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Merge branch 'develop' into t/23211/mark_morphisms_as_coercions
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‎VERSION.txt

+1-1
Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
SageMath version 8.0.beta9, Release Date: 2017-05-31
1+
SageMath version 8.0.beta11, Release Date: 2017-06-15

‎build/bin/sage-spkg

+10-7
Original file line numberDiff line numberDiff line change
@@ -786,13 +786,16 @@ fi
786786
# Mark that the new package has been installed (and tested, if
787787
# applicable).
788788
PKG_NAME_INSTALLED="$SAGE_SPKG_INST/$PKG_NAME"
789-
echo "PACKAGE NAME: $PKG_NAME" > "$PKG_NAME_INSTALLED"
790-
echo "INSTALL DATE: `date`" >> "$PKG_NAME_INSTALLED"
791-
echo "UNAME: `uname -a`" >> "$PKG_NAME_INSTALLED"
792-
if [ -n "$TEST_SUITE_RESULT" ]; then
793-
echo "TEST SUITE: $TEST_SUITE_RESULT" >> "$PKG_NAME_INSTALLED"
794-
fi
795-
cat "$SAGE_ROOT/VERSION.txt" >> "$PKG_NAME_INSTALLED"
789+
cat > "$PKG_NAME_INSTALLED" << __EOF__
790+
{
791+
"package_name": "$PKG_BASE",
792+
"package_version": "$PKG_VER",
793+
"install_date": "$(date)",
794+
"system_uname": "$(uname -a)",
795+
"sage_version": "$(cat "${SAGE_ROOT}/VERSION.txt")",
796+
"test_result": "$TEST_SUITE_RESULT"
797+
}
798+
__EOF__
796799

797800

798801
##################################################################

‎build/pkgs/configure/checksums.ini

+3-3
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
11
tarball=configure-VERSION.tar.gz
2-
sha1=1468ff678f41a3552bce2ba952af0795127d64d8
3-
md5=931c98793b007e28874089c17c40e53d
4-
cksum=1227610551
2+
sha1=e259780779245d47e729ff7f0353d99a2bf51c36
3+
md5=29e6ed6ba6534018c58fb41dcdc89a5e
4+
cksum=2785456807

‎build/pkgs/configure/package-version.txt

+1-1
Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
223
1+
225

‎build/pkgs/cryptominisat/SPKG.txt

+8-7
Original file line numberDiff line numberDiff line change
@@ -15,16 +15,17 @@
1515

1616
== License ==
1717

18-
* GNU General Public License Version 3 or later (see src/COPYING)
18+
MIT License
1919

2020
== Upstream Contact ==
2121

22-
* Authors: Mate Soos
23-
* Email: [email protected]
24-
* Website: http://www.msoos.org/cryptominisat2
22+
* Authors: Mate Soos
23+
* Email: [email protected]
24+
* Website: http://www.msoos.org/
25+
* Releases: https://github.com/msoos/cryptominisat/releases
2526

2627
== Special Update/Build Instructions ==
2728

28-
CryptoMiniSat's tarball is called cmsat-VERSION.tar.gz and unpacks to
29-
cmsat-VERSION. It should be unpacked, renamed to cryptominisat-VERSION and
30-
repackaged.
29+
CryptoMiniSat's tarball downloaded from github is called VERSION.tar.gz
30+
and should be renamed to cryptominisat-VERSION.tar.gz
31+

‎build/pkgs/cryptominisat/checksums.ini

+3-3
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
11
tarball=cryptominisat-VERSION.tar.gz
2-
sha1=3566754f4e1eb5aefec703f7806c74e4c3edda80
3-
md5=6fdabd54dc9076e0e2f28f489f5eab64
4-
cksum=2155609827
2+
sha1=f270bc232dbf273d5059f4c0cb704df7cf1f507d
3+
md5=45203be947368de75b44cf734cbac1d7
4+
cksum=1496245059

‎build/pkgs/cryptominisat/dependencies

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
# no dependencies
1+
$(PYTHON) | cmake sqlite m4ri boost_cropped
22

33
----------
44
All lines of this file are ignored except the first.

