Merge branch 'develop' into t/16561/ticket/16561

VERSION.txt

@@ -1 +1 @@
-SageMath version 7.5.rc0, Release Date: 2016-12-18
+SageMath version 7.6.beta0, Release Date: 2017-01-21

build/bin/sage-pip-install

@@ -15,7 +15,9 @@
 # --no-deps          : Don't install runtime dependencies from PyPI.
 # --no-index         : Don't look at the package index.
 #                      This also disables pip's version self-check.
-pip_install_flags="--ignore-installed --verbose --no-deps --no-index"
+# --isolated         : Don't read configuration files such as
+#                      ~/.pydistutils.cfg
+pip_install_flags="--ignore-installed --verbose --no-deps --no-index --isolated"
 
 # Consume any additional pip install arguments except the last one
 while [ $# -gt 1 ]; do

build/make/deps

@@ -78,7 +78,7 @@ toolchain-deps:
 
 # Everything needed to start up Sage using "./sage".  Of course, not
 # every part of Sage will work.  It does not include Maxima for example.
-SAGERUNTIME = sagelib $(SCRIPTS) $(inst_ipython) $(inst_pexpect)
+SAGERUNTIME = sagelib $(SCRIPTS) $(inst_ipython) $(inst_pexpect) $(inst_psutil)
 
 
 # Start Sage at least once to check that it works

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=dec646cbe7003843d95349386e65ff39ce623561
-md5=8edc28e5ce617646e08dce522c4a733a
-cksum=1353419480
+sha1=6bca962ddef509dfdc793677e04cb36cba0be319
+md5=761bb8747a20cf90685449e6e757f3a6
+cksum=2840043807

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-196
+202

build/pkgs/database_pari/checksums.ini

@@ -1,4 +1,4 @@
 tarball=database_pari-VERSION.tar.bz2
-sha1=92dcb68e7a6def53ffc5fb82e3593d5b80c940cb
-md5=652d36d18ea300193957120815298be7
-cksum=2257060384
+sha1=dd2b168da033a9fca98ce5d9d81ad76fbc1739fb
+md5=0fb372a3c8de787f84c066f81511a276
+cksum=3988008667

build/pkgs/database_pari/package-version.txt

@@ -1 +1 @@
-20140908
+20161017

build/pkgs/eclib/checksums.ini

@@ -1,4 +1,4 @@
 tarball=eclib-VERSION.tar.bz2
-sha1=acd51ec5e7ab7be6a3151fe645320f71c6a11ede
-md5=ac1eee9c42b1b6987173f574b6f43744
-cksum=673064945
+sha1=b5098fe705dcea8f492e5e331ad8a69f5721898f
+md5=af8c339c44155ed813cb40f39fcfe344
+cksum=2757924773

build/pkgs/eclib/package-version.txt

@@ -1 +1 @@
-20160720
+20170104

build/pkgs/enum34/SPKG.txt

@@ -0,0 +1,9 @@
+= enum34 =
+
+== Description ==
+
+Python 3.4 Enum backported to 3.3, 3.2, 3.1, 2.7, 2.6, 2.5, and 2.4
+
+An enumeration is a set of symbolic names (members) bound to unique,
+constant values. Within an enumeration, the members can be compared by
+identity, and the enumeration itself can be iterated over.

build/pkgs/enum34/checksums.ini

@@ -0,0 +1,4 @@
+tarball=enum34-VERSION.tar.gz
+sha1=014ef5878333ff91099893d615192c8cd0b1525a
+md5=5f13a0841a61f7fc295c514490d120d0
+cksum=3196958404

build/pkgs/enum34/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/enum34/package-version.txt

@@ -0,0 +1 @@
+1.1.6

build/pkgs/enum34/spkg-install

@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+
+cd src && $PIP_INSTALL .

build/pkgs/enum34/type

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

build/pkgs/gambit/spkg-install

@@ -21,8 +21,7 @@ if [ $? -ne 0 ]; then
 fi
 
 cd src/python
-python setup.py build
-python setup.py install
+python setup.py --no-user-cfg build install
 
 if [ $? -ne 0 ]; then
     echo "Error installing Python API"

build/pkgs/giac/dependencies

@@ -1,4 +1,4 @@
-readline $(MP_LIBRARY) mpfr mpfi ntl gsl pari
+readline $(MP_LIBRARY) mpfr mpfi ntl gsl pari libpng
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/git/checksums.ini

