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Update to sagemath 6.4.1

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pcpa 2014-12-13 21:05:42 -02:00
parent 3e866bf86e
commit 738094a8d8
27 changed files with 276 additions and 12243 deletions
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187
sagemath-scripts.patch
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@ -1,8 +1,8 @@
diff -up src/bin/sage.orig src/bin/sage
--- src/bin/sage.orig 2014-08-12 13:51:14.714911495 -0300
+++ src/bin/sage 2014-08-12 13:59:39.911930840 -0300
@@ -13,17 +13,14 @@ usage() {
echo " file.<sage|py|spyx> -- run given .sage, .py or .spyx files"
--- src/bin/sage.orig 2014-11-17 17:42:48.321925514 -0200
+++ src/bin/sage 2014-11-17 17:55:52.524955544 -0200
@@ -13,11 +13,9 @@ usage() {
echo " file.[sage|py|spyx] -- run given .sage, .py or .spyx file"
echo " -advanced -- list all command line options"
echo " -c <cmd> -- Evaluates cmd as sage code"
- echo " -experimental -- list all experimental packages that can be installed"
@ -10,16 +10,18 @@ diff -up src/bin/sage.orig src/bin/sage
echo " -gp [...] -- run Sage's PARI/GP calculator with given arguments"
echo " -h, -? -- print this help message"
- echo " -i [packages] -- install the given Sage packages"
echo " -inotebook [...] -- start the *insecure* Sage notebook"
echo " -pip [...] -- invoke pip, the Python package manager"
echo " -inotebook [...] -- start the *insecure* Sage notebook (deprecated)"
echo " -maxima [...] -- run Sage's Maxima with given arguments"
echo " -mwrank [...] -- run Sage's mwrank with given arguments"
echo " -n, -notebook [...] -- start the Sage notebook (options are the same"
echo " as for the notebook command in Sage)"
@@ -25,7 +23,6 @@ usage() {
echo " --notebook=[...] -- start the Sage notebook (valid options are"
echo " 'default', 'sagenb', and 'ipython')"
echo " -n, --notebook -- shortcut for --notebook=default"
- echo " -optional -- list all optional packages that can be installed"
echo " -python [...] -- run the Python interpreter"
echo " -R [...] -- run Sage's R with given arguments"
echo " -singular [...] -- run Sage's singular with given arguments"
@@ -39,10 +36,6 @@ usage() {
@@ -41,10 +38,6 @@ usage() {
echo " --optional - controls which optional tests are run"
echo " --sagenb - test all sagenb files"
echo " --help - show all testing options"
@ -30,32 +32,31 @@ diff -up src/bin/sage.orig src/bin/sage
echo " -v, -version -- print the Sage version"
exit 0
}
@@ -61,16 +54,14 @@ usage_advanced() {
@@ -63,8 +56,6 @@ usage_advanced() {
echo " -preparse <file.sage> -- preparse file.sage and produce corresponding file.sage.py"
echo " -q -- quiet; start with no banner"
echo " -root -- print the Sage root directory"
- echo " -gthread, -qthread, -q4thread, -wthread, -pylab"
- echo " -- pass the option through to ipython"
+ echo " -testall [options] -- test all source files, docs, and examples. options"
+ echo " like -t"
echo " -v, -version -- print the Sage version"
echo
#### 1.......................26..................................................78
#### |.....................--.|...................................................|
echo "Running the notebook:"
@@ -75,8 +66,6 @@ usage_advanced() {
echo " 'default', 'sagenb', and 'ipython'). See the output"
echo " of sage --notebook --help for more details and"
echo " examples of how to pass optional arguments"
- echo " -bn, -build-and-notebook [...] -- build the Sage library then start"
- echo " the Sage notebook"
echo " -inotebook [...] -- start the *insecure* Sage notebook"
echo " -n, -notebook [...] -- start the Sage notebook (options are the same"
echo " as for the notebook command in Sage)"
@@ -87,13 +78,8 @@ usage_advanced() {
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"
@@ -94,13 +83,9 @@ 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"
- echo " -kash [...] -- run Sage's Kash with given arguments"
- command -v kash &>/dev/null || \
- echo " (not installed currently, run sage -i kash)"
echo " (not installed currently, run sage -i kash)"
echo " -lisp [...] -- run Lisp interpreter included with Sage"
echo " -M2 [...] -- run Sage's Macaulay2 with given arguments"
- command -v M2 &>/dev/null || \
@ -63,7 +64,7 @@ diff -up src/bin/sage.orig src/bin/sage
echo " -maxima [...] -- run Sage's Maxima with given arguments"
