Merge tag '7.2' into t/20226/ticket/20226

SageMath version 7.2

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.beta2, Release Date: 2016-04-01
+SageMath version 7.2, Release Date: 2016-05-15

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) \
@@ -191,7 +191,8 @@ $(SAGE_EXTCODE)/%: $(SAGE_SRC)/ext/%
 DOC_DEPENDENCIES = sagelib $(inst_sphinx) $(inst_sagenb) \
 	| $(SAGERUNTIME) $(inst_maxima) $(inst_networkx) $(inst_scipy) \
 	$(inst_matplotlib) $(inst_pillow) $(inst_mathjax) $(inst_mpmath) \
-	$(inst_ipykernel) $(inst_jupyter_client) $(inst_conway_polynomials)
+	$(inst_ipykernel) $(inst_jupyter_client) $(inst_conway_polynomials) \
+	$(inst_tachyon)
 
 doc: doc-html
 

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/babel/SPKG.txt

@@ -0,0 +1,7 @@
+= babel =
+
+== Description ==
+
+Internationalization utilities
+
+A collection of tools for internationalizing Python applications.

build/pkgs/babel/checksums.ini

@@ -0,0 +1,4 @@
+tarball=Babel-VERSION.tar.gz
+sha1=e02392bc9a16f7672686bce23e4e3cdadcc1b1c8
+md5=1b69e4b2ab3795119266ccaa36b36f15
+cksum=2897183559

build/pkgs/babel/dependencies

@@ -0,0 +1,5 @@
+$(PYTHON) | pip pytz
+
+----------
+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/babel/package-version.txt

@@ -0,0 +1 @@
+2.2.0

build/pkgs/babel/spkg-install

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

build/pkgs/babel/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/cddlib/spkg-install

@@ -28,7 +28,7 @@ cd src
 cp ../patches/random.{c,h} lib-src/
 cp ../patches/random.{c,h} lib-src-gmp/
 
-# Required by sage.geometry.polyhedra 
+# Required by sage.geometry.polyhedron
 cp ../patches/cdd_both_reps.c src/
 cp ../patches/cdd_both_reps.c src-gmp/cdd_both_reps.c
 

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=8cf7b09fdc4d8326d489ead1b1b83b5dc58c872c
-md5=e6a347567b1ea00823f489bfc6afa196
-cksum=3730099068
+sha1=425d4430acbc3ee54a2fbe98a4541226c7e44bf5
+md5=81b5e802a06390e189fe08190f6e09d6
+cksum=2177259732

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-156
+164

build/pkgs/csdp/type

@@ -1 +1 @@
-experimental
+optional

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/cython/checksums.ini

@@ -1,4 +1,4 @@
 tarball=Cython-VERSION.tar.gz
-sha1=ee455e4f6bedb8d02325da1d4810ab906c3ddc1d
-md5=66b62989a67c55af016c916da36e7514
-cksum=3621634163
+sha1=32f12b8dd976111668ef8ba7e716a850869a0bf6
+md5=14fbc970f4a856845e633cbc09e61048
+cksum=2292891014

build/pkgs/cython/package-version.txt

@@ -1 +1 @@
-0.23.5
+0.24.p0

build/pkgs/database_gap/dependencies

@@ -0,0 +1 @@
+gap

build/pkgs/database_mutation_class/SPKG.txt

@@ -0,0 +1,23 @@
+= Mutation class database =
+
+== Description ==
+
+ Contains a database of all exceptional mutation classes of quivers.
+
+ Every file in the database is of the form ``mutation_classes_n.dig6`` for some ``n`` and
+ - contains a ``cPickle.dump`` of a dictionary where
+   - the keys are tuples representing irreducible exceptional quiver mutation types of rank ``n``, and
+   - the values are all quivers in the given mutation class stored in canonical form as ``(dig6,edges)`` where
+     - ``dig6`` is the dig6 data of the given ``DiGraph``, and
+     - ``edges`` are the non-simply-laced edges thereof.
+ - is obtained by running the function
+ ``sage.combinat.cluster_algebra_quiver.quiver_mutation_type._save_data_dig6(n, types='Exceptional', verbose=False)``
+
+== SPKG Maintainers ==
+
+ * C. Stump <christian.stump@gmail.com>
+
+== Dependencies ==
+
+ * None
+

build/pkgs/database_mutation_class/checksums.ini

@@ -0,0 +1,4 @@
+tarball=database_mutation_class-VERSION.tar.gz
+sha1=0e7eb2e89e1d4a612cb60e3d6be14d42f3e55678
+md5=8186b8f75eae76825399f3a9e6378c7b
+cksum=364985299

build/pkgs/database_mutation_class/dependencies

@@ -0,0 +1 @@
+# no dependencies

build/pkgs/database_mutation_class/package-version.txt

@@ -0,0 +1 @@
+1.0

build/pkgs/database_mutation_class/spkg-install

@@ -0,0 +1,17 @@
+#!/usr/bin/env bash
+
+cd src
+
+if [ -z "$SAGE_LOCAL" ]; then
+    echo >&2 "SAGE_LOCAL undefined database_mutation_class-1.0 exiting"
+    echo >&2 "Maybe run 'sage --sh'?"
+    exit 1
+fi
+
+mkdir -p $SAGE_SHARE/cluster_algebra_quiver && cp src/* $SAGE_SHARE/cluster_algebra_quiver
+
+if [ $? -ne 0 ]; then
+    echo >&2 "Error: Failed to copy the data to $SAGE_SHARE/cluster_algebra_quiver. database_mutation_class-1.0 exiting"
+    exit 1
+fi
+

build/pkgs/database_mutation_class/type

@@ -0,0 +1 @@
+optional

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/flask/SPKG.txt

@@ -0,0 +1,8 @@
+= Flask =
+
+== Description ==
+
+A microframework based on Werkzeug, Jinja2 and good intentions
+
+Flask is a microframework for Python based on Werkzeug, Jinja 2 and good
+intentions. And before you ask: It’s BSD licensed!

build/pkgs/flask/checksums.ini

@@ -0,0 +1,4 @@
+tarball=Flask-VERSION.tar.gz
+sha1=d3d078262b053f4438e2ed3fd6f9b923c2c92172
+md5=378670fe456957eb3c27ddaef60b2b24
+cksum=2901487846

build/pkgs/flask/dependencies

@@ -0,0 +1,5 @@
+$(PYTHON) | pip werkzeug jinja2 itsdangerous
+
+----------
+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.