Merge sage 7.5.rc0

.dir-locals.el

@@ -0,0 +1,9 @@
+;;; Directory Local Variables
+;;; For more information see (info "(emacs) Directory Variables")
+
+((nil
+  ;; Use space instead of tabs for indentation
+  (indent-tabs-mode . nil))
+ (makefile-mode
+  ;; But use tabs in Makefiles
+  (indent-tabs-mode . t)))

COPYING.txt

@@ -8,6 +8,9 @@ free open source license as defined at http://www.opensource.org/.
 The whole Sage software distribution is licensed under the General
 Public License, version 3 (no other versions!).
 
+All Sage documentation is licensed under Creative Commons 3.0 BY-SA
+License.
+
 Some of the code available in *optional* Sage packages (not included
 in sage-*.tar) are licensed under more restrictive conditions.
 

VERSION.txt

@@ -1 +1 @@
-SageMath version 7.5.beta2, Release Date: 2016-11-09
+SageMath version 7.5.rc0, Release Date: 2016-12-18

build/bin/sage-apply-patches

@@ -0,0 +1,78 @@
+#!/usr/bin/env bash
+#
+# sage-apply-patches [-p<num>] [-d patch-subdir] [patch-dir] -- [...]
+#
+# Apply any patches to original spkg sources.  Patch files must have
+# the .patch extension.
+#
+# By default the patches are applied from ../patches/ using the -p1
+# option, and it is assumed that the patches are being applied from
+# the root of the package source.
+#
+# An optional patch subdirectory may be specified with the -d flag.
+# For example `sage-apply-patches -d cygwin` applies only those
+# patches under <patch-dir>/cygwin.
+#
+# The -p<num> arg is the argument accepted by the `patch` command,
+# and overrides the default -p1
+#
+# Any additional arguments following " -- " are passed directly
+# to the `patch` command.
+#
+#***************************************************************************
+#
+#  Distributed under the terms of the GNU General Public License (GPL)
+#  as published by the Free Software Foundation; either version 2 of
+#  the License, or (at your option) any later version.
+#                  http://www.gnu.org/licenses/
+#***************************************************************************
+
+patchdir="../patches"
+patch_subdir=""
+patch_strip="-p1"
+patch_args_sep=""
+patch_args="--no-backup-if-mismatch"
+
+while [[ $# > 0 ]]; do
+    if [[ -z "$patch_args_sep" ]]; then
+        case $1 in
+            -d)
+                patch_subdir="${2%/}"
+                shift
+                ;;
+            -p[0-9])
+                patch_strip="$1"
+                ;;
+            --)
+                patch_args_sep="$1"
+                ;;
+            *)
+                patchdir="${1%/}"
+                ;;
+        esac
+    else
+        patch_args="$patch_args $1"
+    fi
+
+    shift
+done
+
+patchdir="${patchdir}/${patch_subdir}"
+patchdir="${patchdir%/}"
+patches=( "${patchdir}"/*.patch )
+
+if [[ -r "${patches[0]}" ]]; then
+    echo "Applying patches from ${patchdir}..."
+    for patch in ${patches[@]}; do
+        # Skip non-existing or non-readable patches
+        [ -r "$patch" ] || continue
+        echo "Applying $patch"
+        patch $patch_strip $patch_args < "$patch"
+        if [ $? -ne 0 ]; then
+            echo >&2 "Error applying '$patch'"
+            exit 1
+        fi
+    done
+else
+    >&2 echo "No patch files found in $patchdir"
+fi

build/bin/sage-spkg

@@ -625,6 +625,10 @@ fi
 
 echo "Finished extraction"
 
+cd src
+sage-apply-patches || exit 1
+cd ..
+
 ##################################################################
 # The package has been extracted, prepare for installation
 ##################################################################

build/make/deps

@@ -1,4 +1,4 @@
-###############################################################################
+## -*- Makefile -*- ###########################################################
 # This file ($SAGE_ROOT/build/make/deps) will be copied into
 # $SAGE_ROOT/build/make/Makefile by $SAGE_ROOT/build/make/install
 ###############################################################################

build/pkgs/arb/spkg-install

@@ -2,15 +2,6 @@
 
 cd src
 
-for patch in ../patches/*.patch; do
-    [ -r "$patch" ] || continue  # Skip non-existing or non-readable patches
-    patch -p1 <"$patch"
-    if [ $? -ne 0 ]; then
-        echo >&2 "Error applying '$patch'"
-        exit 1
-    fi
-done
-
 # The git head of arb now honors LDFLAGS; The following workaround can
 # be removed in arb >= 2.8 when it is released
 export EXTRA_SHARED_FLAGS=$LDFLAGS

build/pkgs/atlas/package-version.txt

@@ -1 +1 @@
-3.10.2.p2
+3.10.2.p3

build/pkgs/atlas/spkg-install

@@ -223,20 +223,11 @@ if 'SAGE_ATLAS_LIB' in os.environ:
 
     sys.exit(0)
 
