Merge branch 'develop' into public/monoids/15289-indexed

* develop: (163 commits) Updated Sage version to 6.2.beta3 fix incorrect permissions for install-sh Prevent python from using system hg and svn during its installation. Do not hardcode the non-posix install program poison proxy environment variables Slight modifications of gap related pkgs SPKG.txt files. * Remove now git recorded old changelog. * Put patches description into subsections. remove nose from dependencies undefine FORTIFY_SOURCE udpate to GAP-4.7.4 reviewer changes with Travis added the affine factorization crystal to the documentation Fix modular exponentiation of polynomials over finite field extensions. Reenable previously failing doctests for modular exponentiation of polynomials over finite field extensions. fix trivial doctest failure apply sparc patch also to libgap add SPARC alignment fix remove duplicated changelog reverted changes in k_tableaux finished affine factorization crystal fixed rep ... Conflicts: src/sage/combinat/sf/kschur.py
sagemath · Mar 4, 2014 · 03057a4 · 03057a4
2 parents 760c939 + ccab985
commit 03057a4
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diff --git a/COPYING.txt b/COPYING.txt
@@ -88,6 +88,8 @@ pari                        GPLv2+
 patch                       GPLv2+
 pexpect                     Python License
 pil                         Similar to MIT and modified BSD (see below)
+pkgconf                     ISC License (equivalent to Simplified BSD)
+pkgconfig                   MIT License
 polybori                    GPLv2+
 polytopes_db                None (database)
 ppl                         GPLv3+

diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-Sage version 6.2.beta2, released 2014-02-15
+Sage version 6.2.beta3, released 2014-03-03
diff --git a/build/deps b/build/deps
@@ -81,6 +81,8 @@ all-sage: \
      $(INST)/$(PARI) \
      $(INST)/$(PEXPECT) \
      $(INST)/$(PILLOW) \
+     $(INST)/$(PKGCONF) \
+     $(INST)/$(PKGCONFIG) \
      $(INST)/$(POLYBORI) \
      $(INST)/$(POLYTOPES_DB) \
      $(INST)/$(PPL) \
@@ -501,6 +503,12 @@ $(INST)/$(GCC): $(INST)/$(MPIR) $(INST)/$(MPFR) $(INST)/$(MPC) \
 $(INST)/$(PILLOW): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
 	+$(PIPE) "$(SAGE_SPKG) $(PILLOW) 2>&1" "tee -a $(SAGE_LOGS)/$(PILLOW).log"
 
+$(INST)/$(PKGCONF): 
+	+$(PIPE) "$(SAGE_SPKG) $(PKGCONF) 2>&1" "tee -a $(SAGE_LOGS)/$(PKGCONF).log"
+
+$(INST)/$(PKGCONFIG): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
+	+$(PIPE) "$(SAGE_SPKG) $(PKGCONFIG) 2>&1" "tee -a $(SAGE_LOGS)/$(PKGCONFIG).log"
+
 $(INST)/$(NUMPY): $(INST)/$(PYTHON) $(INST)/$(ATLAS)
 	+$(PIPE) "$(SAGE_SPKG) $(NUMPY) 2>&1" "tee -a $(SAGE_LOGS)/$(NUMPY).log"
 
@@ -521,6 +529,7 @@ $(INST)/$(CEPHES):
 # setuptools forgets to update easy-install.pth during parallel
 # builds, so we build the relevant packages serially.
 
+$(INST)/$(PILLOW): $(INST)/$(PKGCONFIG)
 $(INST)/$(SQLALCHEMY): $(INST)/$(PILLOW)
 $(INST)/$(PYGMENTS): $(INST)/$(SQLALCHEMY)
 $(INST)/$(JINJA2): $(INST)/$(PYGMENTS)

diff --git a/build/install b/build/install
@@ -65,32 +65,6 @@ mkdir -p "$SAGE_SHARE"
 # Determine whether to install GCC (gcc, g++, gfortran).
 ###############################################################################
 
