Merge branch 'develop' of git://trac.sagemath.org/sage into t/24577/i…

…s_genus_for_torsion_quadratic_modules

Conflicts:
	src/sage/modules/torsion_quadratic_module.py

Makefile

@@ -11,10 +11,14 @@ default: all
 
 build: all-build
 
+# The --stop flag below is just a random flag to induce graceful
+# breakage with non-GNU versions of make.
+# See https://trac.sagemath.org/ticket/24617
+
 # Defer unknown targets to build/make/Makefile
 %::
 	@if [ -x relocate-once.py ]; then ./relocate-once.py; fi
-	$(MAKE) build/make/Makefile
+	$(MAKE) build/make/Makefile --stop
 	+build/bin/sage-logger \
 		"cd build/make && ./install '$@'" logs/install.log
 

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.2.beta4, Release Date: 2018-01-27
+SageMath version 8.2.beta6, Release Date: 2018-02-18

build/pkgs/arb/checksums.ini

@@ -1,4 +1,4 @@
 tarball=arb-VERSION.tar.gz
-sha1=2f06bfb433cdaecde0e824c5e638094fd666a0d1
-md5=d63cdd1147104790826c93bc8651104f
-cksum=2745482665
+sha1=27476d0529e48a07d92da90bd0fb80dd18f443e3
+md5=733285d9705d10b8024e551ffa81952f
+cksum=2391183744

build/pkgs/arb/package-version.txt

@@ -1 +1 @@
-2.11.1.p0
+2.12.0.p0

build/pkgs/atlas/dependencies

@@ -1,4 +1,4 @@
-| $(PYTHON)
+gfortran | $(PYTHON)
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/backports_functools_lru_cache/SPKG.txt

@@ -0,0 +1,5 @@
+= backports.functools_lru_cache =
+
+== Description ==
+
+A backport of functools.lru_cache from Python 3.3 as published at ActiveState.

build/pkgs/backports_functools_lru_cache/checksums.ini

@@ -0,0 +1,4 @@
+tarball=backports.functools_lru_cache-VERSION.tar.gz
+sha1=8a546e7887e961c2873c9b053f4e2cd2a96bd71d
+md5=b954e7d5e2ca0f0f66ad2ed12ba800e5
+cksum=2013684405

build/pkgs/backports_functools_lru_cache/dependencies

@@ -0,0 +1,5 @@
+$(PYTHON) | setuptools_scm 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/backports_functools_lru_cache/package-version.txt

@@ -0,0 +1 @@
+1.4

build/pkgs/backports_functools_lru_cache/spkg-install

@@ -0,0 +1,3 @@
+cd src
+
+sdh_pip_install .

build/pkgs/backports_functools_lru_cache/type

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

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=499badf9321c53c458652ca71580585463e574a3
-md5=e483eb587a1be5886b718e24f54a84a5
-cksum=3889320352
+sha1=5c564595c8dab9d93e86dcc43141b956086d9e16
+md5=9125aedb54d788ec1acb8f3112c5a04e
+cksum=251192083

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-252
+254

build/pkgs/coxeter3/SPKG.txt

@@ -44,6 +44,6 @@ by spkg-install:
   its data and messages from the Sage installation tree
 - makefile.patch: handle compilation flags for Darwin and Cygwin
 - warning.patch: remove deprecation warnings
-- sage.cpp: add a function for Bruhat invervals which is simpler to
+- sage.cpp: add a function for Bruhat intervals which is simpler to
   code in C++ than Cython
 

build/pkgs/cypari/checksums.ini

@@ -1,4 +1,4 @@
 tarball=cypari2-VERSION.tar.gz
-sha1=9e1848b5dc566133edad79437fd39e298e336642
-md5=f268f870d255bb98bd4e917f0d74a463
-cksum=3159551499
+sha1=d27b8a80470514471a59e38f3e7248c677c58abb
+md5=38149046fbdbecc390ce45e28fc10f8a
+cksum=296167081