‎build/pkgs/cryptominisat/package-version.txt

+1-1
Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
2.9.6
1+
5.0.1

‎build/pkgs/cryptominisat/patches/osx_install_nameQA.patch

+35
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,35 @@
1+
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
2+
index 4c1e235..284e348 100644
3+
--- a/src/CMakeLists.txt
4+
+++ b/src/CMakeLists.txt
5+
@@ -2,6 +2,8 @@ include_directories(
6+
${PROJECT_SOURCE_DIR}
7+
)
8+
9+
+include(GNUInstallDirs)
10+
+
11+
if(Boost_FOUND)
12+
include_directories(${Boost_INCLUDE_DIRS})
13+
endif()
14+
@@ -129,6 +131,8 @@ target_link_libraries(libcryptominisat5
15+
)
16+
set_target_properties(libcryptominisat5 PROPERTIES
17+
OUTPUT_NAME cryptominisat5
18+
+ MACOSX_RPATH TRUE
19+
+ INSTALL_NAME_DIR "${CMAKE_INSTALL_FULL_LIBDIR}"
20+
PUBLIC_HEADER "${cryptominisat5_public_headers}"
21+
VERSION ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}
22+
SOVERSION ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}
23+
@@ -185,9 +189,9 @@ endforeach()
24+
25+
install(TARGETS libcryptominisat5
26+
EXPORT ${CRYPTOMINISAT5_EXPORT_NAME}
27+
- LIBRARY DESTINATION "${CMAKE_INSTALL_PREFIX}/lib"
28+
- ARCHIVE DESTINATION "${CMAKE_INSTALL_PREFIX}/lib"
29+
- PUBLIC_HEADER DESTINATION "${CMAKE_INSTALL_PREFIX}/include/cryptominisat5"
30+
+ LIBRARY DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}"
31+
+ ARCHIVE DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}"
32+
+ PUBLIC_HEADER DESTINATION "${CMAKE_INSTALL_FULL_INCLUDEDIR}/cryptominisat5"
33+
)
34+
35+
if (NOT ONLY_SIMPLE)

‎build/pkgs/cryptominisat/spkg-install

+10-65
Original file line numberDiff line numberDiff line change
@@ -1,76 +1,21 @@
11
#!/usr/bin/env bash
22

3-
if [ "$SAGE_LOCAL" = "" ]; then
4-
echo "SAGE_LOCAL undefined ... exiting"
5-
echo "Maybe run 'sage -sh'?"
6-
exit 1
7-
fi
8-
9-
unset RM
10-
11-
INCLUDES="-I$SAGE_LOCAL/include"
12-
LIBDIRS="-L$SAGE_LOCAL/lib"
13-
14-
CXXFLAGS="$CXXFLAGS $INCLUDES $LIBDIRS -g"
15-
16-
COMPILER=`testcc.sh $CC`
17-
18-
if [ "x$COMPILER" = "xGNU" ] ; then
19-
CXXFLAGS="$CXXFLAGS -fPIC -Wall -pedantic"
20-
elif [ "x$COMPILER" = "xSun_on_Solaris" ] ; then
21-
CXXFLAGS="$CXXFLAGS -Kpic"
22-
elif [ "x$COMPILER" = "xHP_on_HPUX" ] ; then
23-
CXXFLAGS="$CXXFLAGS + z"
24-
fi
25-
26-
CPPFLAGS="$INCLUDES"
27-
28-
if [ "x$SAGE_DEBUG" = "xyes" ]; then
29-
CXXFLAGS="$CXXFLAGS -O0"
30-
ENABLE_DEBUG="--enable-debug"
31-
else
32-
CXXFLAGS="$CXXFLAGS -O2"
33-
ENABLE_DEBUG=""
34-
fi
3+
fail () {
4+
echo -e >&2 $1
5+
exit 1
6+
}
357

36-
if [ "x$SAGE64" = "xyes" ]; then
37-
CXXFLAGS="$CXXFLAGS -m64"
38-
CPPFLAGS="$CPPFLAGS -m64"
39-
# FIXME: Do we need LDFLAGS here, too?
40-
# But looks as if all linking is performed by libtool/
41-
# gcc, so we do not really need it here.
8+
if [ "$SAGE_LOCAL" = "" ]; then
9+
fail "SAGE_LOCAL undefined ... exiting\nMaybe run 'sage -sh'?"
4210
fi
4311

44-
export CXXFLAGS
45-
export CPPFLAGS
46-
47-
48-
#build CryptoMiniSat
49-
5012
cd src
5113

52-
$MAKE clean
53-
54-
./configure --prefix=$SAGE_LOCAL $ENABLE_DEBUG
55-
56-
if [ $? -ne 0 ]; then
57-
echo "Error configuring cryptominisat"
58-
exit 1
59-
fi
14+
cmake -DCMAKE_INSTALL_PREFIX="${SAGE_LOCAL}" -DUSE_GAUSS='ON' -DZLIB_ROOT="${SAGE_LOCAL}" . || fail 'Error configuring cryptominisat'
6015