-# Give a deprecation message whenever SAGE_FORTRAN or SAGE_FORTRAN_LIB
-# is set to something. See Trac #13349.
-if [ -n "$SAGE_FORTRAN" ] || [ -n "$SAGE_FORTRAN_LIB" ]; then
-cat >&2 <<EOF
-WARNING: the environment variables SAGE_FORTRAN and SAGE_FORTRAN_LIB
-are deprecated since sage-5.3.
-
-The GNU Compiler Collection (GCC) is included in Sage and will be
-installed if you do not have a Fortran compiler. If you do have a
-Fortran compiler installed and you want to specify its path, you can
-use the standard environment variable FC (instead of SAGE_FORTRAN) to
-point to the Fortran compiler.
-
-As replacement to SAGE_FORTRAN_LIB, you can either add the directory
-containing the Fortran library to LIBRARY_PATH and/or LD_LIBRARY_PATH,
-or copy/symlink the Fortran library into \$SAGE_ROOT/local/lib. In most
-cases, none of this is needed as the compiler/linker should find the
-Fortran library by itself.
-
-Support for SAGE_FORTRAN and SAGE_FORTRAN_LIB might be removed from
-future versions of Sage. Moreover, these variables are not tested
-anymore and might not work as you expect.
-EOF
-sleep 5
-fi
-
 # Determine various compilers.  These variables should not be exported,
 # they are only used in this build/install script to determine whether to
 # install GCC.  The "real" $CC, $CXX,... variables for building Sage are
@@ -107,9 +81,7 @@ if [ -z "$CXX" ]; then
 fi
 
 if [ -z "$FC" ]; then
-    if [ -n "$SAGE_FORTRAN" ]; then
-        FC="$SAGE_FORTRAN"
-    elif command -v gfortran >/dev/null 2>/dev/null; then
+    if command -v gfortran >/dev/null 2>/dev/null; then
         FC=gfortran
     elif command -v g95 >/dev/null 2>/dev/null; then
         FC=g95
@@ -264,12 +236,11 @@ fi
 # Create the sage_fortran script.
 ###############################################################################
 
-# Don't use FC and SAGE_FORTRAN_LIB if we are installing GCC or have
+# Don't use FC if we are installing GCC or have
 # installed gfortran, as that can cause compatibility problems.
 # We want to use the Fortran compiler that we build as part of GCC.
 if [ "$need_to_install_gcc" = yes ] || [ -x "$SAGE_LOCAL/bin/gfortran" ]; then
     unset FC
-    unset SAGE_FORTRAN_LIB
 fi
 
 # Write sage_fortran script.
@@ -301,11 +272,6 @@ fi
 EOF
 chmod +x "$SAGE_LOCAL/bin/sage_fortran"
 
-# Make the fortran library symlink if requested
-if [ -f "$SAGE_FORTRAN_LIB" ]; then
-    ( cd "$SAGE_LOCAL/lib" && ln -sf "$SAGE_FORTRAN_LIB" . )
-fi
-
 ###############################################################################
 # Create $SAGE_ROOT/build/Makefile starting from build/deps
 ###############################################################################
@@ -413,6 +379,8 @@ PARI_SEADATA_SMALL=`newest_version pari_seadata_small`
 PATCH=`newest_version patch`
 PEXPECT=`newest_version pexpect`
 PILLOW=`newest_version pillow`
+PKGCONF=`newest_version pkgconf`
+PKGCONFIG=`newest_version pkgconfig`
 POLYBORI=`newest_version polybori`
 POLYTOPES_DB=`newest_version polytopes_db`
 PPL=`newest_version ppl`

