Merge branch 'develop' into public/combinat/partitions_constraints-15525

* develop: (338 commits)
  Updated Sage version to 6.1.beta2
  fix latex
  fix documentation
  minor typography
  Trac 13101: mark doctest as "long time"
  trac 13101 better doctest
  Trac 13101: Fix bug in enumerate_totallyreal_fields_all
  #9706: review patch.
  trac 9706: Propose new class structure
  Symbolic Chebyshev polynomials: reviewer patch
  trac 9706: Collective patch. Bugfixes, extensions, optimizations, documentation, doctests for chebyshev_T, chebyshev_U and base class for ortho polys
  Updated Sage version to 6.1.beta1
  Fixing Whitespace errors
  Use bash as SHELL for build/Makefile
  allow numpy arrays in list_plot, line, points
  Run Jmol from current directory
  Trac #12322: Add a doctest for the correct behavior introduced in trac #12737.
  Trac #14186 coerce_binop errors with keyword arguments
  trac #15553: Broken links in the doc of graph/ and numerical/
  bug fix : importing BooleanPolynomialRing at the top-level prevents sage from starting
  ...

Conflicts:
	src/sage/combinat/partition.py

VERSION.txt

@@ -1 +1 @@
-Sage version 5.13.rc0, released 2013-12-11
+Sage version 6.1.beta2, released 2013-12-23

build/deps

@@ -6,6 +6,7 @@
 # Let e.g. SAGE_ROOT/build/install pass options to sage-spkg, i.e. currently
 # "-f", to force rebuilding dependent packages during an upgrade (#9896).
 
+# Do not put an explicit path for sage-spkg here, it will be found in $PATH.
 SAGE_SPKG = sage-spkg $${SAGE_SPKG_OPTS}
 PIPE = $(SAGE_ROOT)/build/pipestatus
 
@@ -108,10 +109,10 @@ all-sage: \
      $(INST)/$(NCURSES) \
      $(INST)/$(ZLIB) \
      $(INST)/$(ZNPOLY) \
-     scripts \
-     sage \
-     csage \
-     extcode
+     $(INST)/sage \
+     $(INST)/csage \
+     $(EXTCODE) \
+     $(SCRIPTS)
 
 # TOOLCHAIN consists of dependencies determined by build/install,
 # including for example the GCC package.
@@ -132,7 +133,7 @@ toolchain-deps:
 
 # Everything needed to start up Sage using "./sage".  Of course, not
 # every part of Sage will work.  It does not include Maxima for example.
-SAGERUNTIME = scripts sage $(INST)/$(SAGENB) $(INST)/$(IPYTHON) $(INST)/$(GAP)
+SAGERUNTIME = $(SCRIPTS) $(INST)/sage $(INST)/$(SAGENB) $(INST)/$(IPYTHON)
 
 ###############################################################################
 # Building the base system
@@ -147,12 +148,8 @@ base: $(INST)/$(PREREQ) $(INST)/$(BZIP2) $(INST)/$(PATCH)
 $(INST)/$(PREREQ):
 	$(PIPE) "base/$(PREREQ)-install 2>&1" "tee -a $(SAGE_LOGS)/$(PREREQ).log"
 
-# If we are upgrading from a version 4.x of Sage, don't build bzip2.
-# This is because the old sage-spkg script cannot install the new bzip2
-# spkg (which is gzip compressed).  We continue using the old bzip2
-# installation (which is version 1.0.5 since sage-3.3), which is fine.
 $(INST)/$(BZIP2): $(INST)/$(PREREQ)
-	$(PIPE) "$(SAGE_SPKG) $(BZIP2) 2>&1" "tee -a $(SAGE_LOGS)/$(BZIP2).log"; \
+	+$(PIPE) "$(SAGE_SPKG) $(BZIP2) 2>&1" "tee -a $(SAGE_LOGS)/$(BZIP2).log"
 
