Merge branch 'master' into 23257

Makefile

@@ -59,7 +59,7 @@ misc-clean:
 	rm -rf logs
 	rm -rf dist
 	rm -rf tmp
-	rm -f aclocal.m4 config.log config.status confcache src/bin/sage-env-config
+	rm -f aclocal.m4 config.log config.status confcache
 	rm -rf autom4te.cache
 	rm -f build/make/Makefile build/make/Makefile-auto
 	rm -f .BUILDSTART
@@ -71,6 +71,7 @@ distclean: build-clean
 	$(MAKE) misc-clean
 	@echo "Deleting all remaining output from build system ..."
 	rm -rf local
+	rm -f src/bin/sage-env-config
 
 # Delete all auto-generated files which are distributed as part of the
 # source tarball

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.0.beta9, Release Date: 2017-05-31
+SageMath version 8.0.beta12, Release Date: 2017-06-22

build/bin/sage-spkg

@@ -786,13 +786,16 @@ fi
 # Mark that the new package has been installed (and tested, if
 # applicable).
 PKG_NAME_INSTALLED="$SAGE_SPKG_INST/$PKG_NAME"
-echo "PACKAGE NAME: $PKG_NAME" > "$PKG_NAME_INSTALLED"
-echo "INSTALL DATE: `date`" >> "$PKG_NAME_INSTALLED"
-echo "UNAME: `uname -a`" >> "$PKG_NAME_INSTALLED"
-if [ -n "$TEST_SUITE_RESULT" ]; then
-    echo "TEST SUITE: $TEST_SUITE_RESULT" >> "$PKG_NAME_INSTALLED"
-fi
-cat "$SAGE_ROOT/VERSION.txt" >> "$PKG_NAME_INSTALLED"
+cat > "$PKG_NAME_INSTALLED" << __EOF__
+{
+    "package_name": "$PKG_BASE",
+    "package_version": "$PKG_VER",
+    "install_date": "$(date)",
+    "system_uname": "$(uname -a)",
+    "sage_version": "$(cat "${SAGE_ROOT}/VERSION.txt")",
+    "test_result": "$TEST_SUITE_RESULT"
+}
+__EOF__
 
 
 ##################################################################

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=1468ff678f41a3552bce2ba952af0795127d64d8
-md5=931c98793b007e28874089c17c40e53d
-cksum=1227610551
+sha1=33d69da374ac82d1595caf1ec2465f21f6d13be5
+md5=e0941bb6701f76d6f7f76879e0364e39
+cksum=2690640362

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-223
+226

build/pkgs/cryptominisat/SPKG.txt

@@ -15,16 +15,17 @@
 
 == License ==
 
- * GNU General Public License Version 3 or later (see src/COPYING)
+MIT License
 
 == Upstream Contact ==
 
- * Authors: Mate Soos
- * Email:   soos.mate@gmail.com
- * Website: http://www.msoos.org/cryptominisat2
+ * Authors:  Mate Soos
+ * Email:    soos.mate@gmail.com
+ * Website:  http://www.msoos.org/
+ * Releases: https://github.com/msoos/cryptominisat/releases
 
 == Special Update/Build Instructions ==
 
-CryptoMiniSat's tarball is called cmsat-VERSION.tar.gz and unpacks to
-cmsat-VERSION. It should be unpacked, renamed to cryptominisat-VERSION and
-repackaged.
+CryptoMiniSat's tarball downloaded from github is called VERSION.tar.gz
+and should be renamed to cryptominisat-VERSION.tar.gz
+

build/pkgs/cryptominisat/checksums.ini

@@ -1,4 +1,4 @@
 tarball=cryptominisat-VERSION.tar.gz
-sha1=3566754f4e1eb5aefec703f7806c74e4c3edda80
-md5=6fdabd54dc9076e0e2f28f489f5eab64
-cksum=2155609827
+sha1=f270bc232dbf273d5059f4c0cb704df7cf1f507d
+md5=45203be947368de75b44cf734cbac1d7
+cksum=1496245059

build/pkgs/cryptominisat/dependencies

@@ -1,4 +1,4 @@
-# no dependencies
+$(PYTHON) | cmake sqlite m4ri boost_cropped
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/cryptominisat/package-version.txt