build/pkgs/cypari/package-version.txt

@@ -1 +1 @@
-1.1.3
+1.1.4

build/pkgs/flint/package-version.txt

@@ -1 +1 @@
-2.5.2.p1
+2.5.2.p2

build/pkgs/flint/patches/linking_SunOS_FreeBSD.patch

@@ -0,0 +1,42 @@
+diff --git a/Makefile.in b/Makefile.in
+index 2d0475d..a8b2b44 100644
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -118,6 +118,7 @@ $(FLINT_LIB): $(LOBJS) $(LIB_SOURCES) $(EXT_SOURCES) $(HEADERS) $(EXT_HEADERS) |
+ 		$(LDCONFIG) -n "$(CURDIR)"; \
+ 	fi
+ 	ln -sf "$(FLINT_LIB)" "$(FLINT_LIBNAME)"; \
++	ln -sf "$(FLINT_LIB)" "$(FLINT_LIBNAME).$(FLINT_MAJOR)"; \
+
+ libflint.a: $(OBJS) $(LIB_SOURCES) $(EXT_SOURCES) $(HEADERS) $(EXT_HEADERS) | build build/interfaces
+ 	$(AT)$(foreach ext, $(EXTENSIONS), $(foreach dir, $(filter-out %templates, $(patsubst $(ext)/%.h, %, $(wildcard $(ext)/*.h))), mkdir -p build/$(dir); BUILD_DIR=$(CURDIR)/build/$(dir); export BUILD_DIR; MOD_DIR=$(dir); export MOD_DIR; $(MAKE) -f $(CURDIR)/Makefile.subdirs -C $(ext)/$(dir) static || exit $$?;))
+diff --git a/configure b/configure
+index 424ab0a..959a650 100755
+--- a/configure
++++ b/configure
+@@ -450,7 +450,7 @@ fi
+
+ # sometimes LDCONFIG is not to be found in the path. Look at some common places.
+ case "$OS" in
+-   MINGW*|CYGWIN*|Darwin)
++   MINGW*|CYGWIN*|Darwin|FreeBSD)
+       LDCONFIG="true";;
+    *)
+       if [ -z "$LDCONFIG" ]; then
+@@ -551,6 +551,8 @@ if [ -z "$CFLAGS" ]; then
+       CFLAGS="-O2 -funroll-loops -g -D _WIN64 $POPCNT_FLAG $ABI_FLAG"
+    elif [ "$MACHINE" = "mips64" ]; then
+       CFLAGS="-O2 -funroll-loops -g $POPCNT_FLAG $ABI_FLAG"
++   elif [ "$KERNEL" = FreeBSD ]; then
++      CFLAGS="-std=c99 -pedantic -Wall -O2 -funroll-loops -g $POPCNT_FLAG $ABI_FLAG $OPENMP_FLAG"
+    else
+       CFLAGS="-ansi -pedantic -Wall -O2 -funroll-loops -g $POPCNT_FLAG $ABI_FLAG"
+    fi
+@@ -715,6 +717,7 @@ echo "FLINT_SHARED=$SHARED" >> Makefile
+ echo "FLINT_LIB=$FLINT_LIB" >> Makefile
+ echo "FLINT_LIBNAME=$FLINT_LIBNAME" >> Makefile
+ echo "FLINT_SOLIB=$FLINT_SOLIB" >> Makefile
++echo "FLINT_MAJOR=$FLINT_MAJOR" >> Makefile
+ echo "EXEEXT=$EXEEXT" >> Makefile
+ echo "PREFIX=$PREFIX" >> Makefile
+ echo "" >> Makefile