 $(INST)/$(PATCH): $(INST)/$(BZIP2)
 	+$(PIPE) "$(SAGE_SPKG) $(PATCH) 2>&1" "tee -a $(SAGE_LOGS)/$(PATCH).log"
@@ -199,12 +196,7 @@ $(INST)/$(GRAPHS):
 $(INST)/$(GLPK): $(INST)/$(MPIR) $(INST)/$(ZLIB)
 	+$(PIPE) "$(SAGE_SPKG) $(GLPK) 2>&1" "tee -a $(SAGE_LOGS)/$(GLPK).log"
 
-# Python links against -lbz2.  Technically speaking, we should add
-# BZIP2 as dependency here.  But we don't do that to avoid needless
-# recompiles of Python when upgrading.  Since bzip2 is part of the
-# "base" target, we are guaranteed anyway that some version of bzip2
-# is present.
-$(INST)/$(PYTHON): $(INST)/$(ZLIB) \
+$(INST)/$(PYTHON): $(INST)/$(ZLIB) $(INST)/$(BZIP2) \
 		   $(INST)/$(READLINE) $(INST)/$(SQLITE) $(INST)/$(LIBPNG)
 	+$(PIPE) "$(SAGE_SPKG) $(PYTHON) 2>&1" "tee -a $(SAGE_LOGS)/$(PYTHON).log"
 
@@ -316,7 +308,7 @@ $(INST)/$(SQLITE): $(INST)/$(READLINE)
 	+$(PIPE) "$(SAGE_SPKG) $(SQLITE) 2>&1" "tee -a $(SAGE_LOGS)/$(SQLITE).log"
 
 # To build SageTeX, you just need Python, but to test (SAGE_CHECK=yes)
-# SageTeX, you actually need to run sage, produce plots,...
+# SageTeX, you actually need to run Sage, produce plots,...
 $(INST)/$(SAGETEX): $(INST)/$(PYTHON) \
                     $(SAGERUNTIME) $(INST)/$(MAXIMA) $(INST)/$(SCIPY) \
                     $(INST)/$(MATPLOTLIB) $(INST)/$(PIL) $(INST)/$(TACHYON)
@@ -416,8 +408,7 @@ $(INST)/$(SPHINX): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS) $(INST)/$(DOCUTILS) \
                    $(INST)/$(JINJA2) $(INST)/$(PYGMENTS)
 	+$(PIPE) "$(SAGE_SPKG) $(SPHINX) 2>&1" "tee -a $(SAGE_LOGS)/$(SPHINX).log"
 
-$(INST)/$(JINJA2): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS) $(INST)/$(DOCUTILS) \
-
+$(INST)/$(JINJA2): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS) $(INST)/$(DOCUTILS)
 	+$(PIPE) "$(SAGE_SPKG) $(JINJA2) 2>&1" "tee -a $(SAGE_LOGS)/$(JINJA2).log"
 