61-
$MAKE
16+
$MAKE VERBOSE=ON || fail 'Error building cryptominisat'
6217

63-
if [ $? -ne 0 ]; then
64-
echo "Error building cryptominisat"
65-
exit 1
66-
fi
67-
68-
$MAKE install
69-
70-
if [ $? -ne 0 ]; then
71-
echo "Error installing cryptominisat"
72-
exit 1
73-
fi
18+
$MAKE VERBOSE=ON install || fail 'Error installing cryptominisat'
7419

75-
cd ..
20+
exit 0
7621

‎build/pkgs/cryptominisat/type

+1-1
Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
experimental
1+
optional

‎build/pkgs/cython/patches/dd0b10c7e31ea136632bfcfd46c925adcf4c4af6.patch

+105
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,105 @@
1+
From dd0b10c7e31ea136632bfcfd46c925adcf4c4af6 Mon Sep 17 00:00:00 2001
2+
From: Robert Bradshaw <[email protected]>
3+
Date: Tue, 24 Jan 2017 15:53:43 -0800
4+
Subject: [PATCH] Work around numpy build formatting differences.
5+
6+
---
7+
tests/run/numpy_test.pyx | 22 ++++++++++++----------
8+
1 file changed, 12 insertions(+), 10 deletions(-)
9+
10+
diff --git a/tests/run/numpy_test.pyx b/tests/run/numpy_test.pyx
11+
index a813085f3..5fca12574 100644
12+
--- a/tests/run/numpy_test.pyx
13+
+++ b/tests/run/numpy_test.pyx
14+
@@ -4,6 +4,7 @@
15+
cimport numpy as np
16+
cimport cython
17+
18+
+import re
19+
import sys
20+
21+
from libc.stdlib cimport malloc
22+
@@ -133,7 +134,7 @@ try:
23+
Traceback (most recent call last):
24+
...
25+
ValueError: ndarray is not C...contiguous
26+
-
27+
+
28+
>>> test_dtype('b', inc1_byte)
29+
>>> test_dtype('B', inc1_ubyte)
30+
>>> test_dtype('h', inc1_short)
31+
@@ -142,7 +143,7 @@ try:
32+
>>> test_dtype('I', inc1_uint)
33+
>>> test_dtype('l', inc1_long)
34+
>>> test_dtype('L', inc1_ulong)
35+
-
36+
+
37+
>>> test_dtype('f', inc1_float)
38+
>>> test_dtype('d', inc1_double)
39+
>>> test_dtype('g', inc1_longdouble)
40+
@@ -172,11 +173,11 @@ try:
41+
Traceback (most recent call last):
42+
...
43+
ValueError: ...
44+
-
45+
+
46+
47+
48+
>>> test_recordarray()
49+
-
50+
+
51+
>>> print(test_nested_dtypes(np.zeros((3,), dtype=np.dtype([\
52+
('a', np.dtype('i,i')),\
53+
('b', np.dtype('i,i'))\
54+
@@ -198,12 +199,12 @@ try:
55+
56+
The output changed in Python 3:
57+
>> print(test_unpacked_align(np.zeros((1,), dtype=np.dtype('b,i', align=True))))
58+
- array([(22, 23)],
59+
+ array([(22, 23)],
60+
dtype=[('f0', '|i1'), ('', '|V3'), ('f1', '!i4')])
61+
62+
->
63+
64+
- array([(22, 23)],
65+
+ array([(22, 23)],
66+
dtype={'names':['f0','f1'], 'formats':['i1','!i4'], 'offsets':[0,4], 'itemsize':8, 'aligned':True})
67+
68+
69+
@@ -234,7 +235,7 @@ try:
70+
8,16
71+
72+
>>> test_point_record()
73+
- array([(0.0, 0.0), (1.0, -1.0), (2.0, -2.0)],
74+
+ array([(0., 0.), (1., -1.), (2., -2.)],
75+
dtype=[('x', '!f8'), ('y', '!f8')])
76+
77+
"""
78+
@@ -352,7 +353,7 @@ def inc1_clongdouble(np.ndarray[long double complex] arr): arr[1] = arr[1] + (1
79+
def inc1_cfloat_struct(np.ndarray[np.cfloat_t] arr):
80+
arr[1].real += 1
81+
arr[1].imag += 1
82+
-
83+
+
84+
def inc1_cdouble_struct(np.ndarray[np.cdouble_t] arr):
85+
arr[1].real += 1
86+
arr[1].imag += 1
87+
@@ -382,7 +383,7 @@ def inc1_uintp_t(np.ndarray[np.uintp_t] arr): arr[1] += 1
88+
def inc1_int32_t(np.ndarray[np.int32_t] arr): arr[1] += 1
89+
def inc1_float64_t(np.ndarray[np.float64_t] arr): arr[1] += 1
90+
91+
-
92+
+
93+
def test_dtype(dtype, inc1):
94+
if dtype in ("g", np.longdouble,
95+
"G", np.clongdouble):
96+
@@ -518,7 +519,8 @@ def test_point_record():
97+
for i in range(3):
98+
test[i].x = i
99+
test[i].y = -i
100+
- print repr(test).replace('<', '!').replace('>', '!')
101+
+ print re.sub(
102+
+ r'\.0+\b', '.', repr(test).replace('<', '!').replace('>', '!'))
103+
104+
# Test fused np.ndarray dtypes and runtime dispatch
105+
@testcase