build/pkgs/fplll/package-version.txt

@@ -1 +1 @@
-5.2.0.p0
+5.2.0.p1

build/pkgs/fplll/patches/GCC-PR10200.patch

@@ -0,0 +1,74 @@
+commit f9ea48c350feb9054c7176c2adec9c8e4a06f503
+Author: Jeroen Demeyer <jdemeyer@cage.ugent.be>
+Date:   Mon Feb 5 11:24:14 2018 +0100
+
+    Work around https://gcc.gnu.org/bugzilla/show_bug.cgi?id=10200
+
+    This shows up in particular on Solaris systems with GCC-5.4.0
+
+diff --git a/fplll/sieve/sieve_gauss_2sieve.cpp b/fplll/sieve/sieve_gauss_2sieve.cpp
+index 83eb817..625c6f0 100644
+--- a/fplll/sieve/sieve_gauss_2sieve.cpp
++++ b/fplll/sieve/sieve_gauss_2sieve.cpp
+@@ -33,7 +33,7 @@ template <class ZT, class F> Z_NR<ZT> GaussSieve<ZT, F>::update_p_2reduce(ListPo
+     for (lp_it = List.begin(); lp_it != List.end(); ++lp_it)
+     {
+       v = *lp_it;
+-      if (p->norm < v->norm)
++      if ((p->norm) < v->norm)
+         break;
+
+       /* if there is one reduction the vector should re-pass the list */
+diff --git a/fplll/sieve/sieve_gauss_3sieve.cpp b/fplll/sieve/sieve_gauss_3sieve.cpp
+index 3c3716c..3fdbca6 100644
+--- a/fplll/sieve/sieve_gauss_3sieve.cpp
++++ b/fplll/sieve/sieve_gauss_3sieve.cpp
+@@ -27,7 +27,7 @@ GaussSieve<ZT, F>::update_p_3reduce_2reduce(ListPoint<ZT> *p,
+     for (lp_it = List.begin(); lp_it != List.end(); ++lp_it)
+     {
+       v = *lp_it;
+-      if (p->norm < v->norm)
++      if ((p->norm) < v->norm)
+         break;
+       if (half_2reduce(p, v))
+       {
+@@ -166,7 +166,7 @@ template <class ZT, class F> Z_NR<ZT> GaussSieve<ZT, F>::update_p_3reduce(ListPo
+         continue;
+       }
+       ++lp_it2;
+-      if (v1->norm < p->norm)
++      if ((v1->norm) < p->norm)
+       {
+         vnew2 = new_listpoint<ZT>(nc);
+         if (check_3reduce(v1, p, v2, vnew2) != 1)
+diff --git a/fplll/sieve/sieve_gauss_4sieve.cpp b/fplll/sieve/sieve_gauss_4sieve.cpp
+index 9eb586e..f2758a4 100644
+--- a/fplll/sieve/sieve_gauss_4sieve.cpp
++++ b/fplll/sieve/sieve_gauss_4sieve.cpp
+@@ -15,7 +15,7 @@ void GaussSieve<ZT, F>::update_p_4reduce_aux(ListPoint<ZT> *p,
+   for (lp_it = List.begin(); lp_it != List.end(); ++lp_it)
+   {
+     v = *lp_it;
+-    if (p->norm < v->norm)
++    if ((p->norm) < v->norm)
+       break;
+   }
+   lp_it_k = lp_it;
+@@ -119,7 +119,7 @@ template <class ZT, class F> Z_NR<ZT> GaussSieve<ZT, F>::update_p_4reduce_3reduc
+         continue;
+       }
+       ++lp_it2;
+-      if (v1->norm < p->norm)
++      if ((v1->norm) < p->norm)
+       {
+         /*cout << "#   --- here 1 " << endl;
+         cout << v1->norm << endl;
+@@ -274,7 +274,7 @@ template <class ZT, class F> Z_NR<ZT> GaussSieve<ZT, F>::update_p_4reduce(ListPo
+         }
+         ++lp_it3;
+         /* (v1, p, v2, v3) or (v1, v2, p, v3) */
+-        if (v1->norm < p->norm)
++        if ((v1->norm) < p->norm)
+         {
+           /* (v1, p, v2, v3) */
+           if (v2->norm > p->norm)

