Merge branch 'develop' into t/17790/builtinfunction_doesn_t_pass_non_…

…sr_coercible_arguments_to_function_code

.gitignore

@@ -14,8 +14,6 @@
 /config.log
 /config.status
 /configure
-/build/Makefile-auto
-/build/Makefile-auto.in
 
 ###################
 # Temporary Files #
@@ -70,3 +68,16 @@ $RECYCLE.BIN/
 
 # SublimeText
 *.sublime-workspace
+
+#################
+# SageMathCloud #
+#################
+*.sage-chat
+*.sage-history
+*.syncdoc*
+
+###########
+# Jupyter #
+###########
+.ipynb_checkpoints
+Untitled*.ipynb

COPYING.txt

@@ -28,6 +28,7 @@ the licenses of the components of Sage are included below as well.
 
 SOFTWARE                    LICENSE
 -----------------------------------------------------------------------
+arb                         GPLv2+
 atlas                       Modified BSD
 boehm_gc                    MIT-like license (see below)
 backports_ssl_match_hostname  Python License
@@ -54,7 +55,6 @@ freetype                    FreeType License (similar to BSD; see below)
 gap                         GPLv2+
 gcc                         GPLv3+
 gd                          Custom (BSD-ish)
-gdmodule                    Custom (BSD-ish)
 genus2reduction             GPLv2+
 gfan                        GPLv2 or GPLv3
 gf2x                        GPLv2+
@@ -67,6 +67,7 @@ iml                         COPYING is GPLv2, source files state modified BSD
 ipython                     Modified BSD
 jinja2                      Modified BSD
 jmol                        LGPLv2.1+
+jsonschema                  MIT License
 lcalc                       GPLv2+
 libfplll                    LGPLv2.1+
 libgap                      GPLv3+
@@ -75,8 +76,11 @@ linbox                      LGPLv2.1+
 lrcalc                      GPLv2+
 m4ri                        GPLv2+
 m4rie                       GPLv2+
+markupsafe                  Simplified BSD
+mathjax                     Apache License 2.0
 matplotlib                  Matplotlib License (BSD compatible, see below)
 maxima                      See below
+mistune                     Modified BSD
 mpc                         LGPLv3+
 mpfi                        COPYING is GPLv2, source files state LGPLv2.1+
 mpfr                        LGPLv3+
@@ -85,6 +89,7 @@ mpmath                      Modified BSD
 networkx                    Modified BSD
 ntl                         GPLv2+
 numpy                       Modified BSD
+openblas                    Modified BSD
 palp                        GPLv3
 pari                        GPLv2+
 patch                       GPLv2+
@@ -93,6 +98,7 @@ 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+
@@ -125,6 +131,7 @@ sympow                      Modified BSD
 sympy                       Modified BSD
 tachyon                     Modified BSD
 termcap                     GPLv2+
+threejs                     MIT License
 tornado                     Apache License
 zlib                        Custom (Modified BSD)
 zn_poly                     GPLv2 or GPLv3 (no later versions, see below)
@@ -945,19 +952,6 @@ documentation.
 
 ================================================================================
 
-gdmodule:
-(http://newcenturycomputers.net/projects/gdmodule.html)
-
-Permission granted for unlimited use, provided that the Quest Center
-at Cold Spring Harbor Labs is given credit for the library in the
-user-visible documentation of your software. If you modify gd, we ask
-that you share the modifications with us so they can be added to the
-distribution. See gd.html for details.  (The rest of the notice is in
-the package gdmodule spkg, which is a bzip2'd tarball included in the
-Sage source distribution.)
-
-================================================================================
-
 genus2reduction:
 (http://www.math.u-bordeaux.fr/~liu/G2R/)
 Copyright Qing LIU. See PARI for the license terms.

