Merge branch 'build_system' of git://github.com/sagemath/sage into bu…

…ild_system

Makefile

@@ -62,30 +62,14 @@ doc-pdf: build
 	$(PIPE) "./sage --docbuild all pdf $(SAGE_DOCBUILD_OPTS) 2>&1" "tee -a logs/docpdf.log"
 
 doc-clean:
-	@echo "Deleting generated docs..."
-	rm -rf src/doc/en/reference/*/sage
-	rm -rf src/doc/en/reference/*/sagenb
-	rm -rf src/doc/en/reference/sage
-	rm -rf src/doc/en/reference/sagenb
-	rm -rf src/doc/output
+	cd src/doc && $(MAKE) clean
 
 clean:
 	@echo "Deleting package build directories..."
 	rm -rf local/var/tmp/sage/build
 
 lib-clean:
-	@echo "Deleting Sage library build artifacts..."
-	rm -f src/c_lib/.sconsign.dblite
-	find src/c_lib -name '*.os' | xargs rm -f
-	find src/c_lib -name '*.so' | xargs rm -f
-	rm -rf src/build
-	find src -name '*.pyc' | xargs rm -f
-	find src -name '*.pyx' | sed 's/pyx$$/c/' | xargs rm -f
-	find src -name '*.pyx' | sed 's/pyx$$/cpp/' | xargs rm -f
-	rm -rf src/sage/libs/pari/gen.h
-	rm -rf src/sage/modular/arithgroup/farey_symbol.h
-	rm -rf src/sage/rings/real_mpfi.h
-	rm -rf src/sage/symbolic/pynac.h
+	cd src && $(MAKE) clean
 
 bdist-clean: clean
 	@echo "Deleting miscellaneous artifacts generated by build system ..."
@@ -101,7 +85,7 @@ distclean: clean doc-clean lib-clean bdist-clean
 
 micro_release: bdist-clean lib-clean
 	@echo "Stripping binaries ..."
-	find local/lib local/bin -type f -exec strip '{}' ';' |& grep -v "File format not recognized" |  grep -v "File truncated" || true
+	LC_ALL=C find local/lib local/bin -type f -exec strip '{}' ';' 2>&1 | grep -v "File format not recognized" |  grep -v "File truncated" || true
 
 TESTPRELIMS = local/bin/sage-starts
 TESTALL = ./sage -t --all

VERSION.txt

@@ -1 +1 @@
-Sage version 5.12.beta2, released 2013-08-20
+Sage version 5.12.rc0, released 2013-10-01

build/deps

@@ -1,16 +1,11 @@
 ###############################################################################
-# This file ($SAGE_ROOT/spkg/standard/deps) will be copied into
-# $SAGE_ROOT/spkg/Makefile by $SAGE_ROOT/spkg/install
+# This file ($SAGE_ROOT/build/deps) will be copied into
+# $SAGE_ROOT/build/Makefile by $SAGE_ROOT/build/install
 ###############################################################################
 
-# Let e.g. SAGE_ROOT/spkg/install pass options to sage-spkg, i.e. currently
+# 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).
-#
-# When upgrading from a 4.x version of Sage, the script "sage-spkg" will be
-# found in SAGE_ROOT/local/bin until the new sage_root repo is installed.
-# After that, it will be found in SAGE_ROOT/spkg/bin
-# (SAGE_ROOT/spkg/bin is added to the PATH in spkg/install).
-# Therefore, do not put an explicit path for sage-spkg here.
+
 SAGE_SPKG = sage-spkg $${SAGE_SPKG_OPTS}
 PIPE = $(SAGE_ROOT)/build/pipestatus
 
@@ -118,7 +113,7 @@ all-sage: \
      csage \
      extcode
 
-# TOOLCHAIN consists of dependencies determined by spkg/install,
+# TOOLCHAIN consists of dependencies determined by build/install,
 # including for example the GCC package.
 toolchain: $(TOOLCHAIN)
 

build/install

@@ -15,7 +15,7 @@ SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed"
 SAGE_VERSION=`cat $SAGE_ROOT/VERSION.txt | sed 's+.*\ \(.*\),.*+\1+'`
 PATH="$SAGE_ROOT/src/bin:$SAGE_LOCAL/bin:$PATH"
 PYTHONPATH="$SAGE_LOCAL"
-export SAGE_ROOT SAGE_SRC SAGE_LOCAL SAGE_LOGS SAGE_SPKG_INST SAGE_VERSION PATH PYTHONPATH
+export SAGE_ROOT SAGE_SRC SAGE_LOCAL SAGE_EXTCODE SAGE_LOGS SAGE_SPKG_INST SAGE_VERSION PATH PYTHONPATH
 