@@ -1 +1 @@
-2.9.6
+5.0.1

build/pkgs/cryptominisat/patches/osx_install_nameQA.patch

@@ -0,0 +1,35 @@
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 4c1e235..284e348 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -2,6 +2,8 @@ include_directories(
+     ${PROJECT_SOURCE_DIR}
+ )
+
++include(GNUInstallDirs)
++
+ if(Boost_FOUND)
+     include_directories(${Boost_INCLUDE_DIRS})
+ endif()
+@@ -129,6 +131,8 @@ target_link_libraries(libcryptominisat5
+ )
+ set_target_properties(libcryptominisat5 PROPERTIES
+     OUTPUT_NAME cryptominisat5
++    MACOSX_RPATH TRUE
++    INSTALL_NAME_DIR "${CMAKE_INSTALL_FULL_LIBDIR}"
+     PUBLIC_HEADER "${cryptominisat5_public_headers}"
+     VERSION ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}
+     SOVERSION ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}
+@@ -185,9 +189,9 @@ endforeach()
+
+ install(TARGETS libcryptominisat5
+     EXPORT ${CRYPTOMINISAT5_EXPORT_NAME}
+-    LIBRARY DESTINATION "${CMAKE_INSTALL_PREFIX}/lib"
+-    ARCHIVE DESTINATION "${CMAKE_INSTALL_PREFIX}/lib"
+-    PUBLIC_HEADER DESTINATION "${CMAKE_INSTALL_PREFIX}/include/cryptominisat5"
++    LIBRARY DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}"
++    ARCHIVE DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}"
++    PUBLIC_HEADER DESTINATION "${CMAKE_INSTALL_FULL_INCLUDEDIR}/cryptominisat5"
+ )
+
+ if (NOT ONLY_SIMPLE)

build/pkgs/cryptominisat/spkg-install

@@ -1,76 +1,21 @@
 #!/usr/bin/env bash
 
-if [ "$SAGE_LOCAL" = "" ]; then
-   echo "SAGE_LOCAL undefined ... exiting"
-   echo "Maybe run 'sage -sh'?"
-   exit 1
-fi
-
-unset RM
-
-INCLUDES="-I$SAGE_LOCAL/include"
-LIBDIRS="-L$SAGE_LOCAL/lib"
-
-CXXFLAGS="$CXXFLAGS $INCLUDES $LIBDIRS -g"
-
-COMPILER=`testcc.sh $CC`
-
-if [ "x$COMPILER"  = "xGNU" ] ; then
-   CXXFLAGS="$CXXFLAGS -fPIC -Wall -pedantic"
-elif [ "x$COMPILER" = "xSun_on_Solaris" ] ; then
-   CXXFLAGS="$CXXFLAGS -Kpic"
-elif [ "x$COMPILER" = "xHP_on_HPUX" ] ; then
-   CXXFLAGS="$CXXFLAGS + z"
-fi
-
-CPPFLAGS="$INCLUDES"
-
-if [ "x$SAGE_DEBUG" = "xyes" ]; then
-   CXXFLAGS="$CXXFLAGS -O0"
-   ENABLE_DEBUG="--enable-debug"
-else
-   CXXFLAGS="$CXXFLAGS -O2"
-   ENABLE_DEBUG=""
-fi
+fail () {
+    echo -e >&2 $1
+    exit 1
+}
 
-if [ "x$SAGE64" = "xyes" ]; then
-    CXXFLAGS="$CXXFLAGS -m64"
-    CPPFLAGS="$CPPFLAGS -m64"
-    # FIXME: Do we need LDFLAGS here, too?
-    #        But looks as if all linking is performed by libtool/
-    #        gcc, so we do not really need it here.
+if [ "$SAGE_LOCAL" = "" ]; then
+    fail "SAGE_LOCAL undefined ... exiting\nMaybe run 'sage -sh'?"
 fi
 
-export CXXFLAGS
-export CPPFLAGS
-
-
-#build CryptoMiniSat
-
 cd src
 
-$MAKE clean
-
-./configure --prefix=$SAGE_LOCAL $ENABLE_DEBUG
-
-if [ $? -ne 0 ]; then
-    echo "Error configuring cryptominisat"
-    exit 1
-fi
+cmake -DCMAKE_INSTALL_PREFIX="${SAGE_LOCAL}" -DUSE_GAUSS='ON' -DZLIB_ROOT="${SAGE_LOCAL}" . || fail 'Error configuring cryptominisat'
 
-$MAKE
+$MAKE VERBOSE=ON || fail 'Error building cryptominisat'
 
-if [ $? -ne 0 ]; then
-    echo "Error building cryptominisat"
-    exit 1
-fi
-
-$MAKE install
-
-if [ $? -ne 0 ]; then
-    echo "Error installing cryptominisat"
-    exit 1
-fi
+$MAKE VERBOSE=ON install || fail 'Error installing cryptominisat'
 
