Merge branch 'develop' into t/20312/parent_of_argument_lost_with_func…

…tions

Makefile

@@ -43,6 +43,9 @@ download:
 	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
@@ -91,34 +94,37 @@ test: all
 check: test
 
 testall: all
-	$(TESTALL) --optional=all --logfile=logs/testall.log
+	$(TESTALL) --optional=sage,optional,external --logfile=logs/testall.log
 
 testlong: all
 	$(TESTALL) --long --logfile=logs/testlong.log
 
 testalllong: all
-	$(TESTALL) --long --optional=all --logfile=logs/testalllong.log
+	$(TESTALL) --long --optional=sage,optional,external --logfile=logs/testalllong.log
 
 ptest: all
 	$(PTESTALL) --logfile=logs/ptest.log
 
 ptestall: all
-	$(PTESTALL) --optional=all --logfile=logs/ptestall.log
+	$(PTESTALL) --optional=sage,optional,external --logfile=logs/ptestall.log
 
 ptestlong: all
 	$(PTESTALL) --long --logfile=logs/ptestlong.log
 
 ptestalllong: all
-	$(PTESTALL) --long --optional=all --logfile=logs/ptestalllong.log
-
+	$(PTESTALL) --long --optional=sage,optional,external --logfile=logs/ptestalllong.log
 
-testoptional: testall # just an alias
+testoptional: all
+	$(TESTALL) --optional=sage,optional --logfile=logs/testoptional.log
 
-testoptionallong: testalllong # just an alias
+testoptionallong: all
+	$(TESTALL) --long --optional=sage,optional --logfile=logs/testoptionallong.log
 
-ptestoptional: ptestall # just an alias
+ptestoptional: all
+	$(PTESTALL) --optional=sage,optional --logfile=logs/ptestoptional.log
 
-ptestoptionallong: ptestalllong # just an alias
+ptestoptionallong: all
+	$(PTESTALL) --long --optional=sage,optional --logfile=logs/ptestoptionallong.log
 
 configure: configure.ac src/bin/sage-version.sh m4/*.m4
 	./bootstrap -d

VERSION.txt

@@ -1 +1 @@
-SageMath version 7.2.beta5, Release Date: 2016-04-21
+SageMath version 7.2.rc0, Release Date: 2016-05-05

build/make/deps

@@ -50,7 +50,7 @@ all-sage: \
 # option to make forces all targets to be built unconditionally)
 download-for-sdist: base
 	env SAGE_INSTALL_FETCH_ONLY=yes $(MAKE) -B SAGERUNTIME= \
-		$(STANDARD_PACKAGES) gcc mpir python2
+		$(SDIST_PACKAGES)
 
 # TOOLCHAIN consists of dependencies determined by configure.
 # These are built after the "base" target but before anything else.
@@ -102,7 +102,7 @@ base: $(inst_bzip2) $(inst_patch) $(inst_pkgconf)
 # dependencies for Cython files (e.g. PARI, NTL, MP_LIBRARY).
 sagelib: \
 		$(inst_arb) \
-		$(inst_atlas) \
+		$(BLAS) \
 		$(inst_brial) \
 		$(inst_cephes) \
 		$(inst_cliquer) \

build/pkgs/alabaster/SPKG.txt

@@ -0,0 +1,13 @@
+= alabaster =
+
+== Description ==
+
+Alabaster is a visually (c)lean, responsive, configurable theme for the Sphinx
+documentation system. It is Python 2+3 compatible.
+
+It began as a third-party theme, and is still maintained separately, but as of
+Sphinx 1.3, Alabaster is an install-time dependency of Sphinx and is selected
+as the default theme.
+
+Live examples of this theme can be seen on paramiko.org, fabfile.org and
+pyinvoke.org.

build/pkgs/alabaster/checksums.ini

@@ -0,0 +1,4 @@
+tarball=alabaster-VERSION.tar.gz
+sha1=ff3e575ee7eb4ba1721f17d91ec5a54b16283603
+md5=957c665d7126dea8121f98038debcba7
+cksum=738605178

build/pkgs/alabaster/dependencies

@@ -0,0 +1,5 @@
+$(PYTHON) | pip
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

build/pkgs/alabaster/package-version.txt

@@ -0,0 +1 @@
+0.7.7

build/pkgs/alabaster/spkg-install

@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+
+cd src && python setup.py install