echo " -mwrank [...] -- run Sage's mwrank with given arguments"
echo " -python [...] -- run the Python interpreter"
@@ -107,75 +93,10 @@ usage_advanced() {
@@ -114,74 +99,10 @@ usage_advanced() {
echo
#### 1.......................26..................................................78
#### |.....................--.|...................................................|
@ -82,6 +83,7 @@ diff -up src/bin/sage.orig src/bin/sage
- echo " -info [packages] -- print the SPKG.txt of the given packages"
- echo " -optional -- list all optional packages that can be installed"
- echo " -standard -- list all standard packages that can be installed"
- echo " -installed -- list all installed packages"
- #echo " -update -- download latest non-optional Sage packages (do not build them)"
- #echo " -update-build -- build and install all downloaded non-optional Sage packages"
- echo " -upgrade [version] -- download, build and install the given version. Here,"
@ -93,20 +95,17 @@ diff -up src/bin/sage.orig src/bin/sage
- #### 1.......................26..................................................78
- #### |.....................--.|...................................................|
- echo "Building and testing the Sage library:"
- echo " -b [branch] -- build Sage library. If branch is given, switch to"
- echo " branch in devel/sage-branch and build that branch"
- echo " -ba [branch] -- same as -b and rebuild all Cython code"
- echo " -ba-force [branch] -- same as -ba, but don't query before rebuilding"
- echo " -br [branch] -- switch to, build, and run Sage given branch"
- echo " -b -- build Sage library."
- echo " -ba -- same as -b and rebuild all Cython code"
- echo " -ba-force -- same as -ba, but don't query before rebuilding"
- echo " -br -- build and run Sage"
- echo " -bt [...] -- build and test, options like -t below"
- echo " -btp <N> [...] -- build and test parallel, options like -tp below"
- echo " -btnew [...] -- build and test modified files, options like -tnew"
- echo " -fixdoctests <file.py> [output_file] [--long]"
- echo " -- writes a new version of file.py to output_file"
- echo " (defaults: to file.py.out) that will pass the doctests."
- echo " With the optional --long argument the long time tests"
- echo " are also checked."
- echo " A patch for the new file is printed to stdout."
- echo " -- replace failing doctests with the actual output. With"
- echo " optional output_file: redirect there. With the --long"
- echo " option: include #long time tests."
- 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"
@ -123,6 +122,7 @@ diff -up src/bin/sage.orig src/bin/sage
- echo " --failed - only test files that failed last test"
- echo " --sagenb - test all sagenb files"
- echo " --help - show all testing options"
- echo " --warn-long [timeout] - warning if doctest is slow"
- echo " -tp <N> [...] -- like -t above, but tests in parallel using N threads"
- echo " with 0 interpreted as a sensible default"
- echo " -testall [options] -- test all source files, docs, and examples. options"
@ -139,7 +139,7 @@ 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"
@@ -195,16 +116,6 @@ usage_advanced() {
@@ -201,16 +122,6 @@ usage_advanced() {
echo
#### 1.......................26..................................................78
#### |.....................--.|...................................................|
@ -156,7 +156,7 @@ 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"
@@ -218,9 +129,6 @@ usage_advanced() {
@@ -224,9 +135,6 @@ 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"
@ -166,7 +166,7 @@ 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'."
@@ -240,34 +148,6 @@ if [ "$1" = '--nodotsage' ]; then
@@ -246,65 +154,14 @@ if [ "$1" = '--nodotsage' ]; then
exit $status
fi
@ -198,14 +198,16 @@ diff -up src/bin/sage.orig src/bin/sage
-fi
-
-
if [ $# -gt 0 ]; then
if [ "$1" = '-h' -o "$1" = '-?' -o "$1" = '-help' -o "$1" = '--help' ]; then
usage
@@ -277,28 +157,13 @@ if [ $# -gt 0 ]; then
fi
fi
-if [ $# -gt 0 ]; then
- if [ "$1" = '-h' -o "$1" = '-?' -o "$1" = '-help' -o "$1" = '--help' ]; then
- usage
- fi
- if [ "$1" = "-advanced" -o "$1" = "--advanced" ]; then
- usage_advanced
- fi
-fi
-
# Prepare for running Sage, either interactively or non-interactively.
sage_setup() {
- # Check that we're not in a source tarball which hasn't been built yet (#13561).
