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Update to sagemath 7.5.1

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pcpa 2017-04-06 08:02:52 -04:00
parent ac3aa7f6b7
commit 056e08d023
24 changed files with 481 additions and 439 deletions
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156
sagemath-scripts.patch
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@ -1,6 +1,6 @@
diff -up src/bin/sage.orig src/bin/sage
--- src/bin/sage.orig 2016-12-30 06:31:16.930949819 -0500
+++ src/bin/sage 2016-12-30 06:31:50.812950266 -0500
--- src/bin/sage.orig 2017-03-04 12:58:43.035411519 -0500
+++ src/bin/sage 2017-03-04 13:08:11.111433272 -0500
@@ -1,5 +1,16 @@
#!/usr/bin/env bash
@ -62,16 +62,16 @@ diff -up src/bin/sage.orig src/bin/sage
echo
#### 1.......................26..................................................78
@@ -78,8 +78,6 @@ usage_advanced() {
echo " 'default', 'sagenb', and 'jupyter'). See the output"
echo " of sage --notebook --help for more details and"
echo " examples of how to pass optional arguments"
@@ -79,8 +79,6 @@ usage_advanced() {
echo " See the output of sage --notebook --help"
echo " for more details and examples of how to pass"
echo " optional arguments"
- echo " -bn, -build-and-notebook [...] -- build the Sage library then start"
- echo " the Sage notebook"
echo " -inotebook [...] -- start the *insecure* Sage notebook (deprecated)"
echo " -n, -notebook [...] -- start the default Sage notebook (options are the"
echo " same as for the notebook command in Sage). See the"
@@ -98,18 +96,12 @@ usage_advanced() {
@@ -99,17 +97,13 @@ usage_advanced() {
echo " -gp [...] -- run Sage's PARI/GP calculator with given arguments"
echo " -ipython [...] -- run Sage's IPython using the default environment (not"
echo " Sage), passing additional options to IPython"
@ -81,16 +81,15 @@ diff -up src/bin/sage.orig src/bin/sage
echo " -lisp [...] -- run Lisp interpreter included with Sage"
echo " -M2 [...] -- run Sage's Macaulay2 with given arguments"
- command -v M2 &>/dev/null || \
- echo " (not installed currently, run sage -i macaulay2)"
echo " (not installed currently, run sage -i macaulay2)"
echo " -maxima [...] -- run Sage's Maxima with given arguments"
echo " -mwrank [...] -- run Sage's mwrank with given arguments"
echo " -polymake [...] -- run Sage's Polymake with given arguments"
- command -v polymake &>/dev/null || \
- echo " (not installed currently, run sage -i polymake)"
echo " (not installed currently, run sage -i polymake)"
echo " -python [...] -- run the Python interpreter"
echo " -R [...] -- run Sage's R with given arguments"
echo " -scons [...] -- run Sage's scons"
@@ -121,49 +113,7 @@ usage_advanced() {
@@ -122,55 +116,7 @@ usage_advanced() {
echo
#### 1.......................26..................................................78
#### |.....................--.|...................................................|
@ -107,6 +106,12 @@ diff -up src/bin/sage.orig src/bin/sage
- echo " if they are already installed"
- echo " -s -- do not delete the temporary build directories"
- echo " after a successful build"
- echo " -y -- reply yes to prompts about experimental"
- echo " and old-style packages; warning: there"
- echo " is no guarantee that these packages will"
- echo " build correctly; use at your own risk"
- echo " -n -- reply no to prompts about experimental"
- echo " and old-style packages"
- echo " -p [opts] [packages]-- install the given Sage packages, without dependency"
- echo " checking and with support for old-style spkgs."
- echo " Options are -c, -d and -s with the same meaning as"
@ -141,7 +146,7 @@ diff -up src/bin/sage.orig src/bin/sage
echo " -startuptime [module] -- display how long each component of Sage takes to"
echo " start up; optionally specify a module to get more"
echo " details about that particular module"
@@ -193,7 +143,6 @@ usage_advanced() {
@@ -200,7 +146,6 @@ usage_advanced() {
echo " -coverage <files> -- give info about doctest coverage of files"
echo " -coverageall -- give summary info about doctest coverage of all"
echo " files in the Sage library"
@ -149,7 +154,7 @@ diff -up src/bin/sage.orig src/bin/sage
echo " -search_src <string> -- search through all the Sage library code for string"
echo " -search_doc <string> -- search through the Sage documentation for string"
echo " -grep <string> -- same as -search_src"
@@ -213,16 +162,6 @@ usage_advanced() {
@@ -220,16 +165,6 @@ usage_advanced() {
echo
#### 1.......................26..................................................78
#### |.....................--.|...................................................|
@ -166,7 +171,7 @@ diff -up src/bin/sage.orig src/bin/sage
echo "Valgrind memory debugging:"
echo " -cachegrind -- run Sage using Valgrind's cachegrind tool. The log"
echo " files are named sage-cachegrind.PID can be found in"
@@ -236,9 +175,6 @@ usage_advanced() {
@@ -243,9 +178,6 @@ usage_advanced() {
echo " -memcheck -- run Sage using Valgrind's memcheck tool. The log"
echo " files are named sage-memcheck.PID can be found in"
echo " $DOT_SAGE"
@ -176,10 +181,27 @@ diff -up src/bin/sage.orig src/bin/sage
echo " -valgrind -- this is an alias for -memcheck"
echo
echo "You can also use -- before a long option, e.g., 'sage --optional'."