 $(INST)/$(PYGMENTS): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
@@ -427,7 +418,7 @@ $(INST)/$(PYGMENTS): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
 # on the one hand, programs needed for the build/install process of the
 # Sage library (e.g. JINJA2), and on the
 # other hand all dependencies for Cython files (e.g. PARI, NTL, MPIR).
-sage: \
+$(INST)/sage: \
 		 $(INST)/$(ATLAS) \
 		 $(INST)/$(CEPHES) \
 		 $(INST)/$(CLIQUER) \
@@ -465,21 +456,25 @@ sage: \
 		 $(INST)/$(SINGULAR) \
 		 $(INST)/$(SYMMETRICA) \
 		 $(INST)/$(ZNPOLY) \
-		 csage
-	+$(PIPE) "{ if [ -z $(SAGE_INSTALL_FETCH_ONLY) ]; then  cd $(SAGE_SRC) && . ./bin/sage-env && time python setup.py install; fi; } 2>&1" "tee -a $(SAGE_LOGS)/sage-$(SAGE_VERSION).log"
-
-scripts: $(SCRIPT_TARGETS)
-
-extcode: $(EXTCODE_TARGETS)
-
-csage: $(INST)/$(SCONS) \
+		 $(INST)/csage
+	if [ -z "$$SAGE_INSTALL_FETCH_ONLY" ]; then \
+		cd $(SAGE_SRC) && source bin/sage-env && \
+		$(PIPE) 'time python setup.py install 2>&1' 'tee -a $(SAGE_LOGS)/sage-$(SAGE_VERSION).log' && \
+		touch $@; \
+	fi
+
+$(INST)/csage: $(INST)/$(SCONS) \
        $(INST)/$(MPIR) \
        $(INST)/$(NTL) \
        $(INST)/$(PARI) \
        $(INST)/$(POLYBORI) \
        $(INST)/$(PYNAC) \
        $(INST)/$(PYTHON)
-	+$(PIPE) "{ if [ -z $(SAGE_INSTALL_FETCH_ONLY) ]; then cd $(SAGE_SRC)/c_lib && . ../bin/sage-env && time scons -Q install; fi; } 2>&1" "tee -a $(SAGE_LOGS)/csage-$(SAGE_VERSION).log"
+	if [ -z "$$SAGE_INSTALL_FETCH_ONLY" ]; then \
+		cd $(SAGE_SRC) && source bin/sage-env && cd c_lib && \
+		$(PIPE) 'time scons -Q install 2>&1' 'tee -a $(SAGE_LOGS)/csage-$(SAGE_VERSION).log' && \
+		touch $@; \
+	fi
 
 $(INST)/ccache: $(BASE) $(INST)/$(ZLIB)
 	+$(PIPE) "$(SAGE_SPKG) ccache 2>&1" "tee -a $(SAGE_LOGS)/ccache.log"

build/install

@@ -23,21 +23,22 @@ export SAGE_ROOT SAGE_SRC SAGE_LOCAL SAGE_EXTCODE SAGE_LOGS SAGE_SPKG_INST SAGE_
 echo `date -u "+%s"` > "$SAGE_ROOT/.BUILDSTART"
 
 ########################################################################
-# Fixes for upgraded Sage versions
+# Support for upgrading
 ########################################################################
-# The script 'pipestatus' used to be autogenerated by this file.  It
-# should be present in any version of Sage starting with 4.5.  In
-# #11073, the autogeneration was removed, so we just check to see if
-# the file is missing.
-if [ ! -f pipestatus ]; then
-    cat >&2 <<EOF
-Error: the script 'pipestatus' is missing.  If you are trying to
-upgrade, your original version of Sage is too old, so upgrading to a
-5.x version of Sage won't work.  Your options are:
- - Upgrading first to sage-4.8 and then upgrading again to sage-5.x.
- - Downloading a new binary version of Sage.
- - Building a new source version from scratch.
-
+# Check that we aren't accidentally upgrading from old (< 6.0)
+# versions of Sage. See #14715.
+# The file $SAGE_ROOT/spkg/install no longer exists in Sage 6.0,
+# but it did exist in all earlier versions.
+if [ -f "$SAGE_ROOT/spkg/install" ]; then
+cat >&2 <<EOF
+************************************************************************
+Error: it is impossible to upgrade your version of Sage to version 6.0
+or later.  It is recommended to install the latest version of Sage from
+scratch.  If you currently have Sage 4.5 or later and really insist on
+upgrading, it should still be possible to upgrade to Sage 5.13 with the
+following command:
+./sage -upgrade http://boxen.math.washington.edu/home/release/sage-5.13/sage-5.13
+************************************************************************
 EOF
     exit 2
 fi
@@ -46,40 +47,6 @@ if [ "$SAGE_UPGRADING" = yes ]; then
     # We're doing an upgrade. Let build/Makefile call sage-spkg with
     # "-f" to force rebuilding dependent packages, too:
     export SAGE_SPKG_OPTS="-f"
-
-    # Avoid RM being set to "rm" (older versions of Sage did this):
-    #   http://trac.sagemath.org/sage_trac/ticket/3537
-    if [ "$RM" = rm ]; then
-        export RM="rm -f"
-    fi
-
-    # Unset AS and LD if they are set to their default values,
-    # otherwise the AS and LD test from #14296 below will fail.
-    if [ "$AS" = as ]; then
-        unset AS
-    fi
-    if [ "$LD" = ld ]; then
-        unset LD
-    fi
-
-    # If we have an old version of sage-location,
-    # then manually fix the .la (libtool) files.
-    if grep 'lib64' "$SAGE_LOCAL/bin/sage-location" &>/dev/null; then
-        # sage-location does check lib64, so everything is fine.
-        true
-    else
-        echo "Found an old version of sage-location, manually fixing some Libtool files."
-        for d in "$SAGE_LOCAL/lib32" "$SAGE_LOCAL/lib64"; do
-            for la_file in "$d"/*.la; do
-                [ -w "$la_file" ] || continue
-                sed -i "s ^libdir=.* libdir='$d' " "$la_file"
-            done
-        done
-    fi
-
-    # The old sage-make_relative script is troublesome (#13407 and #14027).
-    # We simply delete it, its role is taken over by sage-location.
-    rm -f "$SAGE_LOCAL/bin/sage-make_relative"
 fi
 
