Merge branch 't/17715/asy/asymptoticTerm' into t/17716/asy/asymptotic…

…Expression

* t/17715/asy/asymptoticTerm: (2391 commits)
  add asymptotic_expansions index
  Updated Sage version to 6.9.beta5
  Trac 19906: reviewer comments
  Trac #19006: transcendental function of polynomials
  Trac #19006: more flint declarations
  Trac 19005: two * current -> current + current
  Trac 19005: on -> over
  Trac 19005: check that prec is positive
  19005: inverse_series -> inverse_series_trunc
  Trac 19005: a SEEALSO block
  Trac 19005: fix a doctest
  Trac 19005: inverse_series over noncommutative rings
  Trac 19005: is_unit for matrices
  fix doc mis-formatting in Singleton category
  Organize a few parts of the reference manual
  doc: Easier to distinguish heading levels
  trac #19090: unify documentation
  trac #19090: Fix doc (links + latex formatting)
  trac #19109: Tastes and colors ...
  trac #19109: Broken doctest
  ...

.gitignore

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

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

@@ -7,20 +7,15 @@
 # See below for targets to build the documentation in other formats,
 # to run various types of test suites, and to remove parts of the build etc.
 
-PIPE = build/pipestatus
+default: all
 
+build: all-build
 
-all: start doc  # indirectly depends on build
-
-logs:
-	mkdir -p $@
-
-build: logs configure
-	+cd build && \
-	"../$(PIPE)" \
-		"env SAGE_PARALLEL_SPKG_BUILD='$(SAGE_PARALLEL_SPKG_BUILD)' ./install all 2>&1" \
-		"tee -a ../logs/install.log"
-	+./sage -b
+# Defer unknown targets to build/make/Makefile
+%::
+	$(MAKE) configure
+	+build/bin/sage-logger \
+		"cd build/make && ./install '$@'" logs/install.log
 
 # Preemptively download all standard upstream source tarballs.
 download:
@@ -36,73 +31,28 @@ 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
-	[ -f local/etc/sage-started.txt ] || local/bin/sage-starts
-
-# You can choose to have the built HTML version of the documentation link to
-# the PDF version. To do so, you need to build both the HTML and PDF versions.
-# To have the HTML version link to the PDF version, do
-#
-# $ ./sage --docbuild all html
-# $ ./sage --docbuild all pdf
-#
-# For more information on the docbuild utility, do
-#
-# $ ./sage --docbuild -H
-doc: doc-html
-
-doc-html: build
-	$(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: build doc-clean
-	$(PIPE) "./sage --docbuild --no-pdf-links --no-plot all html $(SAGE_DOCBUILD_OPTS) 2>&1" "tee -a logs/dochtml.log"
-
-doc-html-mathjax: build
-	$(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: build
-	$(PIPE) "./sage --docbuild all pdf $(SAGE_DOCBUILD_OPTS) 2>&1" "tee -a logs/docpdf.log"
-
-doc-clean:
-	cd src/doc && $(MAKE) clean
-
-clean:
-	@echo "Deleting package build directories..."
-	rm -rf local/var/tmp/sage/build
-
-lib-clean:
-	cd src && $(MAKE) clean
-
-bdist-clean: clean
+misc-clean:
 	@echo "Deleting miscellaneous artifacts generated by build system ..."
 	rm -rf logs
 	rm -rf dist
 	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
 
-distclean: clean doc-clean lib-clean bdist-clean
+bdist-clean: clean
+	$(MAKE) misc-clean
+
+distclean: build-clean
+	$(MAKE) misc-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
+	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
@@ -112,42 +62,33 @@ 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
 
 
@@ -182,8 +123,7 @@ install:
 	"$(DESTDIR)"/bin/sage -c # Run sage-location
 
 
-.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 bootstrap-clean maintainer-clean \
+.PHONY: default build install micro_release \
+	misc-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 6.7, released 2015-05-17
+Sage version 6.9.beta5, released 2015-09-04

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-logger

@@ -0,0 +1,40 @@
+#!/usr/bin/env bash
+#
+# sage-logger COMMAND LOGFILE
+#
+# Evaluate shell command COMMAND while logging stdout and stderr to
+# LOGFILE. If either the command or the logging failed, return a
+# non-zero exit status.
+#
+# AUTHOR:
+#
+# - Jeroen Demeyer (2015-07-26): initial version based on old pipestatus
+#   script (#18953)
+#
+#*****************************************************************************
+#       Copyright (C) 2015 Jeroen Demeyer <jdemeyer@cage.ugent.be>
+#
+#  Distributed under the terms of the GNU General Public License (GPL)
+#  as published by the Free Software Foundation; either version 2 of
+#  the License, or (at your option) any later version.
+#                  http://www.gnu.org/licenses/
+#*****************************************************************************
+
+cmd="$1"
+logfile="$2"
+logdir=`dirname "$logfile"`
+
+mkdir -p "$logdir"
+
+# Redirect stdout and stderr to a subprocess running tee.
+# We trap SIGINT such that SIGINT interrupts the main process being
+# run, not the logging.
+( exec 2>&1; eval "$cmd" ) | ( trap '' SIGINT; tee -a "$logfile" )
+
+pipestatus=(${PIPESTATUS[*]})
+
+if [ ${pipestatus[1]} -ne 0 ]; then
+    exit ${pipestatus[1]}
+else
+    exit ${pipestatus[0]}
+fi

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()