Merge remote-tracking branch 'trac/public/lie_algebras/base_class_nil…

…ponent-26074' into u/gh-ehaka/free_nilpotent_lie_algebras-26076

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.4.beta0, Release Date: 2018-08-05
+SageMath version 8.4.beta1, Release Date: 2018-08-14

build/bin/sage-pip-install

@@ -17,7 +17,10 @@
 #                      This also disables pip's version self-check.
 # --isolated         : Don't read configuration files such as
 #                      ~/.pydistutils.cfg
-pip_install_flags="--ignore-installed --verbose --no-deps --no-index --isolated"
+# --no-build-isolation:Build the package in the usual Python environment
+#                      (containing the dependencies) instead of an
+#                      "isolated" environment
+pip_install_flags="--ignore-installed --verbose --no-deps --no-index --isolated --no-build-isolation"
 
 # Consume any additional pip install arguments except the last one
 while [ $# -gt 1 ]; do
@@ -66,19 +69,18 @@ LOCK="$SAGE_LOCAL/var/lock/$PIP.lock"
 while true; do
     out=$(sage-flock -x $LOCK $PIP uninstall --disable-pip-version-check -y "$name" 2>&1)
     if [ $? -ne 0 ]; then
+        # Uninstall failed
+        echo >&2 "$out"
+        exit 1
+    fi
+
+    # Uninstall succeeded, which may mean that the package was not
+    # installed to begin with.
+    if [[ "$out" != *"not installed" ]]; then
         break
     fi
-    echo "$out"
 done
 
-# Not ideal, but this is the easiest way to check if the package
-# was not installed to begin with (which pip2/3 treats as an error).
-# If it wasn't, then we proceed quietly; if it was installed show the
-# uninstallation output and error out.
-if [[ "$out" != *"not installed" ]]; then
-    echo >&2 "$out"
-    exit 1
-fi
 
 # Finally actually do the installation (the "SHARED" tells pip2/3-lock
 # to apply a shared lock)

build/bin/sage-spkg

@@ -869,9 +869,12 @@ fi
 # 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="${SAGE_DESTDIR_LOCAL%/}/"
+    # Some `find` implementations will put superfluous slashes in the
+    # output if we give them a directory name with a slash; so make sure
+    # any trailing slash is removed; https://trac.sagemath.org/ticket/26013
+    PREFIX="${SAGE_DESTDIR_LOCAL%/}"
 
-    rm -f "$PREFIX"lib/*.la
+    rm -f "$PREFIX"/lib/*.la
     if [ $? -ne 0 ]; then
         error_msg "Error deleting unnecessary libtool archive files"
         exit 1
@@ -882,7 +885,7 @@ if [ -d "$SAGE_DESTDIR" ]; then
     FIRST=1
     old_IFS="$IFS"; IFS=$'\n'
     for filename in $(find "$PREFIX" -type f -o -type l | sort); do
-        filename="${filename#$PREFIX}"
+        filename="${filename#$PREFIX/}"
         if [ $FIRST -eq 1 ]; then
             FILE_LIST="\"$filename\""
             FIRST=0
@@ -893,7 +896,7 @@ if [ -d "$SAGE_DESTDIR" ]; then
         if [ ! -d "$SAGE_LOCAL/$(dirname "$filename")" ]; then
             $SAGE_SUDO mkdir -p "$SAGE_LOCAL/$(dirname "$filename")"
         fi
-        $SAGE_SUDO mv "$PREFIX$filename" "${SAGE_LOCAL%/}/$filename"
+        $SAGE_SUDO mv "$PREFIX/$filename" "${SAGE_LOCAL%/}/$filename"
         if [ $? -ne 0 ]; then
             error_msg "Error moving files for $PKG_NAME."
             exit 1

build/make/deps

@@ -141,7 +141,9 @@ sagelib: \
 		$(inst_jupyter_core) \
 		$(inst_lcalc) \
 		$(inst_lrcalc) \
+		$(inst_libbraiding) \
 		$(inst_libgap) \
+		$(inst_libhomfly) \
 		$(inst_libpng) \
 		$(inst_linbox) \
 		$(inst_m4ri) \