Makefile

@@ -7,27 +7,45 @@
 # 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
-
-
-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
+default: all
+
+build: all-build
+
+# Defer unknown targets to build/make/Makefile
+%::
+	@if [ -x relocate-once.py ]; then ./relocate-once.py; fi
+	$(MAKE) build/make/Makefile
+	+build/bin/sage-logger \
+		"cd build/make && ./install '$@'" logs/install.log
+
+# If configure was run before, rerun it with the old arguments.
+# Otherwise, run configure with argument $PREREQ_OPTIONS.
+build/make/Makefile: configure build/make/deps build/pkgs/*/*
+	rm -f config.log
+	mkdir -p logs/pkgs
+	ln -s logs/pkgs/config.log config.log
+	@if [ -x config.status ]; then \
+		./config.status --recheck && ./config.status; \
+	else \
+		./configure $$PREREQ_OPTIONS; \
+	fi || ( \
+		if [ "x$$SAGE_PORT" = x ]; then \
+			echo "If you would like to try to build Sage anyway (to help porting),"; \
+			echo "export the variable 'SAGE_PORT' to something non-empty."; \
+			exit 1; \
+		else \
+			echo "Since 'SAGE_PORT' is set, we will try to build anyway."; \
+		fi; )
 
 # Preemptively download all standard upstream source tarballs.
 download:
 	export SAGE_ROOT=$$(pwd) && \
 	export PATH=$$SAGE_ROOT/src/bin:$$PATH && \
 	./src/bin/sage-download-upstream
 
+dist: build/make/Makefile
+	./sage --sdist
+
 # ssl: build Sage, and also install pyOpenSSL. This is necessary for
 # running the secure notebook. This make target requires internet
 # access. Note that this requires that your system have OpenSSL
@@ -36,154 +54,91 @@ 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
 	rm -rf upstream
 
-micro_release: bdist-clean lib-clean
+micro_release: bdist-clean sagelib-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) --optional=all --logfile=logs/testall.log
+testall: all
+	$(TESTALL) --optional=sage,optional,external --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)
-	$(TESTALL) --long --optional=all --logfile=logs/testalllong.log
+testalllong: all
+	$(TESTALL) --long --optional=sage,optional,external --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) --optional=all --logfile=logs/ptestall.log
+ptestall: all
+	$(PTESTALL) --optional=sage,optional,external --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)
-	$(PTESTALL) --long --optional=all --logfile=logs/ptestalllong.log
+ptestalllong: all
+	$(PTESTALL) --long --optional=sage,optional,external --logfile=logs/ptestalllong.log
 
+testoptional: all
+	$(TESTALL) --optional=sage,optional --logfile=logs/testoptional.log
 
-testoptional: testall # just an alias
+testoptionallong: all
+	$(TESTALL) --long --optional=sage,optional --logfile=logs/testoptionallong.log
 
-testoptionallong: testalllong # just an alias
+ptestoptional: all
+	$(PTESTALL) --optional=sage,optional --logfile=logs/ptestoptional.log
 
-ptestoptional: ptestall # just an alias
+ptestoptionallong: all
+	$(PTESTALL) --long --optional=sage,optional --logfile=logs/ptestoptionallong.log
 
-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
+configure: configure.ac src/bin/sage-version.sh m4/*.m4
 	./bootstrap -d
 
 install:
-	echo "Experimental use only!"
-	if [ "$(DESTDIR)" = "" ]; then \
-		echo >&2 "Set the environment variable DESTDIR to the install path."; \
-		exit 1; \
-	fi
-	# Make sure we remove only an existing directory. If $(DESTDIR)/sage is
-	# a file instead of a directory then the mkdir statement later will fail
-	if [ -d "$(DESTDIR)"/sage ]; then \
-		rm -rf "$(DESTDIR)"/sage; \
-	fi
-	mkdir -p "$(DESTDIR)"/sage
-	mkdir -p "$(DESTDIR)"/bin
-	cp -Rp * "$(DESTDIR)"/sage
-	rm -f "$(DESTDIR)"/bin/sage
-	ln -s ../sage/sage "$(DESTDIR)"/bin/sage
-	"$(DESTDIR)"/bin/sage -c # Run sage-location
-
-
-.PHONY: all build build-serial start install micro_release \
-	doc doc-html doc-html-jsmath doc-html-mathjax doc-pdf \
-	doc-clean clean lib-clean bdist-clean distclean bootstrap-clean maintainer-clean \
+	@echo "******************************************************************"
+	@echo "The '$@' target is no longer supported:"
+	@echo "either build SageMath in-place or use the binary packaging scripts"
+	@echo "from https://github.com/sagemath/binary-pkg"
+	@echo "******************************************************************"
+	@exit 1
+
+
+.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