 # Storing the start time of the build process. The time is stored in
 # seconds since 1970-01-01 in a hidden file called
@@ -456,10 +456,10 @@ EOF
 
 # $(TOOLCHAIN) variable containing prerequisites for the build
 echo >&3 -n 'TOOLCHAIN ='
-if [ "$SAGE_INSTALL_CCACHE" == yes ]; then
+if [ "$SAGE_INSTALL_CCACHE" = yes ]; then
     echo >&3 -n ' $(INST)/ccache'
 fi
-if [ "$need_to_install_gcc" == yes ]; then
+if [ "$need_to_install_gcc" = yes ]; then
     echo >&3 -n ' $(INST)/$(GCC)'
     # Use this option for the prereq configure script, such that it
     # will skip all compiler checks.
@@ -469,32 +469,34 @@ echo >&3
 
 echo >&3 'SCRIPT_SOURCES = \'
 for file in "$SAGE_SRC/bin/"*; do
-    echo >&3 "                 $file \\"
+    echo >&3 "                 \$(SAGE_SRC)${file#$SAGE_SRC} \\"
 done
 echo >&3
 echo >&3 'SCRIPT_TARGETS = \'
 for file in "$SAGE_SRC/bin/"*; do
-    echo >&3 "                 ${SAGE_LOCAL}${file#$SAGE_SRC} \\"
+    echo >&3 "                 \$(SAGE_LOCAL)${file#$SAGE_SRC} \\"
 done
 echo >&3
 echo >&3 'EXTCODE_SOURCES = \'
 for file in `find "$SAGE_SRC"/ext -type f`; do
-    echo >&3 "                  $file \\"
+    echo >&3 "                  \$(SAGE_SRC)${file#$SAGE_SRC} \\"
 done
 echo >&3
 echo >&3 'EXTCODE_TARGETS = \'
 for file in `find "$SAGE_SRC"/ext -type f`; do
-    echo >&3 "                  ${SAGE_EXTCODE}${file#$SAGE_SRC/ext} \\"
+    echo >&3 "                  \$(SAGE_EXTCODE)${file#$SAGE_SRC/ext} \\"
 done
 echo >&3
 
 cat >&3 <<EOF
 # don't just use \`install\` since we don't want to change permissions
-$SAGE_LOCAL/bin/%: $SAGE_SRC/bin/%
+\$(SAGE_LOCAL)/bin/%: \$(SAGE_SRC)/bin/%
 	cp \$< \$@
 
 # don't just use \`install -D\` since we don't want to change permissions
-$SAGE_EXTCODE/%: $SAGE_SRC/ext/%
+# cp won't correctly setup the SAGE_EXTCODE directory structure (unlike install)
+# so we need a mkdir here to cp can copy into an existing folder
+\$(SAGE_EXTCODE)/%: \$(SAGE_SRC)/ext/%
 	@mkdir -p "\$(@D)"
 	cp \$< \$@
 EOF

build/pkgs/atlas/SPKG.txt

@@ -36,6 +36,9 @@ Solaris, but should also work on OSX and Cygwin.
  * patches/threads.patch: Avoid thread-related symbols
    ATL_(Set|Reset|Free|Dec)AtomicCount symbols in single-threaded
    library.
+ * patches/do_not_force_mutex.patch: always use assembly over mutex
+   since the mutex version fails to build a shared library. See #15045
+   for details.
  * lapack-x.y.z.tgz: The netlib lapack tarball. If you update this,
    make sure you also update the LAPACK_TARBALL variable in
    spkg-install.
@@ -92,6 +95,14 @@ The package can be configured via three environment variables:
 
