diff -up src/bin/sage.orig src/bin/sage

--- src/bin/sage.orig	2014-02-07 11:02:57.653623604 -0200

+++ src/bin/sage	2014-02-07 11:08:54.765637279 -0200

@@ -11,17 +11,14 @@ usage() {

     echo "  file.<sage|py|spyx> -- run given .sage, .py or .spyx files"

     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"

     echo "  -gap [...]          -- run Sage's Gap with given arguments"

     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 "  -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)"

-    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"

@@ -37,10 +34,6 @@ usage() {

     echo "                           --optional - controls which optional tests are run"

     echo "                           --sagenb - test all sagenb files"

     echo "                           --help - show all testing options"

-    echo "  -upgrade [version]  -- download, build and install the given version. Here,"

-    echo "                         'version' is a git branch or tag name. Useful values"

-    echo "                         are 'master' (the currend development version, this"

-    echo "                         is the default) or a version number like '5.13'."

     echo "  -v, -version        -- print the Sage version"

     exit 0

 }

@@ -64,14 +57,14 @@ usage_advanced() {

     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:"

-    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)"

@@ -88,13 +81,9 @@ 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 "  -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 "  -maxima [...]       -- run Sage's Maxima with given arguments"

     echo "  -mwrank [...]       -- run Sage's mwrank with given arguments"

     echo "  -python [...]       -- run the Python interpreter"

@@ -108,80 +97,10 @@ usage_advanced() {

     echo

     ####  1.......................26..................................................78

     ####  |.....................--.|...................................................|

-    echo "Installing packages and upgrading:"

-    echo "  -experimental       -- list all experimental packages that can be installed"

-    echo "  -f [opts] [packages]-- shortcut for -i -f: force build of the given Sage"

-    echo "                         packages"

-    echo "  -i [opts] [packages]-- install the given Sage packages (unless they are"

-    echo "                         already installed); if no packages are given, print"

-    echo "                         a list of all installed packages.  Options:"

-    echo "                           -c -- run the packages' test suites"

-    echo "                           -f -- force build: install the packages even"

-    echo "                                 if they are already installed"

-    echo "                           -s -- do not delete the spkg/build directories"

-    echo "                                 after a successful build"

-    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 "  -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,"

-    echo "                         'version' is a git branch or tag name. Useful values"

-    echo "                         are 'master' (the currend development version, this"

-    echo "                         is the default) or a version number like '5.13'."

-

-    echo

-    ####  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 "  -sync-build         -- delete old code and other files in the Sage library"

-    echo "                         that have already been deleted from devel/sage but"

-    echo "                         remain in the build directory.  This is sometimes"

-    echo "                         necessary because \`sage -b\` merely copies new or"

-    echo "                         modified files to the target directory."

-    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 "  -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 "  -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"

-    echo "  -t [options] <--all|files|dir>"

-    echo "                      -- test examples in .py, .pyx, .sage, .tex or .rst files"

-    echo "                         selected options:"

-    echo "                           --long - include lines with the phrase 'long time'"

-    echo "                           --verbose - print debugging output during the test"

-    echo "                           --optional - controls which optional tests are run"

-    echo "                           --randorder[=seed] - randomize order of tests"

-    echo "                           --new - only test files modified since last commit"

-    echo "                           --initial - only show the first failure per block"

-    echo "                           --debug - drop into PDB after an unexpected error"

-    echo "                           --failed - only test files that failed last test"

-    echo "                           --sagenb - test all sagenb files"

-    echo "                           --help - show all testing options"

-    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"

-    echo "                         like -t"

-

-    echo

-    ####  1.......................26..................................................78

-    ####  |.....................--.|...................................................|

     echo "Documentation:"

     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"

-    echo "  -docbuild [lang/]<document> <html|pdf|...> -- Build the Sage documentation"

     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"

@@ -201,17 +120,6 @@ usage_advanced() {

     echo

     ####  1.......................26..................................................78

     ####  |.....................--.|...................................................|

-    echo "Making Sage packages or distributions:"

-    echo "  -bdist VER          -- build a binary distribution of Sage"

-    echo "  -combinat [...]     -- run sage-combinat patch management script"

-    echo "  -crap sage-ver.tar  -- detect suspicious garbage in sage source tarball"

-    echo "  -pkg <dir>          -- create Sage package dir.spkg from a given directory"

-    echo "  -pkg_nc <dir>       -- as -pkg, but do not compress the package"

-    echo "  -sdist              -- build a source distribution of Sage"

-

-    echo

-    ####  1.......................26..................................................78

-    ####  |.....................--.|...................................................|

     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"

@@ -225,9 +133,6 @@ 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"

-    echo "  -omega              -- run Sage using Valgrind's omega tool.  The log"

-    echo "                         files are named sage-omega.PID can be found in"

-    echo "                         $DOT_SAGE"

     echo "  -valgrind           -- this is an alias for -memcheck"

     echo

     echo "You can also use -- before a long option, e.g., 'sage --optional'."