 ###############################################################################
@@ -364,6 +331,11 @@ cat >&3 <<EOF
 
 EOF
 
+# Use bash as shell for the Makefile (bash obviously exists, since
+# this build/install script runs under bash).
+echo >&3 "SHELL = `command -v bash`"
+echo >&3
+
 # If the user (or the Makefile) has set SAGE_PARALLEL_SPKG_BUILD=no,
 # then turn off parallel building: disable just building multiple
 # packages at the same time.   Individual packages can still be built
@@ -523,7 +495,7 @@ for file in "$SAGE_SRC/bin/"*; do
     echo >&3 "                 \$(SAGE_SRC)${file#$SAGE_SRC} \\"
 done
 echo >&3
-echo >&3 'SCRIPT_TARGETS = \'
+echo >&3 'SCRIPTS = \'
 for file in "$SAGE_SRC/bin/"*; do
     echo >&3 "                 \$(SAGE_LOCAL)${file#$SAGE_SRC} \\"
 done
@@ -533,7 +505,7 @@ for file in `find "$SAGE_SRC"/ext -type f`; do
     echo >&3 "                  \$(SAGE_SRC)${file#$SAGE_SRC} \\"
 done
 echo >&3
-echo >&3 'EXTCODE_TARGETS = \'
+echo >&3 'EXTCODE = \'
 for file in `find "$SAGE_SRC"/ext -type f`; do
     echo >&3 "                  \$(SAGE_EXTCODE)${file#$SAGE_SRC/ext} \\"
 done
@@ -573,12 +545,12 @@ exec 3>&-
 
 # Set MAKE to "make" if unset
 if [ -z "$MAKE" ]; then
-    MAKE=make
+    export MAKE=make
 fi
 
-# * If "make" doesn't understand the -q option (although we require
-#   GNU make, which supports it), it should exit with a non-zero status
-#   which is not a problem.
+# If "make" doesn't understand the -q option (although we require
+# GNU make, which supports it), it should exit with a non-zero status
+# which is not a problem.
 if $MAKE -q "$@" >/dev/null 2>/dev/null; then
     echo "Nothing to (re)build / all up-to-date."
     exit 0

build/pkgs/atlas/checksums.ini

@@ -1,3 +1,4 @@
+tarball=atlas-VERSION.tar.bz2
 sha1=9084d7bb0580c54dd233f0b164f07f60117e029c
 md5=cae064f152ab5faf0cc61bf2801463ad
 cksum=4284029515

build/pkgs/blas/checksums.ini

@@ -1,3 +1,4 @@
+tarball=blas-VERSION.tar.bz2
 sha1=9fb06551c6154201ff2e77fce66c05534fade2a6
 md5=78eaee691634a3aa37567cf915802b00
 cksum=75369376