 == ChangeLog ==
 
+=== atlas-3.10.1.p5, lapack-3.4.2 (Volker Braun, 30 August 2013) ===
+ * Trac #15045: Another workaround for shared library bug that does
+   not involve static libraries
+
+=== atlas-3.10.1.p4, lapack-3.4.2 (Volker Braun, 14 August 2013) ===
+ * Trac #15045: Workaround for shared library bug,
+   non-deterministically affecting some old platforms
+
 === atlas-3.10.1.p3, lapack-3.4.2 (Volker Braun, 6 July 2013) ===
  * Trac #14781: move untracked files to src/ in preparation for git
  * Added spkg-src to populate the src/ directory

build/pkgs/atlas/package-version.txt

@@ -1 +1 @@
-3.10.1.p3
+3.10.1.p5

build/pkgs/atlas/patches/do_not_force_mutex.patch

@@ -0,0 +1,18 @@
+Always use assembly over mutex since the mutex version fails to build
+a shared library. See #15045 for details.
+
+diff --git a/tune/threads/tune_count.c b/tune/threads/tune_count.c
+index f09717f..4dc3fde 100644
+--- a/tune/threads/tune_count.c
++++ b/tune/threads/tune_count.c
+@@ -241,8 +241,8 @@ int main(int nargs, char **args)
+  */
+       if (tmut < tldec*1.02)
+       {
+-         printf("\nNO REAL ADVANTAGE TO ASSEMBLY, FORCING USE OF MUTEX\n");
+-         ATL_assert(!system("make iForceUseMutex"));
++         printf("\nNO REAL ADVANTAGE TO ASSEMBLY OVER MUTEX\n");
++         printf("\nASSEMBLY/MUTEX ratio is %.2f, but we'll stick with assembly anyway\n", tldec/tmut);
+       }
+    }
+    free(timearr);

build/pkgs/atlas/spkg-install

@@ -536,6 +536,8 @@ rc = make_atlas_library('ptshared')
 if rc!=0:
     print 'Failed to build threaded library, possibly because your'
     print 'system does not support it.'
+else:
+    print 'Installed ATLAS multi-threaded shared library'
 
 
 ######################################################################

build/pkgs/git/checksums.ini

@@ -0,0 +1,3 @@
+sha1=8cce24a390595d6e62c3aa66bef332ab95900173
+md5=9b178a549f64e6f896b634e76ce4c1a6
+cksum=3835145085

build/pkgs/git/package-version.txt

@@ -0,0 +1 @@
+1.7.12.2.p0

build/pkgs/ipython/checksums.ini

@@ -1,3 +1,3 @@
-sha1=1076f8ddcaa3f51e5febac9d8fdb39e789c22a1d
-md5=3108fd91d47e2a87e17b92834f5e79d8
-cksum=2751286105
+sha1=b533236e5c5d4f85bbc654c2bfe890dbb9e68b8e
+md5=29585ef7a2e4396527fa64de11c36e59
+cksum=4222531866

build/pkgs/ipython/package-version.txt

@@ -1 +1 @@
-0.13.1
+0.13.2

build/pkgs/singular/SPKG.txt

@@ -64,6 +64,8 @@ See spkg-src.
  * osx_link.patch: #14415: Fixes linker problems on OS X PPC.
  * sanitize_gmp_header_hack.patch:
    Fix and simplify generation of `factory/cf_gmp.h` (cf. #14737).
+ * pullrequest215.patch: Backport of first 3 patches from
+   https://github.com/Singular/Sources/pull/215
 
 Other notes
  * The option '--without-dynamic-kernel' is used on *all*
@@ -91,6 +93,12 @@ Other notes
 
 == ChangeLog ==
 
+=== singular-3-1-5.p9 (Paul Zimmermann, Jeroen Demeyer, 26 August 2013) ===
+ * #13770: Add upstream pull request 215 for multivariate factorisation.
+ * spkg-install: split apply_patches step in 2 steps: choose_patches and
+   apply_patches; add a few small fixes.
+ * Remove install-sh which is no longer needed.
+
 === singular-3-1-5.p8 (Leif Leonhardy, Volker Braun, 10 July 2013) ===
  * #14737: Fix and simplify generation of `factory/cf_gmp.h`
    (by adding `patches/sanitize_gmp_header_hack.patch`).