@@ -256,17 +161,6 @@ if [ "$1" = '-upgrade' -o "$1" = "--upgr

 fi

-# Source sage-env ($0 is the name of this "sage" script, so we can just

-# append -env to that). We redirect stdout to stderr, which is safer

-# for scripts.

-. "$0-env" >&2

-if [ $? -ne 0 ]; then

-    echo >&2 "Error setting environment variables by sourcing '$0-env';"

-    echo >&2 "possibly contact sage-devel (see http://groups.google.com/group/sage-devel)."

-    exit 1

-fi

-

-

 if [ $# -gt 0 ]; then

   if [ "$1" = '-h' -o "$1" = '-?' -o "$1" = '-help' -o "$1" = '--help' ]; then

      usage

@@ -279,25 +173,11 @@ 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).

-    if [ ! -d "$SAGE_LOCAL/lib/python/site-packages/sage" ]; then

-        echo >&2 '************************************************************************'

-        echo >&2 'It seems that you are attempting to run Sage from an unpacked source'

-        echo >&2 'tarball, but you have not compiled it yet (or maybe the build has not'

-        echo >&2 'finished). You should run `make` in the Sage root directory first.'

-        echo >&2 'If you did not intend to build Sage from source, you should download'

-        echo >&2 'a binary tarball instead. Read README.txt for more information.'

-        echo >&2 '************************************************************************'

-        exit 1

-    fi

-

     # Display the startup banner

     if [ "$SAGE_BANNER" != "no" ]; then

         cat "$SAGE_LOCAL/bin/sage-banner"

     fi

-    maybe_sage_location

-

     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

@@ -308,20 +188,6 @@ 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

-# if Python and sage-location haven't been installed yet.

-maybe_sage_location()

-{

-    if [ -w "$SAGE_LOCAL" ]; then

-        if [ -x "$SAGE_LOCAL/bin/python" ] && [ -x "$SAGE_LOCAL/bin/sage-location" ]; then

-            sage-location || exit $?

-        fi

-    fi

-}

-

-

 # Start an interactive Sage session, this function never returns.

 interactive_sage() {

     sage_setup

@@ -371,11 +237,6 @@ if [ "$1" = '-axiom' -o "$1" = '--axiom'

     exec axiom "$@"

 fi

-if [ "$1" = '-combinat' -o "$1" = '--combinat' ]; then

-    shift

-    exec sage-combinat "$@"

-fi

-

 if [ "$1" = '-gap' -o "$1" = '--gap' ]; then

     shift

     exec gap "$@"

@@ -388,7 +249,7 @@ fi

 if [ "$1" = '-singular' -o "$1" = '--singular' ]; then

     shift

-    exec singular "$@"

+    exec Singular "$@"

 fi

 if [ "$1" = '-sqlite3' -o "$1" = '--sqlite3' ]; then

@@ -416,16 +277,6 @@ if [ "$1" = '-lisp' -o "$1" = '--lisp' ]

     exec ecl "$@"

 fi

-if [ "$1" = '-kash' -o "$1" = '--kash' ]; then

-    shift

-    exec kash "$@"

-fi

-

-if [ "$1" = '-fixdoctests' -o "$1" = '--fixdoctests' ]; then

-    shift

-    exec sage-fixdoctests "$@"

-fi

-

 if [ "$1" = '-maxima' -o "$1" = '--maxima' ]; then

     shift

     exec maxima "$@"

@@ -585,20 +436,6 @@ EOF

 fi

 #####################################################################

-# Test coverage of a module?

-#####################################################################

-

-if [ "$1" = "-coverage" -o "$1" = "--coverage" ]; then

-    shift

-    exec sage-coverage "$@"

-fi

-

-if [ "$1" = "-coverageall" -o "$1" = "--coverageall" ]; then

-    shift

-    exec sage-coverageall "$@"

-fi

-

-#####################################################################

 # File conversion

 #####################################################################

@@ -613,36 +450,15 @@ if [ "$1" = '-rst2sws' -o "$1" = '--rst2

 fi

 #####################################################################

-# Crap

-#####################################################################

-

-if [ "$1" = "-crap" -o "$1" = "--crap" ]; then

-    shift

-    exec sage-crap $@

-fi

-

-#####################################################################

 # Run Sage's versions of the standard Algebra/Geometry etc. software

 #####################################################################

-build_sage() {

-    maybe_sage_location

-    sage-build "$@" || exit $?