diff --git a/build/pkgs/atlas/spkg-install b/build/pkgs/atlas/spkg-install
@@ -136,16 +136,16 @@ if 'SAGE_ATLAS_LIB' in os.environ:
         sym_gfortran = 'gfortran' in symbol_table
         sym_g95 = 'g95' in symbol_table
         if sym_gfortran and conf['fortran'] != 'gfortran':
-            print("Symbols in lib77blas indicate it was build with gfortran \n")
-            print("However SAGE is using a different fortran compiler \n")
-            print("If you wish to use this blas library, make sure SAGE_FORTRAN points \n")
-            print("to a fortran compiler compatible with this library. \n")
+            print("Symbols in lib77blas indicate it was built with gfortran.\n")
+            print("However, Sage is using a different fortran compiler.\n")
+            print("If you wish to use this blas library, make sure FC points\n")
+            print("to a fortran compiler compatible with this library.\n")
             sys.exit(2)
         if sym_g95 and conf['fortran'] != 'g95':
-            print("Symbols in lib77blas indicate it was build with g95 \n")
-            print("However SAGE is using a different fortran compiler \n")
-            print("If you wish to use this blas library, make sure SAGE_FORTRAN points \n")
-            print("to a fortran compiler compatible with this library. \n")
+            print("Symbols in lib77blas indicate it was built with g95 \n")
+            print("However, Sage is using a different fortran compiler.\n")
+            print("If you wish to use this blas library, make sure FC points\n")
+            print("to a fortran compiler compatible with this library.\n")
             sys.exit(2)
 
     SAGE_LOCAL_LIB = os.path.join(conf['SAGE_LOCAL'], 'lib')

diff --git a/build/pkgs/cliquer/SPKG.txt b/build/pkgs/cliquer/SPKG.txt
@@ -6,7 +6,7 @@ weighted graph. It uses an exact branch-and-bound algorithm recently
 developed by Patr Ostergard.
 
 == License ==
-Cliquer is licensed under the GNU General Public License v2 ( June 1991 )
+GNU General Public License v2
 
 == SPKG Maintainers ==
 Nathann Cohen (nathann.cohen@gmail.com)
@@ -18,92 +18,8 @@ http://users.tkk.fi/pat/cliquer.html
 == Dependencies ==
  * None
 