build/pkgs/fplll/patches/pow.patch

@@ -0,0 +1,27 @@
+commit 848a55ec1eaa425d6843303fcc0fac9eda397a83
+Author: Jeroen Demeyer <jdemeyer@cage.ugent.be>
+Date:   Mon Feb 5 11:22:54 2018 +0100
+
+    Fix pow() calls on Solaris
+
+diff --git a/fplll/nr/dpe.h b/fplll/nr/dpe.h
+index 1ad6562..c132378 100644
+--- a/fplll/nr/dpe.h
++++ b/fplll/nr/dpe.h
+@@ -708,14 +708,14 @@ DPE_INLINE void dpe_ugly_log(dpe_t x, const dpe_t y)
+ DPE_INLINE void dpe_ugly_exp(dpe_t x, const dpe_t y)
+ {
+   // printf ("## exp is %ld\n", DPE_EXP(y));
+-  dpe_set_d(x, exp(((double)DPE_MANT(y)) * pow(2, ((double)DPE_EXP(y)))));
++  dpe_set_d(x, exp(((double)DPE_MANT(y)) * pow(2.0, ((double)DPE_EXP(y)))));
+ }
+
+ /* More hacks */
+ /* x = y^k */
+ DPE_INLINE void dpe_pow_si(dpe_t x, const dpe_t y, const unsigned int k)
+ {
+-  DPE_MANT(x) = pow(DPE_MANT(y), k);
++  DPE_MANT(x) = pow(DPE_MANT(y), (double)k);
+   DPE_EXP(x)  = DPE_EXP(y) * k;
+   dpe_normalize(x);
+ }

build/pkgs/gcc/dependencies

@@ -1,4 +1,4 @@
-| $(MP_LIBRARY) mpfr mpc zlib xz
+$(MP_LIBRARY) mpfr mpc zlib | xz
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/gfortran/SPKG.txt

@@ -0,0 +1,25 @@
+= gfortran =
+
+== Description ==
+
+The GNU Compiler Collection, including the C, C++ and Fortran compiler.
+This particular package is meant to only make gfortran available.
+
+== License ==
+
+GPL version 2 or version 3
+
+== Upstream Contact ==
+
+http://gcc.gnu.org/
+
+== Dependencies ==
+
+ * zlib
+ * MPIR
+ * MPFR
+ * MPC
+
+== Special Update/Build Instructions ==
+
+None.