@@ -1,4 +1,4 @@
 tarball=git-VERSION.tar.gz
-sha1=ff32a94936309ca3f0e3d56e479e7510a3c1c925
-md5=da293290da69f45a86a311ad3cd43dc8
-cksum=2025246710
+sha1=21a227ac7f3a8b3c29e6d6fbd13f7a6b958c81ed
+md5=eac9324afcf4c95ab11acb2e2283e376
+cksum=2000477778

build/pkgs/git/package-version.txt

@@ -1 +1 @@
-2.6.2
+2.11.0

build/pkgs/gp2c/checksums.ini

@@ -1,4 +1,4 @@
 tarball=gp2c-VERSION.tar.gz
-sha1=e07cebffcd09c0d644d52335130984f33042b46f
-md5=3f6bb47d41ddca7b6a4938d16abbe4e8
-cksum=3338275717
+sha1=6bce2bbb69227de44fa768619d1dffa861d6470a
+md5=41d3e76fb070ba7f73242b76ae5cb529
+cksum=2256538341

build/pkgs/gp2c/package-version.txt

@@ -1 +1 @@
-0.0.9pl5
+0.0.10

build/pkgs/gsl/package-version.txt

@@ -1 +1 @@
-2.1.p0
+2.1.p1

build/pkgs/gsl/patches/gsl-2.1-gslcblas.patch

@@ -0,0 +1,16 @@
+Do not include gslcblas in .pc. We already have the selected cblas
+added to libs. Which could be an external cblas if someone wanted too.
+
+diff --git a/gsl.pc.in b/gsl.pc.in
+index 5e9ef21..3a70648 100644
+--- a/gsl.pc.in
++++ b/gsl.pc.in
+@@ -2,7 +2,7 @@ prefix=@prefix@
+ exec_prefix=@exec_prefix@
+ libdir=@libdir@
+ includedir=@includedir@
+-GSL_CBLAS_LIB=-lgslcblas
++GSL_CBLAS_LIB=
+
+ Name: GSL
+ Description: GNU Scientific Library

build/pkgs/ipykernel/checksums.ini

@@ -1,4 +1,4 @@
 tarball=ipykernel-VERSION.tar.gz
-sha1=1a16f3366a655edd1c0dc264fc3fe1489cf2c2df
-md5=0b1150602203af298631555509a809bd
-cksum=69264790
+sha1=b94d49af3a9a89eb9b4d32c63868b8fcb689de19
+md5=4048987076b85814202cd29b1dd3fc7b
+cksum=1741951088

build/pkgs/ipykernel/package-version.txt

@@ -1 +1 @@
-4.3.1.p0
+4.5.2

build/pkgs/jupyter_client/checksums.ini

@@ -1,4 +1,4 @@
 tarball=jupyter_client-VERSION.tar.gz
-sha1=909b47a92960364300765a36963c8c9bf9c179ab
-md5=4ae3d5e04baea1e8fa8d3ec24c600c17
-cksum=854482584
+sha1=1455be4a05b45051f83ae30a10d97a432fa5e01e
+md5=8a428a07cbcd4f2e4ca7c2f728b718ea
+cksum=1097112492

build/pkgs/jupyter_client/package-version.txt

@@ -1 +1 @@
-4.3.0.p0
+4.4.0

build/pkgs/jupyter_core/checksums.ini

@@ -1,4 +1,4 @@
 tarball=jupyter_core-VERSION.tar.gz
-sha1=7836ef4bbe750048361624c6a3968ed733bf8f6a
-md5=78f6add824eef72b12e0f6e6940372b3
-cksum=3147890695
+sha1=983a8eca910b3ac4290f1944fe6589770c254b1d
+md5=f707f8693e537177341c4a89081fdac3
+cksum=3375597820

build/pkgs/jupyter_core/package-version.txt

@@ -1 +1 @@
-4.1.0.p0
+4.2.1

build/pkgs/modular_decomposition/type

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

build/pkgs/nbformat/checksums.ini

@@ -1,4 +1,4 @@
 tarball=nbformat-VERSION.tar.gz
-sha1=c823d95938cb12b8e8af918bd2e547d3ca966e4f
-md5=684c4dc3c6fd8036fd1ae1c908003e23
-cksum=3054783982
+sha1=96c8836cc2ef1457b150d61bb7f20cdcab64d66c
+md5=f90f24d317b651226a6b547fa69d8da4
+cksum=159106855