-write_pc_file(['cblas', 'atlas'], 'cblas')
-write_pc_file(['f77blas', 'atlas'], 'blas')
-# The inclusion of cblas is not a mistake. ATLAS' lapack include
-# a custom version of clapack which depends on cblas.
-write_pc_file(['lapack', 'f77blas', 'cblas', 'atlas'], 'lapack')
-
-######################################################################
-### Patch source
-######################################################################
-
-# apply all patches
-for fname in glob.glob(os.path.join(PATCH_DIR,'*.patch')):
-    rc = system_with_flush('patch -p1 -d src/ --input '+os.path.join(PATCH_DIR, fname))
-    assert_success(rc, bad='Applying '+fname+' failed.', good='Applied '+fname+'.')
+# Because blas, cblas and lapack libraries are properly linked
+# with no unknown symbols, no extra libraries needs to be given.
+write_pc_file(['cblas'], 'cblas')
+write_pc_file(['f77blas'], 'blas')
+write_pc_file(['lapack'], 'lapack')
 
 # add extra architectural defaults
 cp('src/ARCHS/*.tar.bz2', 'src/ATLAS/CONFIG/ARCHS/')

build/pkgs/autotools/SPKG.txt

@@ -61,5 +61,5 @@ spkg. If you edit this, you must update Makefile.build using the
 spkg-write-makefile script. After optionally updating the git repos
 using spkg-src, you need to run
   ./spkg-write-makefile >Makefile.build
-This must be run in a Sage shell, with the the autotools spkg
+This must be run in a Sage shell, with the autotools spkg
 installed.

build/pkgs/autotools/spkg-install

@@ -31,19 +31,7 @@ BUILD=`pwd`/build
 # SageMath.  See trac #21047.
 export M4="$SAGE_LOCAL/bin/m4"
 
-########################################################################
-# Apply patch(es)
-########################################################################
-
-cd src
-for patch in ../patches/*.patch; do
-    [ -r "$patch" ] || continue  # Skip non-existing or non-readable patches
-    patch -p1 <"$patch"
-    if [ $? -ne 0 ]; then
-        echo >&2 "Error applying '$patch'"
-        exit 1
-    fi
-done
+cd "$SRC"
 
 ########################################################################
 # Remove old installed versions

build/pkgs/backports_abc/checksums.ini

@@ -1,4 +1,4 @@
 tarball=backports_abc-VERSION.tar.gz
-sha1=76060a68d14f9d1a4198e00c3bb3711467ecb1f4
-md5=0b65a216ce9dc9c1a7e20a729dd7c05b
-cksum=1989294907
+sha1=7f19aefc840301effcd43d9d95e8e59ed8153ea2
+md5=7d1936ec183a3586290adf60f6f96764
+cksum=2833604013

build/pkgs/backports_abc/package-version.txt

@@ -1 +1 @@
-0.4.p0
+0.5

build/pkgs/backports_shutil_get_terminal_size/spkg-install

@@ -2,13 +2,4 @@
 
 cd src
 
-for patch in ../patches/*.patch; do
-    [ -r "$patch" ] || continue  # Skip non-existing or non-readable patches
-    patch -p1 <"$patch"
-    if [ $? -ne 0 ]; then
-        echo >&2 "Error applying '$patch'"
-        exit 1
-    fi
-done
-
 $PIP_INSTALL .

build/pkgs/bliss/spkg-install

@@ -8,14 +8,6 @@ fi
 
 
 cd "src"
-for patch in ../patches/*.patch; do
-    [ -r "$patch" ] || continue  # Skip non-existing or non-readable patches
-    patch -p1 <"$patch"
-    if [ $? -ne 0 ]; then
-        echo >&2 "Error applying '$patch'"
-        exit 1
-    fi
-done
 
 ./configure --prefix="$SAGE_LOCAL" --disable-gmp && $MAKE && $MAKE install
 

build/pkgs/brial/spkg-install

@@ -13,14 +13,6 @@ rm -rf "$SAGE_LOCAL"/include/polybori*
 rm -rf "$SAGE_LOCAL"/share/polybori
 
 cd src
-for patch in ../patches/*.patch; do
-    [ -r "$patch" ] || continue  # Skip non-existing or non-readable patches
-    patch -p1 <"$patch"
-    if [ $? -ne 0 ]; then
-        echo >&2 "Error applying '$patch'"
-        exit 1
-    fi
-done
 
