Merge branch 'master' into 6629-Schubert-Grothendieck-Key-polynomials

Conflicts:
	src/sage/combinat/all.py

.gitignore

@@ -4,3 +4,52 @@
 /local
 /logs
 /upstream
+
+###################
+# Temporary Files #
+###################
+
+# Various editors
+*~
+
+# Emacs
+\#*\#
+.\#*
+
+# Vim
+*.s[a-w][a-z]
+*.un~
+.netrwhist
+
+# PyCharm
+.idea
+.iml
+
+# Eclipse
+*.pydevproject
+.project
+.metadata
+*.tmp
+*.bak
+*.swp
+*~.nib
+.classpath
+.settings/
+.loadpath
+.externalToolBuilders/
+.cproject
+.buildpath
+
+# OSX specific temporary files
+.DS_Store
+._*
+.AppleDouble
+.LSOverride
+.Spotlight-V100
+.Trashes
+
+# Windows
+$RECYCLE.BIN/
+
+# SublimeText
+*.sublime-workspace

Makefile

@@ -21,6 +21,12 @@ build: logs
 		"tee -a ../logs/install.log"
 	./sage -b
 
+# Preemptively download all standard upstream source tarballs.
+download:
+	export SAGE_ROOT=$$(pwd) && \
+	export PATH=$$SAGE_ROOT/src/bin:$$PATH && \
+	./src/bin/sage-download-upstream
+
 # ssl: build Sage, and also install pyOpenSSL. This is necessary for
 # running the secure notebook. This make target requires internet
 # access. Note that this requires that your system have OpenSSL

VERSION.txt

@@ -1 +1 @@
-Sage version 5.13.beta2, released 2013-10-31
+Sage version 6.0, released 2013-12-17

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
 
@@ -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"
 
@@ -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)
@@ -466,7 +457,7 @@ sage: \
 		 $(INST)/$(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"
+	$(PIPE) '{ if [ -z "$(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)
 
@@ -479,7 +470,7 @@ csage: $(INST)/$(SCONS) \
        $(INST)/$(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"
+	$(PIPE) '{ if [ -z "$(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'
 
 $(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
@@ -46,31 +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
-
-    # 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
 
 ###############################################################################
@@ -252,6 +228,48 @@ else
     fi
 fi
 
+# If we are not installing GCC: check that the assembler and linker
+# used by $CC match $AS and $LD.
+# See http://trac.sagemath.org/sage_trac/ticket/14296
+if [ $need_to_install_gcc != yes ]; then
+    if [ "$AS" != "" ]; then
+        CC_as=`$CC -print-file-name=as 2>/dev/null`
+        CC_as=`command -v $CC_as 2>/dev/null`
+        cmd_AS=`command -v $AS`
+
+        if [ "$CC_as" != "" -a "$CC_as" != "$cmd_AS" ]; then
+            echo >&2 "Error: Mismatch of assemblers between"
+            echo >&2 " * $CC using $CC_as"
+            echo >&2 " * \$AS equal to $AS"
+            if [ "$SAGE_PORT" = "" ]; then
+                echo >&2 "Aborting, either change or unset AS or set SAGE_PORT=yes or set"
+                echo >&2 "SAGE_INSTALL_GCC=yes (this GCC would use assembler $AS)"
+                exit 1
+            else
+                echo >&2 "Continuing since SAGE_PORT is set."
+            fi
+        fi
+    fi
+    if [ "$LD" != "" ]; then
+        CC_ld=`$CC -print-file-name=ld 2>/dev/null`
+        CC_ld=`command -v $CC_ld 2>/dev/null`
+        cmd_LD=`command -v $LD`
+
+        if [ "$CC_ld" != "" -a "$CC_ld" != "$cmd_LD" ]; then
+            echo >&2 "Error: Mismatch of linkers between"
+            echo >&2 " * $CC using $CC_ld"
+            echo >&2 " * \$LD equal to $LD"
+            if [ "$SAGE_PORT" = "" ]; then
+                echo >&2 "Aborting, either change or unset LD or set SAGE_PORT=yes or set"
+                echo >&2 "SAGE_INSTALL_GCC=yes (this GCC would use linker $LD)"
+                exit 1
+            else
+                echo >&2 "Continuing since SAGE_PORT is set."
+            fi
+        fi
+    fi
+fi
+
 ###############################################################################
 # Create the sage_fortran script.
 ###############################################################################
@@ -522,12 +540,12 @@ 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/SPKG.txt

@@ -95,6 +95,13 @@ The package can be configured via three environment variables:
 
 == ChangeLog ==
 
+=== atlas-3.10.1.p7, lapack-3.4.2 (Jean-Pierre Flori, 25 November 2013) ===
+ * Trac #14410: Let ATLAS build and install shared libraries on Cygwin.
+ * Bunch of modifications to the autotools project generating shared libraries
+   so that it does not invoke libtool on Cygwin.
+ * Fix a bug in spkg-install.
+ * Cleanup spkg-check.
+
 === atlas-3.10.1.p6, lapack-3.4.2 (Volker Braun, 11 October 2013) ===
  * Trac #15270: Do not give up if the upstream shared library build
    fails

build/pkgs/atlas/checksums.ini

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

build/pkgs/atlas/package-version.txt

@@ -1 +1 @@
-3.10.1.p6
+3.10.1.p7