build/pkgs/gfortran/checksums.ini

@@ -0,0 +1 @@
+../gcc/checksums.ini

build/pkgs/gfortran/dependencies

@@ -0,0 +1 @@
+../gcc/dependencies

build/pkgs/gfortran/package-version.txt

@@ -0,0 +1 @@
+../gcc/package-version.txt

build/pkgs/gfortran/spkg-install

@@ -0,0 +1,77 @@
+if [ -z "$SAGE_LOCAL" ]; then
+    echo >&2 "SAGE_LOCAL undefined ... exiting"
+    echo >&2 "Maybe run 'sage --sh'?"
+    exit 1
+fi
+
+# This spkg shouldn't be installed if gcc is already installed
+if [ -a "$SAGE_LOCAL"/bin/gcc ]; then
+    echo >&2 "Error: gcc is already installed"
+    exit 1
+fi
+
+# Exit on error
+set -e
+
+# Build in a separate directory, not in src/ (a.k.a. a VPATH build).
+# This is the recommended way to build GCC.
+mkdir gcc-build
+cd gcc-build
+
+
+# On OSX:
+if [ "$UNAME" = "Darwin" ]; then
+    # isl/cloog libraries are almost certainly from Homebrew and won't work
+    GCC_CONFIGURE="--without-isl --without-cloog $GCC_CONFIGURE"
+
+    # Use 'bootstrap-debug' build configuration to force stripping of object
+    # files prior to comparison during bootstrap (broken by Xcode 6.3).
+    # See #18156
+    GCC_CONFIGURE="--with-build-config=bootstrap-debug $GCC_CONFIGURE"
+fi
+
+# Let Gfortran build on Raspberry Pi using hard floats.
+if [ `uname -m` = "armv6l" ]; then
+    GCC_CONFIGURE="--with-arch=armv6 --with-fpu=vfp --with-float=hard $GCC_CONFIGURE"
+fi
+
+# Let Gfortran build on more recent ARM boards using hard floats.
+if [ `uname -m` = "armv7l" ]; then
+    GCC_CONFIGURE="--with-arch=armv7-a --with-fpu=vfpv3-d16 --with-float=hard $GCC_CONFIGURE"
+fi
+
+if [ "$SAGE_CHECK" = yes ]; then
+    # Enable internal checks in GCC.  These checks do not affect the
+    # binaries produced by GCC, but they do increase the compile time
+    # of everything compiled with GCC.
+    GCC_CONFIGURE="$GCC_CONFIGURE --enable-checking=yes"
+fi
+
+# Use the assembler/linker specified by $AS/$LD if they differ from the
+# default.
+if [ -n "$AS" -a "$AS" != "as" ]; then
+    CONFIGURE_AS="--with-as=$AS"
+fi
+if [ -n "$LD" -a "$LD" != "ld" ]; then
+    CONFIGURE_LD="--with-ld=$LD"
+fi
+
+../src/configure \
+    --prefix="$SAGE_LOCAL" \
+    --with-local-prefix="$SAGE_LOCAL" \
+    --with-gmp="$SAGE_LOCAL" --with-mpfr="$SAGE_LOCAL" --with-mpc="$SAGE_LOCAL" \
+    --with-system-zlib \
+    --disable-multilib \
+    --disable-nls \
+    --enable-languages=fortran \
+    --disable-bootstrap \
+    --disable-libitm \
+    $GCC_CONFIGURE "$CONFIGURE_AS" "$CONFIGURE_LD"
+
+$MAKE BOOT_LDFLAGS="-Wl,-rpath,$SAGE_LOCAL/lib"
+
+$MAKE install
+
+# The spkg still installs a minimal C compiler that needs to be removed
+# so it doesn't conflict with the configured C compiler.
+rm -f "$SAGE_LOCAL"/bin/gcc "$SAGE_LOCAL"/bin/cpp

build/pkgs/gfortran/type

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

build/pkgs/giac/SPKG.txt

@@ -16,8 +16,11 @@
 
 == Licence ==
 
-GPLv3+ except the french html documentation which is freely redistributable
-       for non commercial only purposes. This doc has been removed in the spkg)
+GPLv3+
+
+Note: except the french html documentation which is freely
+redistributable for non commercial only purposes. This doc has been
+removed in the Sage package, see spkg-src
 
 == Upstream Contact ==
 
@@ -30,12 +33,8 @@ GPLv3+ except the french html documentation which is freely redistributable
   * gettext, readline
   * giac will benefit of ntl, pari, mpfr, gsl, lapack but they should be already installed by sage.
   * giac can also benefit of mpfi for arithmetic on intervals.
-  * The Documentation is  pre-built, hevea or latex or ... are not needed to install the package.
+  * The Documentation is pre-built, hevea or latex or ... are not needed to install the package.
 
 == Special Update/Build Instructions ==
 
-  * The script_subdirectory of the pexpect giac interface is create in spkg-install.
-  * Some gcc 4.7.2 gives a seg fault when compiling giac, but earlier or later version
-    should be fine.
-    http://gcc.gnu.org/bugzilla/show_bug.cgi?id=54986
-  * pari support has been enabled in spkg-install. To allow this, giac have been patched to not always init pari. (See the comments in patches/README.txt for details)
+  * Use spkg-src to update this package

build/pkgs/giac/package-version.txt

@@ -1 +1 @@
-1.4.9.45
+1.4.9.45.p2