Merge branch 'develop' of git://trac.sagemath.org/sage into t/24521/a…

…belian_groups_with_gap

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.2.beta2, Release Date: 2018-01-01
+SageMath version 8.2.beta4, Release Date: 2018-01-27

build/bin/sage-spkg

@@ -21,6 +21,7 @@
 #      SAGE_ROOT      -- root directory of sage install
 #      SAGE_LOCAL     -- $SAGE_ROOT/local
 #      SAGE_DISTFILES -- directory that stores upstream tarballs
+#      SAGE_DESTDIR   -- temporary root the package will be installed to
 #      PKG_BASE       -- the base name of the package itself (e.g. 'patch')
 #      PKG_VER        -- the version number of the package
 #      PKG_NAME       -- $PKG_BASE-$PKG_VER
@@ -804,6 +805,10 @@ export rsync_proxy=$http_proxy
 # Actually install
 ##################################################################
 
+# Set the $SAGE_DESTDIR variable to be passed to the spkg-install
+# script (the script itself could set this, but better to standardize
+# this in one place)
+export SAGE_DESTDIR="${SAGE_BUILD_DIR}/${PKG_NAME}/inst"
 
 if [ -f spkg-build ]; then
     # Package has both spkg-build and spkg-install; execute the latter with SAGE_SUDO
@@ -826,6 +831,46 @@ else
     fi
 fi
 
+# All spkgs should eventually support this, but fall back on old behavior in
+# case DESTDIR=$SAGE_DESTDIR installation was not used
+echo "Copying package files from temporary location $SAGE_DESTDIR to $SAGE_LOCAL"
+if [ -d "$SAGE_DESTDIR" ]; then
+    PREFIX="${SAGE_DESTDIR}${SAGE_LOCAL%/}/"
+
+    rm -f "$PREFIX"lib/*.la
+    if [ $? -ne 0 ]; then
+        error_msg "Error deleting unnecessary libtool archive files"
+        exit 1
+    fi
+
+    # Generate installed file manifest
+    FILE_LIST=""
+    FIRST=1
+    IFS=$'\n'
+    for filename in $(find "$PREFIX" -type f -o -type l | sort); do
+        filename="${filename#$PREFIX}"
+        if [ $FIRST -eq 1 ]; then
+            FILE_LIST="\"$filename\""
+            FIRST=0
+        else
+            FILE_LIST="${FILE_LIST},"$'\n        '"\"${filename}\""
+        fi
+        # Copy file from the temp install path into $SAGE_LOCAL
+        if [ ! -d "$SAGE_LOCAL/$(dirname "$filename")" ]; then
+            mkdir -p "$SAGE_LOCAL/$(dirname "$filename")"
+        fi
+        mv "$PREFIX$filename" "${SAGE_LOCAL%/}/$filename"
+        if [ $? -ne 0 ]; then
+            error_msg "Error moving files for $PKG_BASE."
+            exit 1
+        fi
+    done
+
+    # Remove the $SAGE_DESTDIR entirely once all files have been moved to their
+    # final location.
+    rm -rf "$SAGE_DESTDIR"
+fi
+
 if [ "$UNAME" = "CYGWIN" ]; then
     # Rebase after installing each package--in case any packages load this
     # package at build time we need to ensure during the build that no binaries
@@ -834,7 +879,11 @@ if [ "$UNAME" = "CYGWIN" ]; then
         sage-rebase.sh "$SAGE_LOCAL" 2>/dev/null
 fi
 
-echo "Successfully installed $PKG_NAME"
+
+# Note: spkg-check tests are run after the package has been copied into
+# SAGE_LOCAL.  It might make more sense to run the tests before, but the
+# spkg-check scripts were written before use of DESTDIR installs, and so
+# fail in many cases.  This might be good to change later.
 
 if [ "$SAGE_CHECK" = "yes" ]; then
     if [ -f spkg-check ]; then
@@ -851,11 +900,6 @@ if [ "$SAGE_CHECK" = "yes" ]; then
     fi
 fi
 