-cd ..
+exit 0
 

build/pkgs/cryptominisat/type

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

build/pkgs/cython/patches/dd0b10c7e31ea136632bfcfd46c925adcf4c4af6.patch

@@ -0,0 +1,105 @@
+From dd0b10c7e31ea136632bfcfd46c925adcf4c4af6 Mon Sep 17 00:00:00 2001
+From: Robert Bradshaw <robertwb@gmail.com>
+Date: Tue, 24 Jan 2017 15:53:43 -0800
+Subject: [PATCH] Work around numpy build formatting differences.
+
+---
+ tests/run/numpy_test.pyx | 22 ++++++++++++----------
+ 1 file changed, 12 insertions(+), 10 deletions(-)
+
+diff --git a/tests/run/numpy_test.pyx b/tests/run/numpy_test.pyx
+index a813085f3..5fca12574 100644
+--- a/tests/run/numpy_test.pyx
++++ b/tests/run/numpy_test.pyx
+@@ -4,6 +4,7 @@
+ cimport numpy as np
+ cimport cython
+
++import re
+ import sys
+
+ from libc.stdlib cimport malloc
+@@ -133,7 +134,7 @@ try:
+     Traceback (most recent call last):
+        ...
+     ValueError: ndarray is not C...contiguous
+-    
++
+     >>> test_dtype('b', inc1_byte)
+     >>> test_dtype('B', inc1_ubyte)
+     >>> test_dtype('h', inc1_short)
+@@ -142,7 +143,7 @@ try:
+     >>> test_dtype('I', inc1_uint)
+     >>> test_dtype('l', inc1_long)
+     >>> test_dtype('L', inc1_ulong)
+-    
++
+     >>> test_dtype('f', inc1_float)
+     >>> test_dtype('d', inc1_double)
+     >>> test_dtype('g', inc1_longdouble)
+@@ -172,11 +173,11 @@ try:
+     Traceback (most recent call last):
+        ...
+     ValueError: ...
+-    
++
+
+
+     >>> test_recordarray()
+-    
++
+     >>> print(test_nested_dtypes(np.zeros((3,), dtype=np.dtype([\
+             ('a', np.dtype('i,i')),\
+             ('b', np.dtype('i,i'))\
+@@ -198,12 +199,12 @@ try:
+
+     The output changed in Python 3:
+     >> print(test_unpacked_align(np.zeros((1,), dtype=np.dtype('b,i', align=True))))
+-    array([(22, 23)], 
++    array([(22, 23)],
+           dtype=[('f0', '|i1'), ('', '|V3'), ('f1', '!i4')])
+
+     ->
+
+-    array([(22, 23)], 
++    array([(22, 23)],
+           dtype={'names':['f0','f1'], 'formats':['i1','!i4'], 'offsets':[0,4], 'itemsize':8, 'aligned':True})
+
+
+@@ -234,7 +235,7 @@ try:
+     8,16
+
+     >>> test_point_record()
+-    array([(0.0, 0.0), (1.0, -1.0), (2.0, -2.0)], 
++    array([(0., 0.), (1., -1.), (2., -2.)], 
+           dtype=[('x', '!f8'), ('y', '!f8')])
+
+ """
+@@ -352,7 +353,7 @@ def inc1_clongdouble(np.ndarray[long double complex] arr): arr[1] = arr[1] + (1
+ def inc1_cfloat_struct(np.ndarray[np.cfloat_t] arr):
+     arr[1].real += 1
+     arr[1].imag += 1
+-    
++
+ def inc1_cdouble_struct(np.ndarray[np.cdouble_t] arr):
+     arr[1].real += 1
+     arr[1].imag += 1
+@@ -382,7 +383,7 @@ def inc1_uintp_t(np.ndarray[np.uintp_t] arr):           arr[1] += 1
+ def inc1_int32_t(np.ndarray[np.int32_t] arr):           arr[1] += 1
+ def inc1_float64_t(np.ndarray[np.float64_t] arr):       arr[1] += 1
+
+-    
++
+ def test_dtype(dtype, inc1):
+     if dtype in ("g", np.longdouble,
+                  "G", np.clongdouble):
+@@ -518,7 +519,8 @@ def test_point_record():
+     for i in range(3):
+         test[i].x = i
+         test[i].y = -i
+-    print repr(test).replace('<', '!').replace('>', '!')
++    print re.sub(
++        r'\.0+\b', '.', repr(test).replace('<', '!').replace('>', '!'))
+
+ # Test fused np.ndarray dtypes and runtime dispatch
+ @testcase

build/pkgs/cython/patches/dd9eb10bc5657beed1f66221511c16ec6f4e517d.patch

@@ -0,0 +1,23 @@
+From dd9eb10bc5657beed1f66221511c16ec6f4e517d Mon Sep 17 00:00:00 2001
+From: Robert Bradshaw <robertwb@gmail.com>
+Date: Tue, 24 Jan 2017 16:46:31 -0800
+Subject: [PATCH] More numpy struct format normalization.
+
+---
+ tests/run/numpy_test.pyx | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/tests/run/numpy_test.pyx b/tests/run/numpy_test.pyx
+index 5fca12574..39fe1ffea 100644
+--- a/tests/run/numpy_test.pyx
++++ b/tests/run/numpy_test.pyx
+@@ -520,7 +520,8 @@ def test_point_record():
+         test[i].x = i
+         test[i].y = -i
+     print re.sub(
+-        r'\.0+\b', '.', repr(test).replace('<', '!').replace('>', '!'))
++        r'\.0+\b', '.', repr(test).replace('<', '!').replace('>', '!')
++                                  .replace('( ', '(').replace(',  ', ', '))
+
+ # Test fused np.ndarray dtypes and runtime dispatch
+ @testcase