 # C++11 workaround https://trac.sagemath.org/ticket/20926
 export CXXFLAGS="$CXXFLAGS -std=c++98"

build/pkgs/bzip2/spkg-install

@@ -19,16 +19,6 @@ export CFLAGS="-O2 -g $CFLAGS"
 
 cd src/src
 
-# Patch bzip2
-for patch in ../patches/*.patch; do
-    [ -r "$patch" ] || continue  # Skip non-existing or non-readable patches
-    patch -p1 <"$patch"
-    if [ $? -ne 0 ]; then
-        echo >&2 "Error applying '$patch'"
-        exit 1
-    fi
-done
-
 # Autotoolify bzip2
 cp -r -f ../autotools/* ./
 

build/pkgs/cddlib/spkg-install

@@ -32,16 +32,6 @@ cp ../patches/random.{c,h} lib-src-gmp/
 cp ../patches/cdd_both_reps.c src/
 cp ../patches/cdd_both_reps.c src-gmp/cdd_both_reps.c
 
-# apply patch files
-for patch in ../patches/*.patch; do
-    # skip patches that aren't needed at build time
-    if echo "$patch" | grep 'Makefile.am.patch$' > /dev/null; then
-        continue
-    fi
-    patch -p1 < "$patch" ||
-      die "Error patching cddlib"
-done
-
 # Use newer version of config.guess and config.sub (see Trac #19718)
 cp "$SAGE_ROOT"/config/config.* .
 

build/pkgs/cephes/spkg-install

@@ -11,19 +11,8 @@ if [ "$UNAME" != "FreeBSD" ]; then
     exit 0
 fi
 
-CUR=`pwd`
 cd src
 
-# Apply patches:
-echo "Applying patches (if any)..."
-for patch in ../patches/*.patch; do
-    patch -p1 <"$patch"
-    if [ $? -ne 0 ]; then
-        echo >&2 "Patch '$patch' failed to apply."
-        exit 1
-    fi
-done
-
 echo "Building Cephes..."
 $MAKE
 if [ $? -ne 0 ]; then

build/pkgs/cliquer/spkg-install

@@ -8,18 +8,6 @@ fi
 
 cd src
 
-echo "Applying patches..."
-# Apply all patches
-for patch in ../patches/*.patch; do
-    [ -r "$patch" ] || continue  # Skip non-existing or non-readable patches
-    echo "Applying $patch"
-    patch -p1 <"$patch"
-    if [ $? -ne 0 ]; then
-        echo >&2 "Error applying '$patch'"
-        exit 1
-    fi
-done
-
 echo "Configuring..."
 ./configure --prefix="$SAGE_LOCAL" --disable-static --libdir="$SAGE_LOCAL/lib"
 if [ $? -ne 0 ]; then

build/pkgs/cmake/spkg-install

@@ -2,15 +2,6 @@
 
 cd src
 
-for patch in ../patches/*.patch; do
-    [ -r "$patch" ] || continue  # Skip non-existing or non-readable patches
-    patch -p1 <"$patch"
-    if [ $? -ne 0 ]; then
-        echo >&2 "Error applying '$patch'"
-        exit 1
-    fi
-done
-
 system_curl=""
 
 if [ "$UNAME" = "Darwin" ]; then

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=e2e2814e51821d5ff0562304d3d597301e90b976
-md5=245603edc9bffd08d535ed9be163ba5f
-cksum=3269882326
+sha1=dec646cbe7003843d95349386e65ff39ce623561
+md5=8edc28e5ce617646e08dce522c4a733a
+cksum=1353419480

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-191
+196

build/pkgs/coxeter3/spkg-install

@@ -16,14 +16,6 @@ cd ../src
 cp ../patches/directories.tmpl directories.h
 cp ../patches/sage.cpp ../patches/sage.h .
 cp ../patches/test.input ../patches/test.output.expected .
-for patch in ../patches/*.patch; do
-    [ -r "$patch" ] || continue  # Skip non-existing or non-readable patches
-    patch -p1 <"$patch"
-    if [ $? -ne 0 ]; then
-        echo >&2 "Error applying '$patch'"
-        exit 1
-    fi
-done
 
 # Build
 $MAKE all

build/pkgs/cvxopt/spkg-install

@@ -8,15 +8,6 @@ fi
 
 cd src
 
-# Apply patches.
-for patch in ../patches/*.patch; do
-    patch -p1 <"$patch"
-    if [ $? -ne 0 ]; then
-        echo >&2 "Error applying '$patch'"
-        exit 1
-    fi
-done
-
 # Normally for a 64-bit build the -m64 option is added to
 # gcc, but other compilers will not accept that, so
 # allow it to be configured as something different if need

build/pkgs/cysignals/checksums.ini

@@ -1,4 +1,4 @@
 tarball=cysignals-VERSION.tar.bz2
-sha1=1ad0314a19bfad58dfb689c534087c31241c07f0
-md5=20483b618a1d5c65485d38a2d0002386
-cksum=507747317
+sha1=4394b36d8b30a7afd81df45c6266048d49567af0
+md5=abc98cb7b07c3a40979ee24dead06a38
+cksum=1213194811

build/pkgs/cysignals/dependencies

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

build/pkgs/cysignals/package-version.txt

@@ -1 +1 @@
-1.1.1
+1.3.2