‎build/pkgs/cython/patches/dd9eb10bc5657beed1f66221511c16ec6f4e517d.patch

+23
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,23 @@
1+
From dd9eb10bc5657beed1f66221511c16ec6f4e517d Mon Sep 17 00:00:00 2001
2+
From: Robert Bradshaw <[email protected]>
3+
Date: Tue, 24 Jan 2017 16:46:31 -0800
4+
Subject: [PATCH] More numpy struct format normalization.
5+
6+
---
7+
tests/run/numpy_test.pyx | 3 ++-
8+
1 file changed, 2 insertions(+), 1 deletion(-)
9+
10+
diff --git a/tests/run/numpy_test.pyx b/tests/run/numpy_test.pyx
11+
index 5fca12574..39fe1ffea 100644
12+
--- a/tests/run/numpy_test.pyx
13+
+++ b/tests/run/numpy_test.pyx
14+
@@ -520,7 +520,8 @@ def test_point_record():
15+
test[i].x = i
16+
test[i].y = -i
17+
print re.sub(
18+
- r'\.0+\b', '.', repr(test).replace('<', '!').replace('>', '!'))
19+
+ r'\.0+\b', '.', repr(test).replace('<', '!').replace('>', '!')
20+
+ .replace('( ', '(').replace(', ', ', '))
21+
22+
# Test fused np.ndarray dtypes and runtime dispatch
23+
@testcase

‎build/pkgs/database_gap/spkg-install

+5-6
Original file line numberDiff line numberDiff line change
@@ -6,8 +6,6 @@ if [ -z "$SAGE_LOCAL" ]; then
66
exit 1
77
fi
88

9-
touch "$SAGE_LOCAL/bin/gap_stamp"
10-
119
GAP=`echo 'Print(Concatenation("gap-", GAPInfo.Version));' | gap -q`
1210
if [ -z "$GAP" ]; then
1311
echo >&2 "Error determining the version of GAP installed in Sage."
@@ -24,33 +22,34 @@ echo "********************************************************************"
2422
cd src/
2523

2624
rm -rf "$SAGE_LOCAL/gap/latest/small"
27-
cp -rp small "$SAGE_LOCAL/gap/latest/"
25+
cp -r small "$SAGE_LOCAL/gap/latest/"
2826
if [ $? -ne 0 ]; then
2927
echo >&2 "Error installing small group database."
3028
exit 1
3129
fi
3230
echo "Installed small group database."
3331

3432
rm -rf "$SAGE_LOCAL/gap/latest/prim"
35-
cp -rp prim "$SAGE_LOCAL/gap/latest/"
33+
cp -r prim "$SAGE_LOCAL/gap/latest/"
3634
if [ $? -ne 0 ]; then
3735
echo >&2 "Error installing prim database."
3836
exit 1
3937
fi
4038
echo "Installed prim database."
4139

4240
rm -rf "$SAGE_LOCAL/gap/latest/trans"
43-
cp -rp trans "$SAGE_LOCAL/gap/latest/"
41+
cp -r trans "$SAGE_LOCAL/gap/latest/"
4442
if [ $? -ne 0 ]; then
4543
echo >&2 "Error installing trans database."
4644
exit 1
4745
fi
4846
echo "Installed trans database."
4947

5048
rm -rf "$SAGE_LOCAL/gap/latest/pkg/tomlib"
51-
cp -rp pkg/tomlib "$SAGE_LOCAL/gap/latest/pkg/"
49+
cp -r pkg/tomlib "$SAGE_LOCAL/gap/latest/pkg/"
5250
if [ $? -ne 0 ]; then
5351
echo >&2 "Error installing tomlib database."
5452
exit 1
5553
fi
5654
echo "Installed tomlib database."
55+

‎build/pkgs/ecl/package-version.txt

+1-1
Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
16.1.2.p3
1+
16.1.2.p4

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