build/pkgs/nbformat/package-version.txt

@@ -1 +1 @@
-4.0.1.p0
+4.2.0

build/pkgs/notebook/checksums.ini

@@ -1,4 +1,4 @@
 tarball=notebook-VERSION.tar.gz
-sha1=cec36e2d1aa7835f2b4dda7dde8455d33a06361a
-md5=09e727ba598ab1848327d211fd2ad057
-cksum=2780054946
+sha1=ab665a9b0f42a6fc430dfe61db83a8d54bce3f97
+md5=70cc97ad19c0f9246ad295a653475e2a
+cksum=660926754

build/pkgs/notebook/package-version.txt

@@ -1 +1 @@
-4.2.1.p0
+4.3.1

build/pkgs/numpy/spkg-install

@@ -49,7 +49,9 @@ rm -rf "$SAGE_LOCAL/lib/python/site-packages/numpy"
 # Program around a bug in SciPY's distutils.
 unset CFLAGS
 
-python setup.py install \
+python setup.py \
+        --no-user-cfg \
+       install \
        --single-version-externally-managed \
        --record /dev/null \
        ${NUMPY_FCONFIG}

build/pkgs/openblas/package-version.txt

@@ -1 +1 @@
-0.2.19
+0.2.19.p0

build/pkgs/openblas/patches/openblas-0.2.19-MAKE.patch

@@ -0,0 +1,29 @@
+diff --git a/Makefile b/Makefile
+index 2ae0047..2071e10 100644
+--- a/Makefile
++++ b/Makefile
+@@ -278,13 +278,13 @@ lapack-timing : large.tgz timing.tgz
+ ifndef NOFORTRAN
+ 	(cd $(NETLIB_LAPACK_DIR); $(TAR) zxf ../timing.tgz TIMING)
+ 	(cd $(NETLIB_LAPACK_DIR)/TIMING; $(TAR) zxf ../../large.tgz )
+-	make -C $(NETLIB_LAPACK_DIR)/TIMING
++	$(MAKE) -C $(NETLIB_LAPACK_DIR)/TIMING
+ endif
+
+
+ lapack-test :
+ 	(cd $(NETLIB_LAPACK_DIR)/TESTING && rm -f x* *.out)
+-	make -j 1 -C $(NETLIB_LAPACK_DIR)/TESTING xeigtstc  xeigtstd  xeigtsts  xeigtstz  xlintstc  xlintstd  xlintstds  xlintstrfd  xlintstrfz  xlintsts  xlintstz  xlintstzc xlintstrfs xlintstrfc
++	$(MAKE) -j 1 -C $(NETLIB_LAPACK_DIR)/TESTING xeigtstc  xeigtstd  xeigtsts  xeigtstz  xlintstc  xlintstd  xlintstds  xlintstrfd  xlintstrfz  xlintsts  xlintstz  xlintstzc xlintstrfs xlintstrfc
+ ifneq ($(CROSS), 1)
+ 	( cd $(NETLIB_LAPACK_DIR)/INSTALL; ./testlsame; ./testslamch; ./testdlamch; \
+         ./testsecond; ./testdsecnd; ./testieee; ./testversion )
+@@ -299,7 +299,7 @@ lapack-runtest:
+
+ blas-test:
+ 	(cd $(NETLIB_LAPACK_DIR)/BLAS && rm -f x* *.out)
+-	make -j 1 -C $(NETLIB_LAPACK_DIR) blas_testing
++	$(MAKE) -j 1 -C $(NETLIB_LAPACK_DIR) blas_testing
+ 	(cd $(NETLIB_LAPACK_DIR)/BLAS && cat *.out)
+
+

build/pkgs/openblas/patches/openblas-0.2.19-OSX_DEPLOY.patch

@@ -0,0 +1,14 @@
+diff --git a/Makefile.system b/Makefile.system
+index b05177b..d4b3709 100644
+--- a/Makefile.system
++++ b/Makefile.system
+@@ -217,7 +217,9 @@ endif
+ #
+
+ ifeq ($(OSNAME), Darwin)
++ifndef MACOSX_DEPLOYMENT_TARGET
+ export MACOSX_DEPLOYMENT_TARGET=10.6
++endif
+ MD5SUM = md5 -r
+ endif
+

