Merge tag '7.1.beta1' into symbolics/stieltjes-constants

Sage version 7.1.beta1

VERSION.txt

@@ -1 +1 @@
-Sage version 7.0.beta3, released 2016-01-06
+Sage version 7.1.beta1, released 2016-01-28

build/pkgs/atlas/configuration.py

@@ -161,6 +161,8 @@ def close(self):
 
 conf['generic_binary?'] = (os.environ.get('SAGE_FAT_BINARY', 'no') == 'yes')
 
+conf['user'] = os.environ.get('ATLAS_CONFIGURE', '')
+
 ######################################################################
 ### bit width
 ######################################################################
@@ -253,9 +255,5 @@ def close(self):
 ######################################################################
 
 print("Configuration:")
-for key, value in conf.items():
-    print('    '+str(key)+': '+str(value))
-
-
-
-
+for k in sorted(conf, key=str.lower):
+    print('    {}: {}'.format(k, conf[k]))

build/pkgs/atlas/spkg-install

@@ -346,6 +346,10 @@ def configure(arch=None, isa_ext=None):
         isa_extension = sum(1 << ATLAS_ISAEXT.index(x) for x in isa_ext)
         cmd += ' -V '+str(isa_extension)
 
+    # Custom configure options
+    if conf['user']:
+        cmd += " " + conf['user']
+
     rc = system_with_flush(cmd)
     make_check_enums()
     return rc

build/pkgs/cliquer/SPKG.txt

@@ -16,7 +16,4 @@ http://users.tkk.fi/pat/cliquer.html
  * None
 
 == Patches ==
- * Makefile.patch: Patch the Makefile for Sage. Remove hardcoded
-   compiler and linker flags, allow flags to be set from spkg-install.
-   More importantly, we're building cliquer as a dynamic shared library,
-   instead of a stand-alone program.
+ * autotoolized - see https://github.com/dimpase/autocliquer

build/pkgs/cliquer/checksums.ini

@@ -1,4 +1,4 @@
-tarball=cliquer-VERSION.tar.bz2
-sha1=8239530eb14c1273c32ffcf3b671dd3766084374
-md5=32b97b6689318b58d9c099e2c7769521
-cksum=3641271864
+tarball=cliquer-VERSION.tar.gz
+sha1=930ec79f64facb8ac4035a3e3702ed2b1dabd092
+md5=1d985e0bed876cc69aed43953a814a6a
+cksum=766312376

build/pkgs/cliquer/package-version.txt

@@ -1 +1 @@
-1.21.p2
+1.21.p3

build/pkgs/cliquer/spkg-check

@@ -1,35 +1,18 @@
 #!/usr/bin/env bash
 
-if [ "$SAGE_LOCAL" = "" ]; then
-    echo "SAGE_LOCAL undefined ... exiting";
-    echo "Maybe run 'sage -sh'?"
+if [ -z "$SAGE_LOCAL" ]; then
+    echo >&2 "Error: SAGE_LOCAL undefined - exiting..."
+    echo >&2 "Maybe run 'sage -sh'?"
     exit 1
 fi
 
-OPTIMIZATION_FLAGS="-O3 -funroll-loops -fomit-frame-pointer"
-# Work around a bug in gcc 4.6.0: http://gcc.gnu.org/bugzilla/show_bug.cgi?id=48774
-if [ "`testcc.sh $CC`" = GCC ] ; then
-    if $CC -dumpversion 2>/dev/null |grep >/dev/null '^4\.6\.[01]' ; then
-        echo "Warning: Working around bug in gcc 4.6.0"
-        OPTIMIZATION_FLAGS="$OPTIMIZATION_FLAGS -fno-ivopts"
-    fi
-fi
-
-CFLAGS="$CFLAGS `testcflags.sh -g $OPTIMIZATION_FLAGS -fPIC -KPIC -Wall`"
-CPPFLAGS="$CPPFLAGS -I$SAGE_LOCAL/include"
-LDFLAGS="$LDFLAGS -L$SAGE_LOCAL/lib"
+cd src
 
-# Compile for 64-bit if SAGE64 is set to 'yes'.
-# On 64-bit hardware, we don't need to set this variable to true. A
-# 64-bit cliquer library would be built on such platform.
-if [ "$SAGE64" = yes ]; then
-    CFLAGS="$CFLAGS -m64 "
-    LDFLAGS="$LDFLAGS -m64 "
+echo "Now building and running cliquer's test suite..."
+$MAKE check
+if [ $? -ne 0 ]; then
+    echo >&2 "Error: The cliquer's test suite failed."
+    exit 1
 fi
 
