
+# Usage:
+#
+# * Print the configuration
+#
+#   $ sage-package config
+#   Configuration:
+#     * log = info
+#     * interactive = True
+#
+# * Print a list of all available packages
+#
+#   $ sage-package list | sort
+#   4ti2
+#   arb
+#   atlas
+#   autotools
+#   [...]
+#   zn_poly
+#
+# * Find the package name given a tarball filename
+#
+#   $ sage-package name pari-2.8-1564-gdeac36e.tar.gz
+#   pari
+#
+# * Find the tarball filename given a package name
+#
+#   $ sage-package tarball pari
+#   pari-2.8-1564-gdeac36e.tar.gz
+
+try:
+    import sage_bootstrap
+except ImportError:
+    import os, sys
+    sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
+    import sage_bootstrap
+
+from sage_bootstrap.cmdline import SagePkgApplication
+SagePkgApplication().run()

src/bin/sage-spkg → build/bin/sage-spkg

@@ -106,10 +106,10 @@ fi
 # The following sets environment variables for building packages.
 # Since this is sourced, it returns a non-zero value on errors rather
 # than exiting.  Using dot suggested by W. Cheung.
-. "${0%spkg}env"
+. sage-env
 
 if [ $? -ne 0 ]; then
-    echo >&2 "Error setting environment variables by sourcing '$SAGE_ROOT/spkg/bin/sage-env';"
+    echo >&2 "Error setting environment variables by sourcing sage-env."
     echo >&2 "possibly contact sage-devel (see http://groups.google.com/group/sage-devel)."
     exit 1
 fi
@@ -310,10 +310,7 @@ fi
 if [ ! -f "$PKG_SRC" ]; then
     if [ -n "$PKG_NAME_UPSTREAM" ]; then
         # This is the new-style package way of downloading the tarball
-        sage-download-file $PKG_NAME_UPSTREAM
-        if [ $? -ne 0 ]; then
-            exit 1
-        fi
+        sage-download-file $PKG_NAME_UPSTREAM || exit $?
         PKG_SRC="$SAGE_DISTFILES/$PKG_NAME_UPSTREAM"
     else
         # Handle all the legacy cruft. This branch can be deleted once
@@ -323,7 +320,7 @@ if [ ! -f "$PKG_SRC" ]; then
         else
             echo "Attempting to get on-line info for package $PKG_NAME"
         fi
-        
+
         # Reduce everything to case 4: full URL.
         if [ -n "$PKG_HAS_PATH" ]; then
             PKG_URL="$PKG_SRC"
@@ -341,7 +338,6 @@ if [ ! -f "$PKG_SRC" ]; then
                 repolist="${DOT_SAGE}/${repo}.list"
                 sage-download-file --quiet "$MIRROR/$repo/list" $repolist
                 if [ $? -ne 0 ]; then
-                    echo >&2 "Error: failed to download $MIRROR/$repo/list, aborting"
                     rm -f $repolist
                     exit 1
                 fi
@@ -401,7 +397,7 @@ if [ ! -f "$PKG_SRC" ]; then
                 echo >&2 "Error: could not find a package matching $PKG_NAME on $MIRROR"
                 exit 1
             fi
-    
+
             # Check a second time whether the package is already installed.
             if [ $INFO -eq 0 -a $FORCE -eq 0 -a -f "$SAGE_SPKG_INST/$PKG_NAME" ]; then
                 echo "Package $PKG_NAME is already installed."
@@ -411,15 +407,15 @@ if [ ! -f "$PKG_SRC" ]; then
                 exit 0
             fi
         fi
-    
+
         # Trac #5852: check write permissions
         mkdir -p "$SAGE_DISTFILES"
         if [ ! -w "$SAGE_DISTFILES" ]; then
             echo >&2 "Error: no write access to packages directory $SAGE_PACKAGES."
             exit 1
         fi
         cd "$SAGE_DISTFILES" || exit $?
-    
+
         # Download to a temporary file (such that we don't end up with a
         # corrupted .spkg file).
         PKG_TMP="${PKG_URL##*/}.tmp"
@@ -428,10 +424,9 @@ if [ ! -f "$PKG_SRC" ]; then
         if [ $? -ne 0 ]; then
             # Delete failed download
             rm -f "$PKG_TMP"
-            echo >&2 "Error: failed to download package $PKG_NAME"
             exit 1
         fi
-    
+
         PKG_SRC="`pwd`/${PKG_URL##*/}"
         mv -f "$PKG_TMP" "$PKG_SRC"
     fi

build/make/.gitignore

@@ -0,0 +1,3 @@
+/Makefile
+/Makefile-auto
+/Makefile-auto.in

build/deps → build/make/deps

@@ -1,11 +1,11 @@
 ###############################################################################
-# This file ($SAGE_ROOT/build/deps) will be copied into
-# $SAGE_ROOT/build/Makefile by $SAGE_ROOT/build/install
+# This file ($SAGE_ROOT/build/make/deps) will be copied into
+# $SAGE_ROOT/build/make/Makefile by $SAGE_ROOT/build/make/install
 ###############################################################################
 
