Merge branch 'develop' into t/24889/enumerate_all_genera_of_given_sig…

…nature__determinant_and_bounded_scale_of_a_jordan_block_

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.3.beta0, Release Date: 2018-05-09
+SageMath version 8.3.beta1, Release Date: 2018-05-14

build/make/deps

@@ -157,6 +157,7 @@ sagelib: \
 		$(inst_pkgconfig) \
 		$(inst_planarity) \
 		$(inst_ppl) \
+		$(inst_pycygwin) \
 		$(inst_pynac) \
 		$(inst_python2) \
 		$(inst_python3) \

build/pkgs/atlas/spkg-install.py

@@ -158,7 +158,7 @@ def is_atlas_lib_path(path, libs):
         print('- or liblapack and libblas;')
         print('you wish to use existing ATLAS libraries.')
         print('For more details, see:')
-        print('http://doc.sagemath.org/html/en/installation/source.html#environment-variables')
+        print('https://doc.sagemath.org/html/en/installation/source.html#environment-variables')
         print('Unset SAGE_ATLAS_LIB to build ATLAS from source.')
         print('Then type make.')
         sys.exit(2)

build/pkgs/cmake/checksums.ini

@@ -1,4 +1,4 @@
 tarball=cmake-VERSION.tar.gz
-sha1=4e4bf2e2f3443325f2abaec5e96819840d832427
-md5=e8ef820ddf7a650845252bca846696e7
-cksum=3021330276
+sha1=7851f87185f80e260ea634d5985ec9215fe408c8
+md5=f3ebc79b5dec85b49abe75958ffa1a03
+cksum=1559829871

build/pkgs/cmake/package-version.txt

@@ -1 +1 @@
-3.8.1
+3.11.0

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=12c986c0c792c32279e4e7948e69feba57b51f92
-md5=83a4497b5cce2f0a3a17746f9a6e9528
-cksum=2212091534
+sha1=3895cb984ffb129f2880278a2c57b57c64905dc6
+md5=1f0e379b82ed3a41b23af0efd8a2c88c
+cksum=4081775049

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-263
+264

build/pkgs/curl/package-version.txt

@@ -1 +1 @@
-7.56.1
+7.56.1.p0

build/pkgs/curl/spkg-install

@@ -1,9 +1,3 @@
-if [ -z "$SAGE_LOCAL" ] ; then
-    echo >&2 "Error - SAGE_LOCAL undefined ... exiting"
-    echo >&2 "Maybe run 'sage -sh'?"
-    exit 1
-fi
-
 cd src
 
 if [ "$SAGE_FAT_BINARY" = yes ]; then
@@ -20,21 +14,6 @@ if [ "$UNAME" = "Darwin" ]; then
     fi
 fi
 
-./configure --prefix="$SAGE_LOCAL" --libdir="$SAGE_LOCAL/lib" \
-    $CURL_CONFIGURE
-if [ $? -ne 0 ]; then
-    echo >&2 "Error configuring curl."
-    exit 1
-fi
-
-$MAKE
-if [ $? -ne 0 ]; then
-    echo >&2 "Error building curl."
-    exit 1
-fi
-
-$MAKE install
-if [ $? -ne 0 ]; then
-    echo >&2 "Error installing curl."
-    exit 1
-fi
+sdh_configure $CURL_CONFIGURE
+sdh_make
+sdh_make_install

build/pkgs/freetype/package-version.txt

@@ -1 +1 @@
-2.8.1
+2.8.1.p0

build/pkgs/freetype/spkg-install

@@ -1,29 +1,9 @@
-if [ "$SAGE_LOCAL" = "" ]; then
-   echo "SAGE_LOCAL undefined ... exiting";
-   echo "Maybe run 'sage -sh'?"
-   exit 1
-fi
-
 cd src
 