@@ -263,87 +199,6 @@ if [ "$1" = '--nodotsage' ]; then
exit $status
fi
@@ -253,104 +185,6 @@ usage_advanced() {
exit 0
}
-
-#####################################################################
-# Special options to be processed without sage-env
-#####################################################################
-
-# Check for '--nodotsage' before sourcing sage-env; otherwise sage-env
-# will already have set some environment variables with the old
-# setting for DOT_SAGE.
-if [ "$1" = '--nodotsage' ]; then
- export DOT_SAGE=`mktemp -d ${TMPDIR:-/tmp}/dotsageXXXXXX`
- shift
- command "$0" "$@"
- status=$?
- rm -rf "$DOT_SAGE"
- exit $status
-fi
-
-# Check for '--patchbot' before sourcing sage-env: patchbot needs
-# an unclobbered environment before testing unsafe tickets.
-if [ "$1" = '-patchbot' -o "$1" = "--patchbot" ]; then
@ -264,7 +286,7 @@ diff -up src/bin/sage.orig src/bin/sage
if [ $# -gt 0 ]; then
if [ "$1" = '-h' -o "$1" = '-?' -o "$1" = '-help' -o "$1" = '--help' ]; then
usage
@@ -355,23 +210,10 @@ fi
@@ -362,23 +196,9 @@ fi
# Prepare for running Sage, either interactively or non-interactively.
sage_setup() {
@ -279,7 +301,7 @@ diff -up src/bin/sage.orig src/bin/sage
- echo >&2 '************************************************************************'
- exit 1
- fi
-
# Display the startup banner (unless SAGE_BANNER is explictly "no")
sage_banner
@ -288,7 +310,7 @@ diff -up src/bin/sage.orig src/bin/sage
if [ ! -d "$IPYTHONDIR" ]; then
# make sure that $DOT_SAGE exists so that ipython will happily
# create its config directories there. If DOT_SAGE doesn't
@@ -382,20 +224,6 @@ sage_setup() {
@@ -389,20 +209,6 @@ sage_setup() {
}
@ -309,16 +331,7 @@ diff -up src/bin/sage.orig src/bin/sage
# Start an interactive Sage session, this function never returns.
interactive_sage() {
sage_setup
@@ -472,7 +300,7 @@ fi
if [ "$1" = '-singular' -o "$1" = '--singular' ]; then
shift
- exec singular "$@"
+ exec Singular "$@"
fi
if [ "$1" = '-sqlite3' -o "$1" = '--sqlite3' ]; then
@@ -500,16 +328,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
@@ -507,16 +313,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
exec ecl "$@"
fi
@ -335,10 +348,27 @@ diff -up src/bin/sage.orig src/bin/sage
if [ "$1" = '-maxima' -o "$1" = '--maxima' ]; then
shift
exec maxima "$@"
@@ -560,11 +378,6 @@ if [ "$1" = '-git' -o "$1" = '--git' ];
exec git "$@"
@@ -542,11 +338,6 @@ if [ "$1" = '-pip' -o "$1" = '--pip' ];
exec pip-lock "$@"
fi
-if [ "$1" = '-fix-pkg-checksums' -o "$1" = '--fix-pkg-checksums' ]; then
- shift
- exec sage-fix-pkg-checksums "$@"
-fi
-
if [ "$1" = '-python' -o "$1" = '--python' ]; then
shift
exec python "$@"
@@ -562,16 +353,6 @@ if [ "$1" = '-ipython' -o "$1" = '--ipyt
exec ipython "$@"
fi
-if [ "$1" = '-git' -o "$1" = '--git' ]; then
- shift
- exec git "$@"
-fi
-
-if [ "$1" = '-git-branch' -o "$1" = '--git-branch' ]; then
- shift
- exec git --git-dir="$SAGE_ROOT"/.git rev-parse --abbrev-ref HEAD
@ -347,10 +377,11 @@ diff -up src/bin/sage.orig src/bin/sage
if [ "$1" = '-sh' -o "$1" = '--sh' ]; then
# AUTHORS:
# - Carl Witty and William Stein: initial version
@@ -684,20 +497,6 @@ EOF
@@ -690,19 +471,6 @@ EOF
exit $status
fi
#####################################################################
-#####################################################################
-# Test coverage of a module?