build/pkgs/arb/checksums.ini

@@ -1,4 +1,5 @@
 tarball=arb-VERSION.tar.gz
-sha1=44eda7bf8eaa666c45b1fc2c1b5bd08756d94b58
-md5=fa24de9fffe4394fb6a7a6792e2ecc5f
-cksum=3689220688
+sha1=94680f32c3ccd40cc8ef417cc18d7b74b0c6c522
+md5=8f9a8d57417466080cfd1358bbb41efd
+cksum=3846267256
+

build/pkgs/arb/package-version.txt

@@ -1 +1 @@
-2.13.0.p0
+2.14.0

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=46818a6751e8f22f80cbc3e4a8b098556574ee02
-md5=326ca93c96320a6fbb44058f7c1966bc
-cksum=506204676
+sha1=667d7519a357ef427d102680ec7c6cdd3eecfa31
+md5=7481b39886ab0931671be11b2c0a7aba
+cksum=1575778832

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-277
+278

build/pkgs/ipython/checksums.ini

@@ -1,4 +1,4 @@
 tarball=ipython-VERSION.tar.gz
-sha1=bd8b3f8dab9522e6f5b581945a056a39efc69739
-md5=61f627b9365f630887beb30a002f76fd
-cksum=1322213863
+sha1=987b66cc662db8bd2ae96eee2f2237266d0c92dc
+md5=7014b8824981eef2cb893ea5398d6b8d
+cksum=2260693848

build/pkgs/ipython/package-version.txt

@@ -1 +1 @@
-5.5.0.p0
+5.8.0

build/pkgs/openblas/spkg-check

@@ -1,8 +1,3 @@
-if [ "$SAGE_LOCAL" = "" ]; then
-    echo >&2 "SAGE_LOCAL undefined ... exiting";
-    exit 1
-fi
-
 cd src
 
 # OpenBlas has no proper configure script
@@ -13,9 +8,6 @@ cd src
 # We could also patch the Makefile to use a generic symlink pointing
 # to the archive with a specific name
 
-# See #22021 for issues with multithreading
-OPENBLAS_CONFIGURE="$OPENBLAS_CONFIGURE USE_THREAD=0"
-
 if [ `python -c "from __future__ import print_function; import platform; print(platform.architecture()[0])"` = "32bit" ]; then
     OPENBLAS_CONFIGURE="$OPENBLAS_CONFIGURE BINARY=32"
 fi
@@ -27,23 +19,20 @@ fi
 
 echo "Running OpenBLAS testsuite"
 
-$MAKE tests $OPENBLAS_CONFIGURE
+sdh_make tests $OPENBLAS_CONFIGURE
 if [ $? -ne 0 ]; then
     # First make sure we already didn't set a target
     if [[ $OPENBLAS_CONFIGURE == *"TARGET"* ]]; then
-        echo >&2 "Error while running the OpenBlas testsuite ... exiting"
-        exit 1
+        sdh_die "Error while running the OpenBlas testsuite ... exiting"
     else
         # The recommended TARGET is ATOM if CPU fails
         # See https://github.com/xianyi/OpenBLAS/issues/1204
         OPENBLAS_CONFIGURE="$OPENBLAS_CONFIGURE TARGET=ATOM"
         echo "Error while testing the OpenBLAS testsuite"
         echo "Retrying the OpenBAS testsuit with TARGET=ATOM"
-        $MAKE tests $OPENBLAS_CONFIGURE
+        sdh_make tests $OPENBLAS_CONFIGURE
         if [ $? -ne 0 ]; then
-            echo >&2 "Error while running the OpenBLAS testsuite ... exiting"
-            exit 1
+            sdh_die "Error while running the OpenBLAS testsuite ... exiting"
         fi
     fi
 fi
-

build/pkgs/openblas/spkg-install

@@ -1,8 +1,5 @@
 cd src
 
-# See #22021 for issues with multithreading
-OPENBLAS_CONFIGURE="$OPENBLAS_CONFIGURE USE_THREAD=0"
-
 # OpenBLAS does not build on 32bit Haswell. Upstream suggests to pass BINARY=32 to default to NEHALEM kernels
 # See https://github.com/xianyi/OpenBLAS/issues/657
 # Right now this affect all 32bit CPUs.

build/pkgs/palp/package-version.txt

@@ -1 +1 @@
-2.1.p1
+2.1.p2

build/pkgs/palp/spkg-install

@@ -11,37 +11,25 @@ if [ "$UNAME" = "CYGWIN" ] ; then
   CFLAGS="$CFLAGS -Wl,--stack,8000000"
 fi
 