 # Disabling harfbuzz until upstream properly check for suitable version
-GNUMAKE=${MAKE} ./configure --prefix="$SAGE_LOCAL" --libdir="$SAGE_LOCAL/lib" --with-harfbuzz=no
-
-if [ $? -ne 0 ]; then
-    exit 1;
-fi;
-
-${MAKE}
-
-if [ $? -ne 0 ]; then
-    exit 1;
-fi;
-
-${MAKE} install
-
-if [ $? -ne 0 ]; then
-    exit 1;
-fi;
+GNUMAKE=${MAKE} sdh_configure --with-harfbuzz=no
+sdh_make
+sdh_make_install
 
 # The following file may be present from old builds of freetype, and
 # its presence can break the matplotlib build. So remove it. (The

build/pkgs/gc/package-version.txt

@@ -1 +1 @@
-7.6.4
+7.6.4.p0

build/pkgs/gc/spkg-install

@@ -1,9 +1,3 @@
-if [ -z "$SAGE_LOCAL" ]; then
-    echo >&2 "SAGE_LOCAL undefined ... exiting"
-    echo >&2 "Maybe run 'sage -sh'?"
-    exit 1
-fi
-
 cd src
 
 if [ "$SAGE_DEBUG" = "yes" ]; then
@@ -13,31 +7,15 @@ else
     export CFLAGS="-O2 -g $CFLAGS"
 fi
 
-CONFIGURE_FLAGS="--enable-large-config"
+GC_CONFIGURE="--enable-large-config"
+
 if [ "$UNAME" = "CYGWIN" ]; then
     # See https://trac.sagemath.org/ticket/22694
-    CONFIGURE_FLAGS="$CONFIGURE_FLAGS --enable-threads=posix --enable-handle-fork --enable-shared --disable-static"
+    GC_CONFIGURE="$GC_CONFIGURE --enable-threads=posix --enable-handle-fork --enable-shared --disable-static"
     # Force use of mmap on Cygwin https://trac.sagemath.org/ticket/23973
     export CFLAGS="$CFLAGS -DUSE_MMAP -DUSE_MUNMAP"
 fi
 
-./configure --prefix="$SAGE_LOCAL" --libdir="$SAGE_LOCAL/lib" $CONFIGURE_FLAGS
-
-if [ $? -ne 0 ]; then
-   echo >&2 "Error configuring BoehmGC."
-   exit 1
-fi
-
-$MAKE
-
-if [ $? -ne 0 ]; then
-   echo >&2 "Error building BoehmGC."
-   exit 1
-fi
-
-$MAKE install
-
-if [ $? -ne 0 ]; then
-   echo >&2 "Error installing BoehmGC."
-   exit 1
-fi
+sdh_configure $GC_CONFIGURE
+sdh_make
+sdh_make_install

build/pkgs/ipywidgets/checksums.ini

@@ -1,4 +1,4 @@
 tarball=ipywidgets-VERSION.tar.gz
-sha1=8b32ce2f82665ab500b7f359bf93bbf803731cff
-md5=4538e533c99ac950d9bc39fdb8d07610
-cksum=475923855
+sha1=443148cd72ea1e708f8f0be1ea5de99dd1019808
+md5=de18af90829063fad0990ff89aa3cff5
+cksum=2457014809

build/pkgs/ipywidgets/package-version.txt

@@ -1 +1 @@
-7.1.1
+7.2.0

build/pkgs/ntl/package-version.txt

@@ -1 +1 @@
-10.3.0
+10.3.0.p0

build/pkgs/ntl/spkg-install

@@ -11,11 +11,6 @@
 #
 ###############################################################################
 
-if [ -z "$SAGE_LOCAL" ]; then
-    echo >&2 "Error: SAGE_LOCAL undefined - exiting..."
-    echo >&2 "Maybe run 'sage -sh'?"
-    exit 1
-fi
 
 SRC=`pwd`/src/src
 
@@ -104,12 +99,7 @@ ntl_configure()
         LDFLAGS="$LDFLAGS" LIBTOOL_LINK_FLAGS="$LIBTOOL_LINK_FLAGS" \
         NTL_GMP_LIP=on NTL_GF2X_LIB=on \
         "$DISABLE_NATIVE" \
-        NTL_THREADS=off
-
-    if [ $? -ne 0 ]; then
-        echo >&2 "Error configuring NTL."
-        exit 1
-    fi
+        NTL_THREADS=off || sdh_die "Error configuring NTL."
 }
 
 ntl_build()
@@ -119,12 +109,7 @@ ntl_build()
 
     cd "$SRC"
 