@ -230,11 +232,10 @@ diff -up src/bin/sage.orig src/bin/sage
if [ ! -d "$IPYTHONDIR" ]; then
# make sure that $DOT_SAGE exists so that ipython will happily
# create its config directories there. If DOT_SAGE doesn't
@@ -308,21 +173,6 @@ sage_setup() {
sage-cleaner &>/dev/null &
@@ -315,20 +172,6 @@ sage_setup() {
}
-
-# Check to see if the whole Sage install tree has moved. If so,
-# change various hardcoded paths. Skip this if we don't have write
-# access to $SAGE_LOCAL (e.g. when running as a different user) or
@ -252,7 +253,7 @@ diff -up src/bin/sage.orig src/bin/sage
# Start an interactive Sage session, this function never returns.
interactive_sage() {
sage_setup
@@ -384,7 +234,7 @@ fi
@@ -390,7 +233,7 @@ fi
if [ "$1" = '-singular' -o "$1" = '--singular' ]; then
shift
@ -261,15 +262,10 @@ diff -up src/bin/sage.orig src/bin/sage
fi
if [ "$1" = '-sqlite3' -o "$1" = '--sqlite3' ]; then
@@ -412,16 +262,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]
exec ecl "$@"
@@ -423,11 +266,6 @@ if [ "$1" = '-kash' -o "$1" = '--kash' ]
exec kash "$@"
fi
-if [ "$1" = '-kash' -o "$1" = '--kash' ]; then
- shift
- exec kash "$@"
-fi
-
-if [ "$1" = '-fixdoctests' -o "$1" = '--fixdoctests' ]; then
- shift
- exec sage-fixdoctests "$@"
@ -278,7 +274,23 @@ diff -up src/bin/sage.orig src/bin/sage
if [ "$1" = '-maxima' -o "$1" = '--maxima' ]; then
shift
exec maxima "$@"
@@ -581,20 +421,6 @@ EOF
@@ -448,15 +286,6 @@ if [ "$1" = '-scons' -o "$1" = '--scons'
exec scons "$@"
fi
-if [ "$1" = '-pip' -o "$1" = '--pip' ]; then
- if [ ! -x "$SAGE_LOCAL/bin/pip" ]; then
- echo "Pip is not installed. Run \"sage -i pip\" to install it."
- exit 1
- fi
- shift
- exec pip "$@"
-fi
-
if [ "$1" = '-python' -o "$1" = '--python' ]; then
shift
exec python "$@"
@@ -596,20 +425,6 @@ EOF
fi
#####################################################################
@ -299,7 +311,7 @@ diff -up src/bin/sage.orig src/bin/sage
# File conversion
#####################################################################
@@ -609,36 +435,15 @@ if [ "$1" = '-rst2sws' -o "$1" = '--rst2
@@ -624,23 +439,9 @@ if [ "$1" = '-rst2sws' -o "$1" = '--rst2
fi
#####################################################################
@ -320,23 +332,24 @@ diff -up src/bin/sage.orig src/bin/sage
- sage-build "$@" || exit $?