-rm -f "$SAGE_LOCAL"/lib/*.la
-if [ $? -ne 0 ]; then
-    error_msg "Error deleting unnecessary libtool archive files"
-    exit 1
-fi
 
 # Mark that the new package has been installed (and tested, if
 # applicable).
@@ -867,11 +911,17 @@ cat > "$PKG_NAME_INSTALLED" << __EOF__
     "install_date": "$(date)",
     "system_uname": "$(uname -a)",
     "sage_version": "$(cat "${SAGE_ROOT}/VERSION.txt")",
-    "test_result": "$TEST_SUITE_RESULT"
+    "test_result": "$TEST_SUITE_RESULT",
+    "files": [
+        $FILE_LIST
+    ]
 }
 __EOF__
 
 
+echo "Successfully installed $PKG_NAME"
+
+
 ##################################################################
 # Delete the temporary build directory if required
 ##################################################################

build/pkgs/alabaster/checksums.ini

@@ -1,4 +1,4 @@
 tarball=alabaster-VERSION.tar.gz
-sha1=c80dedaf4a1906410e53b653de059fe9d8b17c68
-md5=346a71e8a6d51dff2e02086fdd9c5ffe
-cksum=2849350596
+sha1=dba599faf1ca5541ef35ab251eb2b365ae2f25c7
+md5=7934dccf38801faa105f6e7b4784f493
+cksum=3227702678

build/pkgs/alabaster/package-version.txt

@@ -1 +1 @@
-0.7.8.p0
+0.7.10

build/pkgs/babel/checksums.ini

@@ -1,4 +1,4 @@
 tarball=Babel-VERSION.tar.gz
-sha1=c92786942f1c920e3c39a057a7678d2aa0d1c44c
-md5=afa20bc55b0e991833030129ad498f35
-cksum=4254002491
+sha1=9adbd49864392713c6a3080aeb0a9e6432577277
+md5=60228b3ce93a203357158b909afe8ae1
+cksum=2035941902

build/pkgs/babel/package-version.txt

@@ -1 +1 @@
-2.3.4.p0
+2.5.1

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=8d46907fc431aaab8b7c378db213fda2dc06ac00
-md5=b815a36b9ad3d256ec2a25b41145f7a7
-cksum=229126322
+sha1=499badf9321c53c458652ca71580585463e574a3
+md5=e483eb587a1be5886b718e24f54a84a5
+cksum=3889320352

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-250
+252

build/pkgs/cython/checksums.ini

@@ -1,4 +1,4 @@
 tarball=Cython-VERSION.tar.gz
-sha1=3f903995b1444d5cbb3af6cd4aeadfd7c1dacc2b
-md5=64abe5847736eb413a525b70b48afd7f
-cksum=949083648
+sha1=688aa815301dd9e710cd847528de31099f3b52c4
+md5=6149238287d662bd5d5e572482252493
+cksum=460741347

build/pkgs/cython/package-version.txt

@@ -1 +1 @@
-0.27.2
+0.27.3

build/pkgs/docutils/checksums.ini

@@ -1,4 +1,4 @@
 tarball=docutils-VERSION.tar.gz
-sha1=c16e14ef18142fa248400cd174edb4fa40e51d5b
-md5=ea4a893c633c788be9b8078b6b305d53
-cksum=137667414
+sha1=32cefb69ac3dab5b04c4d150776f35419cc4c863
+md5=c53768d63db3873b7d452833553469de
+cksum=2981697109