-#####################################################################
-
@ -363,12 +394,10 @@ diff -up src/bin/sage.orig src/bin/sage
- shift
- exec sage-coverageall "$@"
-fi
-
-#####################################################################
# File conversion
#####################################################################
@@ -715,11 +514,6 @@ fi
#####################################################################
# File conversion
@@ -722,11 +490,6 @@ fi
# Run Sage's versions of the standard Algebra/Geometry etc. software
#####################################################################
@ -380,7 +409,7 @@ diff -up src/bin/sage.orig src/bin/sage
if [[ "$1" =~ ^--notebook=.* || "$1" =~ ^-n=.* || "$1" =~ ^-notebook=.* ]] ; then
sage-cleaner &>/dev/null &
exec sage-notebook "$@"
@@ -730,13 +524,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
@@ -737,13 +500,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
exec sage-notebook "$@"
fi
@ -394,7 +423,7 @@ diff -up src/bin/sage.orig src/bin/sage
if [ "$1" = "-inotebook" -o "$1" = '--inotebook' ]; then
shift
sage-cleaner &>/dev/null &
@@ -755,31 +542,12 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
@@ -762,31 +518,12 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
exit 0
fi
@ -427,7 +456,7 @@ diff -up src/bin/sage.orig src/bin/sage
if [ ! -f "$DOT_SAGE"/init.sage ]; then
echo >&2 "init.sage does not exist ... creating"
touch "$DOT_SAGE"/init.sage
@@ -795,10 +563,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
@@ -802,10 +539,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
fi
fi
@ -439,7 +468,7 @@ diff -up src/bin/sage.orig src/bin/sage
shift
SAGE_BANNER=no sage_setup
export PYTHONIOENCODING="utf-8" # Fix encoding for doctests
@@ -824,114 +589,6 @@ if [ "$1" = '--location' ]; then
@@ -831,130 +565,6 @@ if [ "$1" = '--location' ]; then
exit 0
fi
@ -551,10 +580,26 @@ diff -up src/bin/sage.orig src/bin/sage
- exec python -m "sage_setup.docbuild" "$@"
-fi
-
if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
-if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
- shift
- sage_setup
- if [ "$SAGE_DEBUG" = "no" ]; then
- gdb -x "$SAGE_LOCAL/bin/sage-gdb-commands" \
- -args python "$SAGE_LOCAL/bin/sage-ipython" "$@" -i
- else
- # Location of cython_debug directory
- cygdb_dir="$SAGE_SRC/build/cythonized"
- cygdb "$cygdb_dir" "$SAGE_SRC/sage" \
- -- -x "$SAGE_LOCAL/bin/sage-gdb-commands" \
- -args python "$SAGE_LOCAL/bin/sage-ipython" "$@" -i
- fi
- exit $?
-fi
-
if [ "$1" = '-preparse' -o "$1" = "--preparse" ]; then
shift
sage_setup
@@ -980,26 +637,11 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
exec sage-preparse "$@"
@@ -989,21 +599,10 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
exec sage-callgrind "$@"
fi
@ -574,16 +619,11 @@ diff -up src/bin/sage.orig src/bin/sage
-fi
-
if [ $# -ge 1 ]; then
- T=`echo "$1" | sed -e "s/.*\.//"`
- if [ "$T" = "spkg" ]; then
- install "$@"
- fi
SAGE_BANNER=no sage_setup
unset TERM # See Trac #12263
exec sage-run "$@"
T=`echo "$1" | sed -e "s/.*\.//"`
if [ "$T" = "spkg" ]; then
diff -up src/bin/sage-runtests.orig src/bin/sage-runtests
--- src/bin/sage-runtests.orig 2016-12-30 06:31:16.938949819 -0500
+++ src/bin/sage-runtests 2016-12-30 06:31:21.902949885 -0500
--- src/bin/sage-runtests.orig 2017-03-04 13:08:31.712434061 -0500
+++ src/bin/sage-runtests 2017-03-04 13:08:41.887434451 -0500
@@ -56,10 +56,6 @@ if __name__ == "__main__":
help="run doctests using Valgrind's cachegrind tool. The log "
"files are named sage-cachegrind.PID and can be found in " +
@ -596,8 +636,8 @@ diff -up src/bin/sage-runtests.orig src/bin/sage-runtests
parser.add_option("-f", "--failed", action="store_true", default=False,
help="doctest only those files that failed in the previous run")
diff -up src/bin/sage-valgrind.orig src/bin/sage-valgrind
--- src/bin/sage-valgrind.orig 2016-12-30 06:31:16.945949819 -0500
+++ src/bin/sage-valgrind 2016-12-30 06:31:21.903949885 -0500
--- src/bin/sage-valgrind.orig 2017-03-04 13:08:52.937434874 -0500
+++ src/bin/sage-valgrind 2017-03-04 13:09:13.143435648 -0500
@@ -1,16 +1,6 @@
#!/usr/bin/env bash
@ -612,7 +652,7 @@ diff -up src/bin/sage-valgrind.orig src/bin/sage-valgrind
-SUPP+=" --suppressions=$SAGE_EXTCODE/valgrind/sage-additional.supp"
-
-MEMCHECK_FLAGS="--leak-resolution=high --leak-check=full --num-callers=25 $SUPP"
+MEMCHECK_FLAGS="--leak-resolution=high --leak-check=full --num-callers=25 "
+MEMCHECK_FLAGS="--leak-resolution=high --leak-check=full --num-callers=25"
if [ "$SAGE_MEMCHECK_FLAGS" ]; then
echo "Overwriting memcheck flags with: $SAGE_MEMCHECK_FLAGS"