build/pkgs/boehm_gc/checksums.ini

@@ -1,3 +1,4 @@
+tarball=boehm_gc-VERSION.tar.bz2
 sha1=4013e5d6b685e1a3c7ff9b5447405a2b452731be
 md5=48232de5b36573da6415ece66a9b9084
 cksum=2689595432

build/pkgs/boost_cropped/checksums.ini

@@ -1,3 +1,4 @@
+tarball=boost_cropped-VERSION.tar.bz2
 sha1=25daefce8a55f14bb56b72fffd573972cd2379d2
 md5=764a6c0aa03e39b70053135dc6edaa30
 cksum=111720154

build/pkgs/bzip2/checksums.ini

@@ -1,3 +1,4 @@
+tarball=bzip2-VERSION.tar.gz
 sha1=06cd2d25c80bea77582cacc9ea33a5cd1756c74a
 md5=a4e60f6889aa9cb752b15ed64ebbb7f8
 cksum=2233929913

build/pkgs/cddlib/checksums.ini

@@ -1,3 +1,4 @@
+tarball=cddlib-VERSION.tar.bz2
 sha1=6f2ed53a78298521f1e59750161e0129213f893b
 md5=ef586f07f14b0a13b1c508849daff425
 cksum=810190426

build/pkgs/cephes/checksums.ini

@@ -1,3 +1,4 @@
+tarball=cephes-VERSION.tar.bz2
 sha1=ef2fd663d14bb28caaef4a7fd5758cd488aa6752
 md5=0f520990464e6f1892d1262c10fe49f0
 cksum=1279093512

build/pkgs/cliquer/checksums.ini

@@ -1,3 +1,4 @@
+tarball=cliquer-VERSION.tar.bz2
 sha1=8239530eb14c1273c32ffcf3b671dd3766084374
 md5=32b97b6689318b58d9c099e2c7769521
 cksum=3641271864

build/pkgs/conway_polynomials/checksums.ini

@@ -1,3 +1,4 @@
+tarball=conway_polynomials-VERSION.tar.bz2
 sha1=25b7abe5c935d20c3ebcde943308652c412d14dc
 md5=17f061204b3a6133abb21e17b3abea19
 cksum=3204784255

build/pkgs/cvxopt/checksums.ini

@@ -1,3 +1,4 @@
+tarball=cvxopt-VERSION.tar.bz2
 sha1=ded19c9acfa3c256e6cbd738fbaf5a155c7dbc96
 md5=7114b6952d0428da51d237b974ab64bd
 cksum=2074500616

build/pkgs/cython/checksums.ini

@@ -1,3 +1,4 @@
+tarball=cython-VERSION.tar.bz2
 sha1=9728545db586559ff736a18183c57e419ad18b4a
 md5=7838eac2e779d60fe4eefab920f54f31
 cksum=650483743

build/pkgs/cython/patches/gdbout.patch

@@ -0,0 +1,20 @@
+--- src.orig/Cython/Compiler/CmdLine.py	2013-05-11 07:46:55.000000000 +0200
++++ src/Cython/Compiler/CmdLine.py	2013-06-04 19:09:59.000000000 +0200
+@@ -28,6 +28,7 @@ Options:
+   -w, --working <directory>      Sets the working directory for Cython (the directory modules
+                                  are searched from)
+   --gdb                          Output debug information for cygdb
++  --gdb-outdir <directory>       Specify gdb debug information output directory. Implies --gdb.
+
+   -D, --no-docstrings            Strip docstrings from the compiled module.
+   -a, --annotate                 Produce a colorized HTML version of the source.
+@@ -138,6 +125,9 @@ def parse_command_line(args):
+             elif option == "--gdb":
+                 options.gdb_debug = True
+                 options.output_dir = os.curdir
++            elif option == "--gdb-outdir":
++                options.gdb_debug = True
++                options.output_dir = pop_arg()
+             elif option == '-2':
+                 options.language_level = 2
+             elif option == '-3':