build/pkgs/docutils/package-version.txt

@@ -1 +1 @@
-0.13.1
+0.14

build/pkgs/ecl/spkg-install

@@ -81,13 +81,13 @@ sdh_make_install
 # Create symbolic link to lib/ecl-version directory.
 # Also create a symbolic link lib/ecl/ecl -> include/ecl.
 # This is important when the Sage install is moved, see Trac #14662.
-cd "$SAGE_LOCAL/lib/" && rm -f ecl && ln -s ecl-* ecl
+cd "$SAGE_DESTDIR$SAGE_LOCAL/lib/" && rm -f ecl && ln -s ecl-* ecl
 if [ $? -ne 0 ]; then
     echo >&2 "Error - Failed to create symbolic link to ECL library"
     echo >&2 "directory ... exiting"
     exit 1
 fi
-cd "$SAGE_LOCAL/lib/ecl" && rm -f ecl && ln -s ../../include/ecl ecl
+cd "$SAGE_DESTDIR$SAGE_LOCAL/lib/ecl" && rm -f ecl && ln -s ../../include/ecl ecl
 if [ $? -ne 0 ]; then
     echo >&2 "Error - Failed to create symbolic link to ECL include"
     echo >&2 "directory ... exiting"

build/pkgs/fflas_ffpack/spkg-install

@@ -43,6 +43,12 @@ if [ "$SAGE_FAT_BINARY" = yes ]; then
     FFLAS_FFPACK_CONFIGURE="--disable-sse --disable-sse2 --disable-sse3 --disable-ssse3 --disable-sse41 --disable-sse42 --disable-fma --disable-fma4 --disable-avx --disable-avx2 $FFLAS_FFPACK_CONFIGURE"
 fi
 
+# Need to use 'bash' for configure, see
+# https://trac.sagemath.org/ticket/23451
+if [ -z "$CONFIG_SHELL" ]; then
+    export CONFIG_SHELL=`command -v bash`
+fi
+
 # We disable openmp because of build failures, see
 # http://trac.sagemath.org/ticket/17635#comment:67
 sdh_configure --with-default="$SAGE_LOCAL" --with-blas-libs="$LINBOX_BLAS" \

build/pkgs/future/checksums.ini

@@ -1,4 +1,4 @@
 tarball=future-VERSION.tar.gz
-sha1=431bf8ff160e8e785a2f76c3e57c1b6c2b13b41a
-md5=a68eb3c90b3b76714c5ceb8c09ea3a06
-cksum=2554543285
+sha1=86ed881acef874d04576b9df03c29d25ad2cd25f
+md5=3e8e88a2bda48d54b1da7634d04760d7
+cksum=1475858329

build/pkgs/future/package-version.txt

@@ -1 +1 @@
-0.15.2.p0
+0.16.0

build/pkgs/gcc/spkg-install

@@ -123,8 +123,9 @@ $MAKE install
 
 
 # Force re-installation of gmp, mpir, mpfr and mpc with the GCC we just built.
+# Also mark gfortran as not installed.
 cd "$SAGE_SPKG_INST"
-rm -f gmp-* mpir-* mpfr-* mpc-*
+rm -f gmp-* mpir-* mpfr-* mpc-* gfortran-*
 
 # Force re-configuration: the next time that "make" is run, we don't
 # want GCC to be built again, see Trac #19324

build/pkgs/giac/checksums.ini

@@ -1,4 +1,4 @@
 tarball=giac-VERSION.tar.bz2
-sha1=79503a2c2ee1ffe996727d09ebe6c6be3554434c
-md5=ad15340533a7308f30b739bc36991a56
-cksum=2233538356
+sha1=3b61dd5fe79a76c2e0d4ef60ad1ad90dc3c04bd3
+md5=55308225758c547b061b52d699fa8b13
+cksum=2762392051

build/pkgs/giac/package-version.txt

@@ -1 +1 @@
-1.2.3.47.p1
+1.4.9.45

build/pkgs/giac/patches/README.txt

@@ -6,6 +6,3 @@
     (xcas, qcas). http://xcas.e.ujf-grenoble.fr/XCAS/viewtopic.php?f=4&t=1555.
     The macos-ifactor patch enables pari in ifactor under osx because the problem can't be 
     reproduced with the spkg library.
-
-*   the pari2.8 patch is because some outputs in the check suite differs when giac is built
-    with pari 2.8 vs 2.7. (One more keyword and a different ordering in a sum)

build/pkgs/giac/spkg-src

@@ -13,9 +13,8 @@ fi
 # Exit on failure
 set -e
 
-# TODO on the next update: l71 switch from gz to bz2 as wished in #18826
-VERSION="1.2.3"
-VERSIONREV="47"
+VERSION="1.4.9"
+VERSIONREV="45"
 