-}
-
if [ "$1" = "-notebook" -o "$1" = '--notebook' -o "$1" = '-n' ]; then
shift
if [[ "$1" =~ "--notebook="* || "$1" =~ "-n="* || "$1" =~ "-notebook="* ]]; then
sage-cleaner &>/dev/null &
exec sage-notebook "$@"
@@ -652,13 +453,6 @@ if [ "$1" = "-notebook" -o "$1" = '--not
exec sage-notebook --notebook=default "$@"
fi
-if [ "$1" = "-bn" -o "$1" = "--build-and-notebook" ]; then
- shift
- build_sage
- sage-cleaner &>/dev/null &
- exec sage-notebook "$@"
- exec sage-notebook --notebook=default "$@"
-fi
-
if [ "$1" = "-inotebook" -o "$1" = '--inotebook' ]; then
shift
sage-cleaner &>/dev/null &
@@ -657,40 +462,19 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
@@ -677,40 +471,19 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep
exit 0
fi
@ -379,7 +392,7 @@ diff -up src/bin/sage.orig src/bin/sage
shift
exec sage-runtests -p "$@"
else
@@ -699,10 +483,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
@@ -719,10 +492,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"
fi
fi
@ -391,7 +404,7 @@ diff -up src/bin/sage.orig src/bin/sage
shift
SAGE_BANNER="no"
sage_setup
@@ -724,132 +505,6 @@ if [ "$1" = '-c' ]; then
@@ -744,136 +514,6 @@ if [ "$1" = '-c' ]; then
exec sage-eval "$@"
fi
@ -445,15 +458,19 @@ diff -up src/bin/sage.orig src/bin/sage
-}
-
-if [ "$1" = '-optional' -o "$1" = "--optional" ]; then
- exec sage-list-optional
- exec sage-list-packages optional
-fi
-
-if [ "$1" = '-experimental' -o "$1" = "--experimental" ]; then
- exec sage-list-experimental
- exec sage-list-packages experimental
-fi
-
-if [ "$1" = '-standard' -o "$1" = "--standard" ]; then
- exec sage-list-standard
- exec sage-list-packages standard
-fi
-
-if [ "$1" = '-installed' -o "$1" = "--installed" ]; then
- exec sage-list-packages installed
-fi
-
-if [ "$1" = '-i' ]; then
@ -524,7 +541,7 @@ diff -up src/bin/sage.orig src/bin/sage
if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
shift
sage_setup
@@ -898,21 +553,10 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
@@ -922,26 +562,10 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca
exec sage-callgrind "$@"
fi
@ -543,12 +560,17 @@ diff -up src/bin/sage.orig src/bin/sage
- interactive_sage "$@"
-fi
-
if [ "$1" = '-dev' -o "$1" = "--dev" ]; then
shift
exec sage-dev "$@"
-if [ "$1" = '-dev' -o "$1" = "--dev" ]; then
- shift
- exec sage-dev "$@"
-fi
-
if [ $# -ge 1 ]; then
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 2014-08-12 14:00:18.705932326 -0300
+++ src/bin/sage-runtests 2014-08-12 14:00:31.543932818 -0300
--- src/bin/sage-runtests.orig 2014-11-17 17:43:03.195926083 -0200
+++ src/bin/sage-runtests 2014-11-17 17:48:39.236938952 -0200
@@ -54,10 +54,6 @@ if __name__ == "__main__":
help="run doctests using Valgrind's cachegrind tool. The log "
"files are named sage-cachegrind.PID and can be found in " +
@ -561,14 +583,23 @@ 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 2014-08-12 14:00:41.666933205 -0300
+++ src/bin/sage-valgrind 2014-08-12 14:01:14.983934481 -0300
@@ -11,7 +11,7 @@ fi
LOG="$DOT_SAGE"/valgrind/sage-memcheck.%p
echo "Log file is $LOG"
--- src/bin/sage-valgrind.orig 2014-11-17 17:43:14.588926520 -0200
+++ src/bin/sage-valgrind 2014-11-17 17:48:18.884938172 -0200
@@ -1,16 +1,6 @@
#!/usr/bin/env bash
-SUPP=""
-if [ -f "$SAGE_EXTCODE/valgrind/python.supp" ]; then
- SUPP+=" --suppressions=$SAGE_EXTCODE/valgrind/python.supp"
-else
- echo "Python suppressions not found (not installed?), skipping"
-fi
-SUPP+=" --suppressions=$SAGE_EXTCODE/valgrind/pyalloc.supp"
-SUPP+=" --suppressions=$SAGE_EXTCODE/valgrind/sage.supp"
-SUPP+=" --suppressions=$SAGE_EXTCODE/valgrind/sage-additional.supp"
-
-MEMCHECK_FLAGS="--leak-resolution=high --leak-check=full --num-callers=25 $SUPP"
+MEMCHECK_FLAGS="--leak-resolution=high --leak-check=full --num-callers=25"
-MEMCHECK_FLAGS="--leak-resolution=high --log-file=$LOG --leak-check=full --num-callers=25 --suppressions=$SAGE_LOCAL/lib/valgrind/sage.supp "; export MEMCHECK_FLAGS
+MEMCHECK_FLAGS="--leak-resolution=high --log-file=$LOG --leak-check=full --num-callers=25 "; export MEMCHECK_FLAGS
if [ "$SAGE_MEMCHECK_FLAGS" ]; then
echo "Overwriting memcheck flags with:"
echo $SAGE_MEMCHECK_FLAGS
echo "Overwriting memcheck flags with: $SAGE_MEMCHECK_FLAGS"