-}

-

 if [ "$1" = "-notebook" -o "$1" = '--notebook' -o "$1" = '-n' ]; then

     shift

     sage-cleaner &>/dev/null &

     exec sage-notebook "$@"

 fi

-if [ "$1" = "-bn" -o "$1" = "--build-and-notebook" ]; then

-    shift

-    build_sage

-    sage-cleaner &>/dev/null &

-    exec sage-notebook "$@"

-fi

-

 if [ "$1" = "-inotebook" -o "$1" = '--inotebook' ]; then

     shift

     sage-cleaner &>/dev/null &

@@ -661,58 +477,12 @@ if [ "$1" = '-grepdoc' -o "$1" = "--grep

    exit 0

 fi

-if [ "$1" = '-b' ]; then

-    shift

-    time build_sage "$@"

-    exit $?

-fi

-

-if [ "$1" = '-br' -o "$1" = "--br" ]; then

-    shift

-    build_sage "$@"

-    interactive_sage

-fi

-

 if [ "$1" = '-r' ]; then

    shift

    interactive_sage

 fi

-if [ "$1" = '-ba' ]; then

-    shift

-    echo " *** WARNING ***"

-    echo " You are about to rebuild the entire Sage library."

-    echo " This will take a significant amount of time."

-    echo " (Use --ba-force instead of -ba to skip this prompt.)"

-    echo -n " Do you want to proceed? [y/n] "

-    read CHOICE

-    while [ "$CHOICE" != "y" -a "$CHOICE" != "n" ]; do

-        echo -n " Choose one of y, n: "

-        read CHOICE

-    done

-    if [ $CHOICE = 'n' ]; then

-        exit 0

-    fi

-    build_sage -b "$@"

-    exit $?

-fi

-

-if [ "$1" = '-ba-force' -o "$1" = '--ba-force' ]; then

-    shift

-    build_sage -b "$@"

-    exit $?

-fi

-

-if [ "$1" = '-sync-build' -o "$1" = '--sync-build' ]; then

-    shift

-    cd "$SAGE_ROOT"

-    exec sage-sync-build.py "$@"

-fi

-

-if [ "$1" = '-t' -o "$1" = '-bt' -o "$1" = '-tp' -o "$1" = '-btp' ]; then

-    if [ "$1" = '-bt' -o "$1" = '-btp' ]; then

-        build_sage

-    fi

+if [ "$1" = '-t' -o "$1" = '-tp' ]; then

     if [ ! -f  "$DOT_SAGE"/init.sage ]; then

         echo >&2 "init.sage does not exist ... creating"

         touch "$DOT_SAGE"/init.sage

@@ -728,10 +498,7 @@ if [ "$1" = '-t' -o "$1" = '-bt' -o "$1"

     fi

 fi

-if [ "$1" = '-tnew' -o "$1" = '-btnew' ]; then

-    if [ "$1" = '-btnew' ]; then

-        build_sage

-    fi

+if [ "$1" = '-tnew' ]; then

     shift

     SAGE_BANNER="no"

     sage_setup

@@ -745,12 +512,6 @@ if [ "$1" = '-testall' -o "$1" = "--test

     exec sage-runtests -a "$@"

 fi

-if [ "$1" = '-patchbot' -o "$1" = "--patchbot" ]; then

-    shift

-    cd "$SAGE_ROOT"

-    exec "$SAGE_LOCAL/bin/patchbot/patchbot.py" "$@"

-fi

-

 if [ "$1" = '-c' ]; then

     shift

     SAGE_BANNER="no"

@@ -759,124 +520,6 @@ if [ "$1" = '-c' ]; then

     exec sage-eval "$@"

 fi

-install() {

-    maybe_sage_location

-

-    mkdir -p "$SAGE_LOGS"

-    for PKG in "$@"

-    do

-        # Check for options

-        case "$PKG" in

-            -f) OPTF="-f"

-                continue;;

-            -m) OPTS="-s"

-                echo >&2 "Warning: the -m option is deprecated since Sage 5.0.  Use -s instead."