-    $MAKE
-
-    if [ $? -ne 0 ]; then
-        echo >&2 "Error building/tuning NTL."
-        exit 1
-    fi
+    sdh_make
 }
 
 ntl_install()
@@ -139,17 +124,7 @@ ntl_install()
 
     cd "$SRC"
 
-    $MAKE install
-
-    if [ $? -ne 0 ]; then
-        echo >&2 "Error installing NTL."
-        exit 1
-    fi
-
-    # Touch all includes such that dependency checking works properly:
-    # the timestamp of the includes should be *now*, not the time when
-    # the NTL package was created.
-    touch "$SAGE_LOCAL"/include/NTL/*
+    sdh_make_install
 }
 
 ntl_configure

build/pkgs/openblas/package-version.txt

@@ -1 +1 @@
-0.2.20.p1
+0.2.20.p2

build/pkgs/openblas/spkg-install

@@ -1,9 +1,3 @@
-if [ -z "$SAGE_LOCAL" ]; then
-    echo >&2 "SAGE_LOCAL undefined ... exiting"
-    echo >&2 "Maybe run 'sage --sh'?"
-    exit 1
-fi
-
 cd src
 
 # See #22021 for issues with multithreading
@@ -28,33 +22,29 @@ fi
 
 echo "Building OpenBLAS: $MAKE $OPENBLAS_CONFIGURE"
 
-$MAKE libs netlib shared $OPENBLAS_CONFIGURE
-if [ $? -ne 0 ]; then
-    # First make sure we already didn't set a target
+if ! (sdh_make libs netlib shared $OPENBLAS_CONFIGURE); then
     if [[ $OPENBLAS_CONFIGURE == *"TARGET"* ]]; then
-        echo >&2 "Error building OpenBLAS"
-        exit 1
+        sdh_die "Error building OpenBLAS"
     else
         # The recommended TARGET is ATOM if CPU fails
         # See https://github.com/xianyi/OpenBLAS/issues/1204
         OPENBLAS_CONFIGURE="$OPENBLAS_CONFIGURE TARGET=ATOM"
         echo "Error building OpenBLAS"
         echo "Retrying building OpenBLAS: $MAKE $OPENBLAS_CONFIGURE"
-        $MAKE libs netlib shared $OPENBLAS_CONFIGURE
-        if [ $? -ne 0 ]; then
-            echo >&2 "Error building OpenBLAS a second time"
-            exit 1
-        fi
+        sdh_make libs netlib shared $OPENBLAS_CONFIGURE
     fi
-
-fi
-
-$MAKE install PREFIX="$SAGE_LOCAL" NO_STATIC=1 $OPENBLAS_CONFIGURE
-if [ $? -ne 0 ]; then
-    echo >&2 "Error installing OpenBLAS"
-    exit 1
 fi
 
-
+sdh_make_install PREFIX="$SAGE_LOCAL" NO_STATIC=1 $OPENBLAS_CONFIGURE
 cd ..
 ./write_pc_file.py
+
+# OpenBLAS's Makefile has a bug w.r.t. calling install_name_tool when
+# DESTDIR is set.  It should *not* include the DESTDIR in the library's
+# install_name; we set the correct install_name here
+if [ "$UNAME" = "Darwin" ]; then
+    cd "$SAGE_DESTDIR_LOCAL/lib"
+    for dylib in lib*openblas*.dylib; do
+        install_name_tool -id "$SAGE_LOCAL/lib/$dylib" "$dylib"
+    done
+fi

build/pkgs/openblas/write_pc_file.py

@@ -18,12 +18,15 @@
 
 
 try:
-    SAGE_LOCAL=os.environ['SAGE_LOCAL']
+    SAGE_LOCAL = os.environ['SAGE_LOCAL']
 except KeyError:
     raise RuntimeError('must be run in a sage shell')
 