build/pkgs/alabaster/type

@@ -0,0 +1 @@
+standard

build/pkgs/brial/patches/build/cygwin-gnucpp.patch

@@ -0,0 +1,10 @@
+--- a/common.mk	2016-04-07 15:53:44.907758600 +0200
++++ b/common.mk	2016-04-07 15:54:02.599770500 +0200
+@@ -3,6 +3,6 @@
+ 	-I$(top_srcdir)/libpolybori/include
+
+ AM_CFLAGS = -std=c99
+-AM_CXXFLAGS = -std=c++98 -ftemplate-depth-100
++AM_CXXFLAGS = -std=gnu++98 -ftemplate-depth-100
+
+ AM_DEFAULT_SOURCE_EXT = .cc

build/pkgs/brial/patches/cygwin-gnucpp.patch

@@ -0,0 +1,51 @@
+diff --git a/Cudd/cudd/Makefile.in b/Cudd/cudd/Makefile.in
+index 645eb7d..760278b
+--- a/Cudd/cudd/Makefile.in
++++ b/Cudd/cudd/Makefile.in
+@@ -350,7 +350,7 @@ AM_CPPFLAGS = \
+ 	-I$(top_srcdir)/libpolybori/include
+
+ AM_CFLAGS = -std=c99
+-AM_CXXFLAGS = -std=c++98 -ftemplate-depth-100
++AM_CXXFLAGS = -std=gnu++98 -ftemplate-depth-100
+ AM_DEFAULT_SOURCE_EXT = .cc
+ noinst_LTLIBRARIES = libcudd.la
+ libcudd_la_SOURCES = \
+diff --git a/common.mk b/common.mk
+index 7915587..0afda02 100755
+--- a/common.mk
++++ b/common.mk
+@@ -3,6 +3,6 @@ AM_CPPFLAGS = \
+ 	-I$(top_srcdir)/libpolybori/include
+
+ AM_CFLAGS = -std=c99
+-AM_CXXFLAGS = -std=c++98 -ftemplate-depth-100
++AM_CXXFLAGS = -std=gnu++98 -ftemplate-depth-100
+
+ AM_DEFAULT_SOURCE_EXT = .cc
+diff --git a/groebner/src/Makefile.in b/groebner/src/Makefile.in
+index ef7882c..cb3b04f
+--- a/groebner/src/Makefile.in
++++ b/groebner/src/Makefile.in
+@@ -372,7 +372,7 @@ AM_CPPFLAGS = \
+ 	-I$(top_srcdir)/libpolybori/include
+
+ AM_CFLAGS = -std=c99
+-AM_CXXFLAGS = -std=c++98 -ftemplate-depth-100
++AM_CXXFLAGS = -std=gnu++98 -ftemplate-depth-100
+ AM_DEFAULT_SOURCE_EXT = .cc
+ lib_LTLIBRARIES = libpolybori_groebner.la
+ libpolybori_groebner_la_CXXFLAGS = $(AM_CXXFLAGS) $(SIMMD_CFLAGS)
+diff --git a/libpolybori/src/Makefile.in b/libpolybori/src/Makefile.in
+index 4e4e60a..4d110c2
+--- a/libpolybori/src/Makefile.in
++++ b/libpolybori/src/Makefile.in
+@@ -323,7 +323,7 @@ AM_CPPFLAGS = \
+ 	-I$(top_srcdir)/libpolybori/include
+
+ AM_CFLAGS = -std=c99
+-AM_CXXFLAGS = -std=c++98 -ftemplate-depth-100
++AM_CXXFLAGS = -std=gnu++98 -ftemplate-depth-100
+ AM_DEFAULT_SOURCE_EXT = .cc
+ noinst_LTLIBRARIES = libpolybori_base.la
+ libpolybori_base_la_SOURCES = \

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=443f6e49b23bbc1e9004f32c802b83e35abe3a77
-md5=bb7132154839ae45a55ca1c46331289d
-cksum=2428928852
+sha1=e2e8a0a63e2734fca610c1fde383ea8e8b342d8f
+md5=fe01ff42664d309fbafbca6924f1fddd
+cksum=646567598

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-159
+161

build/pkgs/cvxopt/dependencies

@@ -1,4 +1,4 @@
-numpy atlas cephes gsl glpk pkgconfig | matplotlib
+numpy $(BLAS) cephes gsl glpk | pkgconfig matplotlib
 
 matplotlib is needed to test cvxopt (i.e., if SAGE_CHECK=yes). See #12742.
 