-# Export everything
-export CFLAGS
-export CPPFLAGS
-export LDFLAGS
-
-cd src && $MAKE test
+echo "The cliquer's test suite passed successfully."

build/pkgs/cliquer/spkg-install

@@ -1,43 +1,14 @@
 #!/usr/bin/env bash
 
-OPTIMIZATION_FLAGS="-O3 -funroll-loops -fomit-frame-pointer"
-# Work around a bug in gcc 4.6.0: http://gcc.gnu.org/bugzilla/show_bug.cgi?id=48774
-if [ "`testcc.sh $CC`" = GCC ] ; then
-    if $CC -dumpversion 2>/dev/null |grep >/dev/null '^4\.6\.[01]' ; then
-        echo "Warning: Working around bug in gcc 4.6.0"
-        OPTIMIZATION_FLAGS="$OPTIMIZATION_FLAGS -fno-ivopts"
-    fi
-fi
-
-CFLAGS="$CFLAGS `testcflags.sh -g $OPTIMIZATION_FLAGS -fPIC -KPIC -Wall`"
-CPPFLAGS="$CPPFLAGS -I$SAGE_LOCAL/include"
-
-# Compile for 64-bit if SAGE64 is set to 'yes'.
-# On 64-bit hardware, we don't need to set this variable to true. A
-# 64-bit cliquer library would be built on such platform.
-if [ "$SAGE64" = yes ]; then
-    echo "Building a 64-bit version of cliquer"
-    CFLAGS="$CFLAGS -m64 "
-    LDFLAGS="$LDFLAGS -m64 "
-fi
-
-# Flags for building a dynamically linked shared object.
-if [ "$UNAME" = "Darwin" ]; then
-    SAGESOFLAGS="-dynamiclib -single_module -flat_namespace -undefined dynamic_lookup"
-elif [ "$UNAME" = "SunOS" ]; then
-    SAGESOFLAGS="-shared -Wl,-h,libcliquer.so -Wl,-ztext"
-else
-    SAGESOFLAGS="-shared -Wl,-soname,libcliquer.so"
+if [ -z "$SAGE_LOCAL" ]; then
+    echo >&2 "SAGE_LOCAL undefined - exiting..."
+    echo >&2 "Maybe run 'sage -sh'?"
+    exit 1
 fi
 
-# Export everything
-export CFLAGS
-export CPPFLAGS
-export LDFLAGS
-export SAGESOFLAGS
-
 cd src
 
+echo "Applying patches..."
 # Apply all patches
 for patch in ../patches/*.patch; do
     [ -r "$patch" ] || continue  # Skip non-existing or non-readable patches
@@ -49,22 +20,16 @@ for patch in ../patches/*.patch; do
     fi
 done
 
-$MAKE
+echo "Configuring..."
+./configure --prefix="$SAGE_LOCAL" --disable-static --libdir="$SAGE_LOCAL/lib"
 if [ $? -ne 0 ]; then
-    echo >&2 "Failed to compile cliquer"
-    exit 1
+   echo >&2 "Error configuring cliquer"
+   exit 1
 fi
 
-rm -rf "$SAGE_LOCAL/include/cliquer/"
-mkdir -p "$SAGE_LOCAL/include/cliquer/"
-cp *.h "$SAGE_LOCAL/include/cliquer/"
-
-if [ "$UNAME" = "Darwin" ]; then
-    cp -f libcliquer.so "$SAGE_LOCAL/lib/libcliquer.dylib"
-    install_name_tool -id "${SAGE_LOCAL}"/lib/libcliquer.dylib "${SAGE_LOCAL}"/lib/libcliquer.dylib
-elif [ "$UNAME" = "CYGWIN" ]; then
-    cp -f libcliquer.so "$SAGE_LOCAL/lib/libcliquer.dll"
+echo "Building and installing ..."
+$MAKE install
+if [ $? -ne 0 ]; then
+    echo >&2 "Error installing cliquer"
+    exit 1
 fi
-
-# Copy this in all cases, in any case it doesn't hurt.
-cp -f libcliquer.so "$SAGE_LOCAL/lib/libcliquer.so"

build/pkgs/cliquer/spkg-src

@@ -0,0 +1,23 @@
+#!/bin/sh
+#
+# creates the tarball in the current dir, to be moved to ../../../upstream
+
+#PATCHLEVEL=".p0"
+PATCHLEVEL=
+
+rm -rf autocliquer/
+git clone https://github.com/dimpase/autocliquer.git
+cd autocliquer/
+
+VERSION=`autoconf --trace='AC_INIT:$2'`
+autoreconf -fi
+automake --add-missing --copy
+./configure
+
+rm -f cliquer-$VERSION.tar.gz
+make dist
+mv cliquer-$VERSION.tar.gz ../
+cd ..
+rm -rf autocliquer/ 
+
+