+SAGE_DESTDIR = os.environ.get('SAGE_DESTDIR', '')
 
-pkgconfigdir = os.path.join(SAGE_LOCAL, 'lib', 'pkgconfig')
+
+pkgconfigdir = os.path.join(SAGE_DESTDIR, SAGE_LOCAL.lstrip('/'), 'lib',
+                            'pkgconfig')
 if not os.path.isdir(pkgconfigdir):
     os.makedirs(pkgconfigdir)
 

build/pkgs/palp/SPKG.txt

@@ -70,7 +70,7 @@ facet enumeration compares well with existing packages.
  * #8477: Work around apparent GNU make problem when building spkgs in
     parallel.
  * SPKG.txt cleanup. The description is based on the abstract of this
-   paper: http://arxiv.org/abs/math/0204356
+   paper: https://arxiv.org/abs/math/0204356
 
 === palp-1.1.p1 (Tim Abbott, William Stein) ===
 

build/pkgs/perl_term_readline_gnu/checksums.ini

@@ -1,4 +1,4 @@
 tarball=Term-ReadLine-Gnu-VERSION.tar.gz
-sha1=8052543fcdf3ab5ae44a385224d92b8337dd5125
-md5=c3afcf3fc989b2c0a5b6676c65d3a58e
-cksum=3006163947
+sha1=1f57fe986d56c6afa5eb868ca36dc5f0f8dcc3b6
+md5=514619d68bda1618da61b19d04b5cefe
+cksum=677275902

build/pkgs/perl_term_readline_gnu/package-version.txt

@@ -1 +1 @@
-1.34
+1.35

build/pkgs/perl_term_readline_gnu/patches/0001-Always-use-ncurses.patch

@@ -0,0 +1,41 @@
+From e9fbab6c37a1955bdf44d8e7ab3fe125351e4aad Mon Sep 17 00:00:00 2001
+From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
+Date: Fri, 6 Apr 2018 15:17:41 -0500
+Subject: [PATCH] Always use ncurses
+
+---
+ Makefile.PL | 18 ++----------------
+ 1 file changed, 2 insertions(+), 16 deletions(-)
+
+diff --git a/Makefile.PL b/Makefile.PL
+index ffd72c1..208aae0 100644
+--- a/Makefile.PL
++++ b/Makefile.PL
+@@ -74,22 +74,8 @@ if ($Config{osname} eq 'os2') {
+         }
+     }
+
+-    # Search libtermcap, libncurses, or libcurses in this order.
+-    # I emulate the behavior of the configure script for bash, and don't
+-    # know why AIX prefers curses.
+-    # libtermcap.a on HPUX cannot be used for dynamically linked binary.
+-    # Old Cygwin may require setting false (0).
+-    my $PREFER_CURSES = $Config{osname} eq 'aix' || $Config{osname} eq 'hpux'
+-			|| $Config{osname} eq 'cygwin';
+-    my $TERMCAP_LIB = (! $PREFER_CURSES && &search_lib('-ltermcap'))
+-	|| &search_lib('-lncurses')
+-	    || &search_lib('-lcurses');
+-
+-    unless ($TERMCAP_LIB) {
+-	warn "Could not find neither libtermcap.a, libncurses.a, or libcurses.\n";
+-	exit $err;
+-    } 
+- 
++    my $TERMCAP_LIB = '-lncurses';
++
+     $libs = "-lreadline $TERMCAP_LIB";
+     # Latest Perl in FreeBSD does not need this hack. (Dec.2002)
+     $libs .= ' -lcrypt' if ($Config{osname} =~ /freebsd/i);
+-- 
+2.11.0
+

build/pkgs/ppl/SPKG.txt

@@ -20,7 +20,7 @@ It is written in C++, but comes with interfaces to C, Java, OCaml, and
 Prolog. PPL is one of the fastest implementations of polyhedral
 computations.
 
-Benchmarks are included in this paper: http://arxiv.org/abs/cs/0612085
+Benchmarks are included in this paper: https://arxiv.org/abs/cs/0612085
 
 == License ==
 GPL v3+