-                continue;;

-            -s) OPTS="-s"

-                continue;;

-            -c) OPTC="-c"

-                continue;;

-            --check) OPTC="-c"

-                continue;;

-            -info) OPTINFO="--info"

-                continue;;

-            --info) OPTINFO="--info"

-                continue;;

-            -*) echo >&2 "Error: unknown option '$PKG'"

-                exit 2;;

-        esac

-

-        PKG_NAME=`echo "$PKG" | sed -e "s/\.spkg$//"`

-        PKG_NAME=`basename "$PKG_NAME"`

-

-        "$SAGE_ROOT"/build/pipestatus \

-            "sage-spkg $OPTINFO $OPTF $OPTS $OPTC '$PKG' 2>&1" \

-            "(trap '' SIGINT; tee -a '$SAGE_ROOT/logs/install.log' '$SAGE_LOGS/$PKG_NAME.log')"

-        # Do not try to install further packages if one failed

-        if [ $? -ne 0 ]; then

-            exit 1

-        fi

-    done

-    exit 0

-}

-

-if [ "$1" = '-optional' -o "$1" = "--optional" ]; then

-    exec sage-list-optional

-fi

-

-if [ "$1" = '-experimental' -o "$1" = "--experimental" ]; then

-    exec sage-list-experimental

-fi

-

-if [ "$1" = '-standard' -o "$1" = "--standard" ]; then

-    exec sage-list-standard

-fi

-

-if [ "$1" = '-i' ]; then

-    shift

-    # If there are no further arguments, simply list all installed

-    # packages.

-    if [ $# -eq 0 ]; then

-        exec sage-spkg

-    fi

-    install "$@"

-fi

-

-if [ "$1" = '-f' ]; then

-    shift

-    # If there are no further arguments, simply list all installed

-    # packages.

-    if [ $# -eq 0 ]; then

-        exec sage-spkg

-    fi

-    install -f "$@"

-fi

-

-if [ "$1" = '-info' -o "$1" = '--info' ]; then

-    shift

-    for PKG in "$@"

-    do

-        sage-spkg --info "$PKG" || exit $?

-    done

-    exit 0

-fi

-

-if [ "$1" = '-pkg' -o "$1" = '-spkg' -o "$1" = "--pkg" -o "$1" = "--spkg" ]; then

-    shift

-    exec sage-pkg "$@"

-fi

-

-if [ "$1" = '-pkg_nc' -o "$1" = "--pkg_nc" ]; then

-    shift

-    exec sage-pkg -n "$@"

-fi

-

-if [ "$1" = '-sdist' -o "$1" = "--sdist" ]; then

-    maybe_sage_location

-    shift

-    exec sage-sdist "$@"

-fi

-

-if [ "$1" = '-rsyncdist' -o "$1" = "--rsyncdist" ]; then

-    if [ $# -ne 2 ]; then

-        echo >&2 "** MISSING VERSION NUMBER! **"

-        exit 2

-    fi

-    maybe_sage_location

-    exec sage-rsyncdist $2

-fi

-

-if [ "$1" = '-bdist' -o "$1" = "--bdist" ]; then

-    maybe_sage_location

-    shift

-    exec sage-bdist "$@"

-fi

-

-if [ "$1" = "-docbuild" -o "$1" = "--docbuild" ]; then

-    shift

-    exec python "$SAGE_DOC/common/builder.py" "$@"

-fi

-

 if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then

     shift

     sage_setup

@@ -925,12 +568,6 @@ if [ "$1" = '-callgrind' -o "$1" = "--ca

     exec sage-callgrind "$@"

 fi

-if [ "$1" = '-omega' -o "$1" = "--omega" ]; then

-    shift

-    sage_setup

-    exec sage-omega "$@"

-fi

-

 if [ "$1" = '-startuptime' -o "$1" = '--startuptime' ]; then

     exec sage-startuptime.py "$@"

 fi

diff -up src/bin/sage-runtests.orig src/bin/sage-runtests

--- src/bin/sage-runtests.orig	2014-02-07 11:09:24.776638428 -0200

+++ src/bin/sage-runtests	2014-02-07 11:09:41.780639079 -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 " +

                          os.path.join(os.environ["DOT_SAGE"], "valgrind"))

-    parser.add_option("--omega", action="store_true", default=False,

-                      help="run doctests using Valgrind's omega tool.  The log "

-                         "files are named sage-omega.PID and can be found in " +

-                         os.path.join(os.environ["DOT_SAGE"], "valgrind"))

     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	2014-02-07 11:09:56.469639641 -0200

+++ src/bin/sage-valgrind	2014-02-07 11:10:06.804640037 -0200

@@ -11,7 +11,7 @@ fi

 LOG="$DOT_SAGE"/valgrind/sage-memcheck.%p

 echo "Log file is $LOG"

-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