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=740a26d4dab56b5a88fa0e886c9bbed931d6a961
-md5=4d3f1282f9db5dab064822b856b86e99
-cksum=3179103806
+sha1=667c4449d5d193a6520ad38cf9c0f49e209cbc21
+md5=de3e80d1d278a05e430669fd8beefa19
+cksum=3190707453

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-137
+142

build/pkgs/cryptominisat/type

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

build/pkgs/flint/patches/use_ldflags_in_tests.patch

@@ -0,0 +1,25 @@
+Use LDFLAGS for tests, too
+
+Upstream PR: https://github.com/wbhart/flint2/pull/209
+
+
+--- a/Makefile.in	2016-01-09 01:44:52.178779543 +0100
++++ b/Makefile.in	2016-01-09 01:44:19.874183406 +0100
+@@ -227,7 +227,7 @@
+ 	$(QUIET_CC) $(CC) $(CFLAGS) $(INCS) -c $< -o $@;
+
+ build/test/%$(EXEEXT): test/%.c $(HEADERS) | build/test
+-	$(QUIET_CC) $(CC) $(CFLAGS) $(INCS) $< -o $@ $(LIBS)
++	$(QUIET_CC) $(CC) $(CFLAGS) $(INCS) $(LDFLAGS) $< -o $@ $(LIBS)
+
+ build/test:
+ 	mkdir -p build/test
+@@ -242,7 +242,7 @@
+ 	$(QUIET_CXX) $(CXX) $(CXXFLAGS) $(INCS) -c $< -o $@
+
+ build/interfaces/test/t-NTL-interface$(EXEEXT): interfaces/test/t-NTL-interface.cpp build/interfaces/NTL-interface.o
+-	$(QUIET_CXX) $(CXX) $(CXXFLAGS) $(INCS) $< build/interfaces/NTL-interface.o -o $@ $(LIBS)
++	$(QUIET_CXX) $(CXX) $(CXXFLAGS) $(INCS) $(LDFLAGS) $< build/interfaces/NTL-interface.o -o $@ $(LIBS)
+
+ print-%:
+ 	@echo '$*=$($*)'

build/pkgs/flint/spkg-check

@@ -13,7 +13,7 @@ if [ "$SAGE_LOCAL" = "" ]; then
 fi
 
 cd src
-$MAKE check
+$MAKE check AT= QUIET_CC= QUIET_CXX= QUIET_AR=
 
 if [ $? -ne 0 ]; then
     echo >&2 "Error: FLINT failed to pass its test suite."

build/pkgs/flint/spkg-install

@@ -26,15 +26,15 @@ fi
 
 cd src
 
-#echo "Patching FLINT."
-#for patch in ../patches/*.patch; do
-#    [ -f "$patch" ] || continue
-#    patch -p1 <"$patch"
-#    if [ $? -ne 0 ]; then
-#        echo >&2 "Error applying '$patch'"
-#        exit 1
-#    fi
-#done
+echo "Patching FLINT."
+for patch in ../patches/*.patch; do
+   [ -f "$patch" ] || continue
+   patch -p1 <"$patch"
+   if [ $? -ne 0 ]; then
+       echo >&2 "Error applying '$patch'"
+       exit 1
+   fi
+done
 
 echo "Configuring FLINT."
 ./configure \
@@ -50,7 +50,7 @@ if [ $? -ne 0 ]; then
 fi
 
 echo "Building FLINT shared library."
-$MAKE
+$MAKE verbose
 if [ $? -ne 0 ]; then
     echo >&2 "Error: Failed to build FLINT shared library."
     exit 1

build/pkgs/gp2c/checksums.ini

@@ -1,4 +1,4 @@
 tarball=gp2c-VERSION.tar.gz
-sha1=5acb1a13e1ed8ee877ffb34baa3b817e720f3e50
-md5=cb263990e399153aca6a2540930b4600
-cksum=1931194041
+sha1=e07cebffcd09c0d644d52335130984f33042b46f
+md5=3f6bb47d41ddca7b6a4938d16abbe4e8
+cksum=3338275717

build/pkgs/gp2c/package-version.txt

@@ -1 +1 @@
-0.0.9pl3
+0.0.9pl5