build/pkgs/fflas_ffpack/dependencies

@@ -1,4 +1,4 @@
-$(MP_LIBRARY) givaro gsl atlas pkgconf
+$(MP_LIBRARY) givaro gsl $(BLAS) | pkgconf
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/gsl/dependencies

@@ -1,4 +1,4 @@
-atlas
+$(BLAS)
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/imagesize/SPKG.txt

@@ -0,0 +1,5 @@
+= imagesize =
+
+== Description ==
+
+It parses image files' header and return image size.

build/pkgs/imagesize/checksums.ini

@@ -0,0 +1,4 @@
+tarball=imagesize-VERSION.tar.gz
+sha1=cf95cf234c88d5400acfa922cdc3c1f5b6a7e713
+md5=23cb4b0b5ec76fb26942d6cc0b1cf31c
+cksum=40173098

build/pkgs/imagesize/dependencies

@@ -0,0 +1,5 @@
+$(PYTHON) | pip
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

build/pkgs/imagesize/package-version.txt

@@ -0,0 +1 @@
+0.7.0

build/pkgs/imagesize/spkg-install

@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+
+cd src && python setup.py install

build/pkgs/imagesize/type

@@ -0,0 +1 @@
+standard

build/pkgs/iml/dependencies

@@ -1,4 +1,4 @@
-$(MP_LIBRARY) gsl atlas pkgconf
+$(MP_LIBRARY) gsl $(BLAS) | pkgconf
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/numpy/dependencies

@@ -1,4 +1,4 @@
-$(PYTHON) atlas | pkgconfig
+$(PYTHON) $(BLAS) | pkgconfig
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/openblas/dependencies

@@ -1,4 +1,4 @@
-# no dependencies
+| $(PYTHON)
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/r/dependencies

@@ -1,4 +1,4 @@
-atlas iconv readline pkgconf
+$(BLAS) iconv readline | pkgconf
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/sagetex/SPKG.txt

@@ -21,16 +21,13 @@ this license, visit [[http://creativecommons.org/licenses/by-sa/3.0/]]
 or send a letter to Creative Commons, 171 Second Street, Suite 300, San
 Francisco, California, 94105, USA.
 
-The included files `tkz-berge.sty` and `tkz-graph.sty` are from
-[[http://altermundus.com/pages/tkz/]] and are licensed under the "LaTeX
-Project Public License Distributed from CTAN archives in directory
-macros/latex/base/lppl.txt"; see
-[[http://mirror.ctan.org/macros/latex/base/lppl.txt]].
+== SPKG Maintainers ==
+
+Dan Drake (dr.dan.drake at gmail)
 
 == Upstream Contact ==
 
-Author: Dan Drake. Web: [[http://www.bitbucket.org/ddrake/sagetex]] and
-[[http://mathsci.kaist.ac.kr/~drake]].
+Author: Dan Drake. Web: [[https://github.com/dandrake/sagetex]]
 
 == Dependencies ==
 
@@ -43,97 +40,15 @@ it cannot find "latex" in your path.
 To use SageTeX, both Sage and LaTeX need to know about it. SageTeX comes
 standard with Sage, so you only need to make sure LaTeX can find what it
 needs. Full details are in the Sage installation guide at
-http://sagemath.org/doc/installation/ .
+http://sagemath.org/doc/installation/ and
+http://doc.sagemath.org/html/en/tutorial/sagetex.html .
 
-The directory `$SAGE_ROOT/local/share/texmf/tex/generic/sagetex`
-contains documentation and an example file. If you have problems or
-suggestions see [[http://groups.google.com/group/sage-support|the
-sage-support group]].
+The directory `$SAGE_ROOT/local/share/doc/sagetex` contains
+documentation and an example file. See
+`$SAGE_ROOT/local/share/texmf/tex/latex/sagetex` for the source code and
+some possibly useful scripts. If you have problems or suggestions see
+[[http://groups.google.com/group/sage-support|the sage-support group]].
 