+BIN="$SAGE_LOCAL/bin"
+
 for dim in 4 5 6 11; do
     echo Building PALP optimized for $dim dimensions
 
     sed "s/^#define[^a-zA-Z]*POLY_Dmax.*/#define POLY_Dmax $dim/" Global.h-template > Global.h
 
-    $MAKE CC="$CC" CFLAGS="$CFLAGS"
-    if [ $? -ne 0 ]; then
-        echo "Error building PALP."
-        exit 1
-    fi
-
+    sdh_make CC="$CC" CFLAGS="$CFLAGS"
     for file in poly class cws nef mori; do
-        cp -p ${file}.x "$SAGE_LOCAL"/bin/${file}-${dim}d.x
-        if [ $? -ne 0 ]; then
-            echo "Error installing PALP."
-            exit 1
-        fi
+        sdh_install -T "${file}.x" "${BIN}/${file}-${dim}d.x"
     done
 
     # the next step is important to avert races on older file systems
     # for example, ext3 has 1-second timestamp granularity!
-    $MAKE cleanall
-    if [ $? -ne 0 ]; then
-        echo "Error building PALP."
-        exit 1
-    fi
+    sdh_make cleanall
 done
 
 # symlinks for the default dimension
-cd "$SAGE_LOCAL"/bin
+cd "${SAGE_DESTDIR}${BIN}"
 for file in poly class cws nef mori; do
     ln -sf ${file}-6d.x ${file}.x
 done
-

build/pkgs/pip/checksums.ini

@@ -1,4 +1,4 @@
 tarball=pip-VERSION.tar.gz
-sha1=1f5f44d433ca599d40f8e46f440479b2c73802d8
-md5=b15b33f9aad61f88d0f8c866d16c55d8
-cksum=3941571893
+sha1=337f4694bfcd4d698d9b02b38a7520fabc42a1d9
+md5=52f75ceb21e96c258f289859a2996b60
+cksum=3433326775

build/pkgs/pip/package-version.txt

@@ -1 +1 @@
-9.0.3
+18.0

build/pkgs/pip/spkg-install

@@ -1,13 +1,16 @@
 cd src
 
-# pip can install itself!
-#
+
+# pip can install itself! But first we need to ensure that the pip
+# source directory in on the PYTHONPATH
+export PYTHONPATH=`cd src && pwd`
+
 # need to use --upgrade or --ignore-installed; Otherwise pip, which is
 # importing itself, will think itself is already installed
 #
 # Install pip3 first so pip2 overwrites local/bin/pip
 for vers in 3 2; do
     python${vers} -m pip install --verbose --no-index --ignore-installed \
-            --isolated --root="$SAGE_DESTDIR" . || \
+            --no-build-isolation --isolated --root="$SAGE_DESTDIR" . || \
         sdh_die "Error building / installing pip${vers}"
 done

build/pkgs/pyzmq/checksums.ini

@@ -1,4 +1,4 @@
 tarball=pyzmq-VERSION.tar.gz
-sha1=507480d9ca99d2b2b139719852a86bbde5e5f50e
-md5=f4b607d633233318edf2766d1a848322
-cksum=2425144830
+sha1=95e87324075adbcd69f28017c2a12e16e176db6e
+md5=aecdfc328193fbd81f6dc23228319943
+cksum=1545898385

build/pkgs/pyzmq/package-version.txt

@@ -1 +1 @@
-17.0.0b3
+17.1.0

build/pkgs/setuptools/checksums.ini

@@ -1,4 +1,4 @@
 tarball=setuptools-VERSION.zip
-sha1=37328c5a707856eb0fb086da6cf60ceb85a493c2
-md5=e8e05d4f8162c9341e1089c80f742f64
-cksum=1301272111
+sha1=dac21f957c047b1b222a54fd2b2a3053c59cbfce
+md5=260630ae1a64bafa39dcc53404d63829
+cksum=2213770058

build/pkgs/setuptools/package-version.txt

@@ -1 +1 @@
-38.2.4.p0
+40.0.0

build/pkgs/tides/package-version.txt

@@ -1 +1 @@
-2.0
+2.0.p0