build/pkgs/openblas/patches/openblas-0.2.19-SMP_conditional.patch

@@ -0,0 +1,50 @@
+From c6623a8da5f9ff393008876455dfba70c1de1e3f Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Fran=C3=A7ois=20Bissey?= <francois.bissey@canterbury.ac.nz>
+Date: Thu, 15 Dec 2016 15:16:46 +1300
+Subject: [PATCH] More prudent handling of SMP in Makefile.system. It may need
+ to extended to other makefiles.
+
+---
+ Makefile.system | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/Makefile.system b/Makefile.system
+index b05177b..f9c5995 100644
+--- a/Makefile.system
++++ b/Makefile.system
+@@ -297,7 +297,7 @@ ifneq ($(OSNAME), WINNT)
+ ifneq ($(OSNAME), CYGWIN_NT)
+ ifneq ($(OSNAME), Interix)
+ ifneq ($(OSNAME), Android)
+-ifdef SMP
++ifeq ($(SMP), 1)
+ EXTRALIB   += -lpthread
+ endif
+ endif
+@@ -843,7 +843,7 @@ ifeq ($(NO_AVX2), 1)
+ CCOMMON_OPT	+= -DNO_AVX2
+ endif
+
+-ifdef SMP
++ifeq ($(SMP), 1)
+ CCOMMON_OPT	+= -DSMP_SERVER
+
+ ifeq ($(ARCH), mips64)
+@@ -1044,7 +1044,7 @@ LIBSUFFIX = a
+ endif
+
+ ifneq ($(DYNAMIC_ARCH), 1)
+-ifndef SMP
++ifneq ($(SMP), 1)
+ LIBNAME		= $(LIBPREFIX)_$(LIBCORE)$(REVISION).$(LIBSUFFIX)
+ LIBNAME_P	= $(LIBPREFIX)_$(LIBCORE)$(REVISION)_p.$(LIBSUFFIX)
+ else
+@@ -1052,7 +1052,7 @@ LIBNAME		= $(LIBPREFIX)_$(LIBCORE)p$(REVISION).$(LIBSUFFIX)
+ LIBNAME_P	= $(LIBPREFIX)_$(LIBCORE)p$(REVISION)_p.$(LIBSUFFIX)
+ endif
+ else
+-ifndef SMP
++ifneq ($(SMP), 1)
+ LIBNAME		= $(LIBPREFIX)$(REVISION).$(LIBSUFFIX)
+ LIBNAME_P	= $(LIBPREFIX)$(REVISION)_p.$(LIBSUFFIX)
+ else

build/pkgs/openblas/spkg-check

@@ -15,6 +15,9 @@ cd src
 # We could also patch the Makefile to use a generic symlink pointing
 # to the archive with a specific name
 
+# See #22021 for issues with multithreading
+OPENBLAS_CONFIGURE="$OPENBLAS_CONFIGURE USE_THREAD=0"
+
 if [ `python -c "from __future__ import print_function; import platform; print(platform.architecture()[0])"` = "32bit" ]; then
     OPENBLAS_CONFIGURE="$OPENBLAS_CONFIGURE BINARY=32"
 fi

build/pkgs/openblas/spkg-install

@@ -8,6 +8,9 @@ fi
 
 cd src
 
+# See #22021 for issues with multithreading
+OPENBLAS_CONFIGURE="$OPENBLAS_CONFIGURE USE_THREAD=0"
+
 # OpenBLAS does not build on 32bit Haswell. Upstream suggests to pass BINARY=32 to default to NEHALEM kernels
 # See https://github.com/xianyi/OpenBLAS/issues/657
 # Right now this affect all 32bit CPUs.
@@ -27,7 +30,7 @@ fi
 
 echo "Building OpenBLAS: $MAKE $OPENBLAS_CONFIGURE"
 
-$MAKE $OPENBLAS_CONFIGURE
+$MAKE libs netlib shared $OPENBLAS_CONFIGURE
 if [ $? -ne 0 ]; then
     echo >&2 "Error building OpenBLAS"
     exit 1

build/pkgs/pari/checksums.ini

@@ -1,4 +1,4 @@
 tarball=pari-VERSION.tar.gz
-sha1=efd1eb6b8d87066b2b9f3b2c38ecb30bbfdb48d2
-md5=f3f3342913a3b3b306970b3462f4d47d
-cksum=1553747906
+sha1=ad6af366153ae160aaa4cb49edf3a32a69f7afc1
+md5=f997d6b526df6cd9145af0de5b822bf4
+cksum=2625551585

build/pkgs/pari/package-version.txt

@@ -1 +1 @@
-2.8.0.alpha.p2
+2.9.1.p0

build/pkgs/pari/patches/README.txt

@@ -14,8 +14,3 @@ Patches to configuration files:
 C files:
 * stackwarn.patch (Jeroen Demeyer, #19883): do not display warnings
   regarding the stack size (unless DEBUGMEM is set).
-
-Building documentation
-* perl_inc.patch (Francois Bissey, #21622): import upstream patch
-to deal with perl install where "." is not part of @INC anymore
-in perl.