-If you want to help develop SageTeX, please clone the bitbucket
-Mercurial repository (see the "Upstream Contact" above) and send me
+If you want to help develop SageTeX, please clone the github
+repository (see the "Upstream Contact" above) and send me
 patches based on that.
-
-Finally, note that you can actually use SageTeX without Sage! The
-`remote-sagetex.py` script uses any remote Sage server to do the
-computations for you. If you can't or don't want to install Sage on your
-computer, you can use the `remote-sagetex` script to use SageTeX,
-although if you are in such a situation, you probably want to get
-SageTeX [[http://tug.ctan.org/pkg/sagetex|from CTAN]] instead of
-downloading this spkg.
-
-== Changelog ==
-
-=== sagetex-2.3.4 (Dan Drake, 20 Mar 2013) ===
- * Copy example.tex into the doc directory too. (Ticket #14246)
-
-=== sagetex-2.3.3.p2 (John Palmieri, 11 Feb 2012) ===
- * Use "#!/usr/bin/env bash" at the top of spkg-check so it works on
-   OpenSolaris (ticket #12500).
-
-=== sagetex-2.3.3.p1 (Dan Drake, 16 Jan 2012) ===
-
- * Improve mechanism for preventing multiply-defined labels (ticket
-   12267), and also keep track of label names when recording maximum
-   counter seen. Also improve version mismatch checking to be backwards
-   compatible (fixes ticket 8035).
-
-=== sagetex-2.3.1.p1 (Dan Drake, 18 Nov 2011) ===
-
- * Comment out tkz-berge and other TikZ stuff from example file; don't
-   distribute tkz-* with SageTeX; fix spkg-check so that we can actually
-   run and pass checks on this spkg. See #11583.
-
-=== sagetex-2.3.1 (Dan Drake, 27 May 2011) ===
-
- * Include various fixes; see #10146. This now installs the PDFs of the
-   documentation to SAGE_ROOT/local/share/doc/sagetex as a sort of
-   halfway-not-really implementation of the SAGE_SPKG_INSTALL_DOCS
-   stuff. (See #10908 and #11197.)
-
-=== sagetex-2.3 (Dan Drake, 20 Oct 2010) ===
-
- * Now includes the sagecommandline environment by Volker Braun.
-
-=== sagetex-2.2.5 (Dan Drake, 25 Mar 2010) ===
-
- * Better implementation of the sageexample environment; 3D plots now
-   automatically fall back to using PNG.
-
-=== sagetex-2.2.4 (Dan Drake, 14 Mar 2010) ===
-
- * Special spkg for Nicolas Thiery; this includes the sageexample
-   environment and some basic documentation. This spkg won't get
-   distributed with Sage.
-
-=== sagetex-2.2.3.p0 (Dan Drake, 2 Mar 2010) ===
-
- * Couple documentation fixes; spkg-check now bails if it can't find
-   tkz-berge.sty (since the example file needs that)
-
-=== sagetex-2.2.3 (Dan Drake, 30 Dec 2009) ===
-
- * New spkg, with instructions that reflect SageTeX's inclusion as a
-   standard spkg.
-
-=== sagetex-2.2.1 (Dan Drake, 20 June 2009) ===
-
- * Update to version 2.2.1, which includes the remote-sagetex script and
-   synchronizes with the current version available on CTAN.
-
-=== sagetex-2.1.1 (Dan Drake, 28 May 2009) ===
-
- * Update to version 2.1.1, which adds pause/unpause support.
-
-=== sagetex-2.0.2 (Dan Drake, 21 Apr 2008) ===
-
- * Update source, improve spkg-check.
-
-=== sagetex-2.0.p0 (Dan Drake, 9 Jan 2008) ===
-
- * Proper SPKG.txt, spkg-check, md5sums
- * Split repos, get directory structure right
-
-=== sagetex-2.0 (Dan Drake, 18 Dec 2008) ===
-
- * Initial release

build/pkgs/sagetex/checksums.ini

@@ -1,4 +1,4 @@
-tarball=sagetex-VERSION.tar.bz2
-sha1=0d4ff45b97e591a22b225f0d7d1469ff903d4846
-md5=55d2293116a391631daaf7847e618646
-cksum=1506200788
+tarball=sagetex-VERSION.tar.gz
+sha1=b14a1be391d7697b83179d451ea9405a9186c3b6
+md5=89f539ac31dd35555eb4f7959280ff89
+cksum=43653548

build/pkgs/sagetex/package-version.txt

@@ -1 +1 @@
-2.3.4
+3.0

build/pkgs/sagetex/spkg-install

@@ -15,3 +15,5 @@ if [ $? -ne 0 ]; then
    exit 1
 fi
 
+echo "Removing old SageTex version(s)"
+rm -rf $SAGE_LOCAL/share/texmf/tex/generic/sagetex