 # Do not put an explicit path for sage-spkg here, it will be found in $PATH.
 SAGE_SPKG = sage-spkg -f
-PIPE = $(SAGE_ROOT)/build/pipestatus
+PIPE = $(SAGE_ROOT)/build/make/pipestatus
 STARTED = $(SAGE_LOCAL)/etc/sage-started.txt
 
 # Tell make not to look for files with these names:
@@ -46,7 +46,7 @@ all-sage: \
 		$(EXTCODE) \
 		$(SCRIPTS)
 
-# TOOLCHAIN consists of dependencies determined by build/install,
+# TOOLCHAIN consists of dependencies determined by build/make/install,
 # including for example the GCC package.
 toolchain: $(TOOLCHAIN)
 
@@ -76,7 +76,7 @@ start: all-build
 # We make this depend on all standard packages because running
 # sage-starts runs sage-location, which should be run after installing
 # any package.
-$(STARTED): $(STANDARD_PACKES)
+$(STARTED): $(STANDARD_PACKAGES)
 	"$(SAGE_LOCAL)/bin/sage-starts"
 
 
@@ -87,8 +87,8 @@ $(STARTED): $(STANDARD_PACKES)
 ###############################################################################
 base: $(INST)/$(BZIP2) $(INST)/$(PATCH) $(INST)/$(PKGCONF)
 
-$(INST)/prereq: ../configure
-	@cd ..; rm -f config.log; ln -s logs/pkgs/config.log config.log; \
+$(INST)/prereq: ../../configure
+	@cd ../..; rm -f config.log; ln -s logs/pkgs/config.log config.log; \
 	./configure $$PREREQ_OPTIONS || ( \
 		if [ "x$$SAGE_PORT" = x ]; then \
 			echo "If you would like to try to build Sage anyway (to help porting),"; \
@@ -192,28 +192,29 @@ $(SAGE_EXTCODE)/%: $(SAGE_SRC)/ext/%
 # produce plots.
 DOC_DEPENDENCIES = sagelib $(INST)/$(SPHINX) $(INST)/$(SAGENB) \
 	| $(SAGERUNTIME) $(INST)/$(MAXIMA) $(INST)/$(NETWORKX) \
-	$(INST)/$(SCIPY) $(INST)/$(MATPLOTLIB) $(INST)/$(PILLOW)
+	$(INST)/$(SCIPY) $(INST)/$(MATPLOTLIB) $(INST)/$(PILLOW) \
+	$(INST)/$(MATHJAX)
 
 doc: doc-html
 
 doc-html: $(DOC_DEPENDENCIES)
-	cd .. && $(PIPE) "./sage --docbuild --no-pdf-links all html $(SAGE_DOCBUILD_OPTS) 2>&1" "tee -a logs/dochtml.log"
+	cd ../.. && $(PIPE) "./sage --docbuild --no-pdf-links all html $(SAGE_DOCBUILD_OPTS) 2>&1" "tee -a logs/dochtml.log"
 
 # 'doc-html-no-plot': build docs without building the graphics coming
 # from the '.. plot' directive, in case you want to save a few
 # megabytes of disk space. 'doc-clean' is a prerequisite because the
 # presence of graphics is cached in src/doc/output.
 doc-html-no-plot: doc-clean $(DOC_DEPENDENCIES)
-	cd .. && $(PIPE) "./sage --docbuild --no-pdf-links --no-plot all html $(SAGE_DOCBUILD_OPTS) 2>&1" "tee -a logs/dochtml.log"
+	cd ../.. && $(PIPE) "./sage --docbuild --no-pdf-links --no-plot all html $(SAGE_DOCBUILD_OPTS) 2>&1" "tee -a logs/dochtml.log"
 
 doc-html-mathjax: $(DOC_DEPENDENCIES)
-	cd .. && $(PIPE) "./sage --docbuild --no-pdf-links all html -j $(SAGE_DOCBUILD_OPTS) 2>&1" "tee -a logs/dochtml.log"
+	cd ../.. && $(PIPE) "./sage --docbuild --no-pdf-links all html -j $(SAGE_DOCBUILD_OPTS) 2>&1" "tee -a logs/dochtml.log"
 
 # Keep target 'doc-html-jsmath' for backwards compatibility.
 doc-html-jsmath: doc-html-mathjax
 
 doc-pdf: $(DOC_DEPENDENCIES)
-	cd .. && $(PIPE) "./sage --docbuild all pdf $(SAGE_DOCBUILD_OPTS) 2>&1" "tee -a logs/docpdf.log"
+	cd ../.. && $(PIPE) "./sage --docbuild all pdf $(SAGE_DOCBUILD_OPTS) 2>&1" "tee -a logs/docpdf.log"
 
 doc-clean:
 	cd "$(SAGE_SRC)/doc" && $(MAKE) clean