 # The upstream tarball name is: giac"$SOURCEORIG".tar.gz
 SOURCEORIG=_"$VERSION"-"$VERSIONREV"

build/pkgs/ipykernel/checksums.ini

@@ -1,4 +1,4 @@
 tarball=ipykernel-VERSION.tar.gz
-sha1=21b1930141d1652c79d986092556f46c2bcf8024
-md5=1b320ff87a1a0b049e83df2de91b7f7c
-cksum=3573376709
+sha1=2be4eee12e8fcc3e6f51c5a6c04976caa7b81234
+md5=2d597192656fbac76c3c1a95aa18c44e
+cksum=3571810947

build/pkgs/ipykernel/package-version.txt

@@ -1 +1 @@
-4.6.1
+4.7.0

build/pkgs/jinja2/checksums.ini

@@ -1,4 +1,4 @@
 tarball=jinja2-VERSION.tar.gz
-sha1=4a33c1a0fd585eba2507e8c274a9cd113b1d13ab
-md5=edb51693fe22c53cee5403775c71a99e
-cksum=2405780533
+sha1=34b69e5caab12ee37b9df69df9018776c008b7b8
+md5=61ef1117f945486472850819b8d1eb3d
+cksum=3666178370

build/pkgs/jinja2/package-version.txt

@@ -1 +1 @@
-2.8.p0
+2.10

build/pkgs/jsonschema/checksums.ini

@@ -1,4 +1,4 @@
 tarball=jsonschema-VERSION.tar.gz
-sha1=c30d415d250699630f302acb8efd660dd006a7ca
-md5=374e848fdb69a3ce8b7e778b47c30640
-cksum=3533981975
+sha1=97e49df4601f7066d9954c0ec4d8d697887b32f0
+md5=50c6b69a373a8b55ff1e0ec6e78f13f4
+cksum=2742363098

build/pkgs/jsonschema/package-version.txt

@@ -1 +1 @@
-2.5.1.p0
+2.6.0

build/pkgs/jupyter_client/checksums.ini

@@ -1,4 +1,4 @@
 tarball=jupyter_client-VERSION.tar.gz
-sha1=1f226cd2d437eed5f9c45d572c0c9efe53437ea9
-md5=990ab28f63861cc29f90585d3f725b10
-cksum=1587833857
+sha1=2290704671547049ee20b034135a7a191fbc26f1
+md5=03293d63b59a3f71c417ee907852b460
+cksum=3064225526

build/pkgs/jupyter_client/package-version.txt

@@ -1 +1 @@
-5.1.0
+5.2.2

build/pkgs/linbox/spkg-install

@@ -34,6 +34,12 @@ fi
 # See trac ticket #21221.
 LINBOX_CONFIGURE="--without-fplll $LINBOX_CONFIGURE"
 
+# Need to use 'bash' for configure, see
+# https://trac.sagemath.org/ticket/23451
+if [ -z "$CONFIG_SHELL" ]; then
+    export CONFIG_SHELL=`command -v bash`
+fi
+
 # We disable openmp because of build failures, see
 # http://trac.sagemath.org/ticket/17635#comment:67
 sdh_configure --with-default="$SAGE_LOCAL" \

build/pkgs/markupsafe/checksums.ini

@@ -1,4 +1,4 @@
 tarball=markupsafe-VERSION.tar.gz
-sha1=cd5c22acf6dd69046d6cb6a3920d84ea66bdf62a
-md5=f5ab3deee4c37cd6a922fb81e730da6e
-cksum=586757310
+sha1=9072e80a7faa0f49805737a48f3d871eb1c48728
+md5=2fcedc9284d50e577b5192e8e3578355
+cksum=1008490675

build/pkgs/markupsafe/package-version.txt

@@ -1 +1 @@
-0.23.p0
+1.0