-== TODO ==
- * A MAJOR cleanup of this package is required, see #9870, #14349
-
 == Patches ==
- * Makefile.patch: Patch the Makefile for Sage. This custom Makefile
-   contains Sage specific compilation and linking flags. More
-   importantly, we're building cliquer as a dynamic shared library,
-   instead of a stand alone program.
- * cl_c.patch, cl_h.patch: Hook into cliquer to access internal
-   functions. Could probably be done better (see TODO)
-
-== Changelog ==
-
-=== cliquer-1.21.p1 (Volker Braun, Felix Salfelder, 15 July 2013) ===
- * Trac #14892: Track all patches, remove unnecessary graph.c.patch
-
-=== cliquer-1.21.p0 (Nathann Cohen, 4 May 2012) ===
- * Solved memory leaks reported on #12905
- * Incidentally updated Cliquer to version 1.21
- * Incidentally removed Sage's code that was formerly directly
-   inserted in the original files. This code is now inserted during
-   installation from patches located in the patches/ folder. A bit
-   cleaner. A long way to go. But God this code really is messy and
-   full of global variables.
-
-=== cliquer-1.2.p11 (John Palmieri, 23 March 2012) ===
- * #12311: Remove explicit path to testcc.sh in spkg-install.
-
-=== cliquer-1.2.p10 (Karl-Dieter Crisman, 28 June 2011) ===
- * #11547: Make sure that libcliquer.so is copied as both
-   .dll and .so files on Cygwin
-
-=== cliquer-1.2.p9 (Jeroen Demeyer, 4 May 2011) ===
- * #11227: Apply workaround also for versions 4.6.1 of gcc, not only
-   version 4.6.0.  This is to support pre-release versions of
-   gcc 4.6.1, the bug should be fixed in the final gcc 4.6.1.
-
-=== cliquer-1.2.p8 (Jeroen Demeyer, 25 April 2011) ===
- * #11227: When compiling with gcc 4.6.0, add compiler flag -fno-ivopts
-   to work around a gcc bug.
- * Use `patch` for patching the Makefile and put patches/Makefile.patch
-   under hg control.
- * Some minor cleanup of spkg-install and Makefile.
-
-=== cliquer-1.2.p7 David Kirkby, Leif Leonhardy  (14 September 2010) ===
- * #9871 Change flags passed to the linker on Solaris to avoid problems with the
-   link-editor believing the shared library contains text relocations. This
-   problem can be seen on 32-bit builds of Solaris and OpenSolaris using
-   /usr/bin/elfdump, but the problems are much more serious on 64-bit
-   builds of Solaris - in some cases stopping code from building.
- * Added the linker flag -ztext on Solaris too, as -ztest forces a fatal
-   error if any  relocations   against   non-writable,  allocatable  sections
-   remain. This will make it easier to catch any similar bugs in future.
-
-=== cliquer-1.2.p6 Nathann Cohen, David Kirkby (31 August 2010) ===
- * #9766: Additions to SPKG.txt
-      - URL of the original website to the SPKG.txt file
-      - "Special Update/Build Instructions" section
-      - "Dependencies" section
- * Added an entry to SPKG showing when this package was first put into
-   Sage. The first mercurial log is dated 17th July 2009.
- * Added a note on to the cliquer-1.2.p0 entry in SPKG.txt that 'scons'
-   was no longer used.
-
-=== cliquer-1.2.p5 Mike Hansen (15 February 2010) ===
- * Fixed Trac #8279 to make the cliquer spkg work on Cygwin with the Sage library.
-
-=== cliquer-1.2.p4 Mike Hansen, William Stein (12 February 2010) ===
- * Fixed Trac #7308 to make the cliquer spkg work on Cygwin.
-
-=== cliquer-1.2.p3 (Peter Jeremy, 2010-01-25) ===
- * #7824: add FreeBSD support
-
-=== cliquer-1.2.p2 (?, ?) ===
- * changelog lost to history
-
-=== cliquer-1.2.p1 Karl-Dieter Crisman, Georg S. Weber (7th October 2009) ===
- * fix trac #7115: Re-add support for building cliquer on Mac OS X 10.4
-
-=== cliquer-1.2.p0 Minh Van Nguyen (16th September 2009) ===
- * Support for building cliquer 1.2 in 64-bit mode on Mac OS X 10.5.x
-   and 64-bit openSUSE 11.1.
- * Add custom compilation and linking flags on top of the Makefile of
-   cliquer 1.2.
- * Removed dependancy of cliquer on 'scons'
-
-=== cliquer-1.2 Nathann Cohen (17th July 2009) ===
- * First release put into Sage.
-
+ * Makefile.patch: Patch the Makefile for Sage. Remove hardcoded
+   compiler and linker flags, allow flags to be set from spkg-install.
+   More importantly, we're building cliquer as a dynamic shared library,
+   instead of a stand-alone program.
diff --git a/build/pkgs/cliquer/package-version.txt b/build/pkgs/cliquer/package-version.txt
@@ -1 +1 @@
-1.21.p1
+1.21.p2
diff --git a/build/pkgs/cliquer/patches/Makefile.patch b/build/pkgs/cliquer/patches/Makefile.patch
@@ -1,27 +1,32 @@
-diff -ur src/Makefile src.patched/Makefile
---- src/Makefile	2010-02-16 05:26:57.000000000 +0100
-+++ src.patched/Makefile	2011-04-26 09:46:41.000000000 +0200
-@@ -1,14 +1,17 @@
-
- ##### Configurable options:
-
-+# Don't need to set any of these compiler variables. They have already been
-+# set when running SAGE_ROOT/local/bin/sage-env as part of installing a
-+# package.
- ## Compiler:
+diff -ru src/Makefile b/Makefile
+--- src/Makefile	2010-01-22 08:53:21.000000000 +0100
++++ b/Makefile	2014-01-16 14:55:51.977047191 +0100
+@@ -1,24 +1,3 @@
+-
+-##### Configurable options:
+-
+-## Compiler:
 -CC=gcc
-+#CC=gcc
- #CC=cc
-
- ## Compiler flags:
-
- # GCC:  (also -march=pentium etc, for machine-dependent optimizing)
+-#CC=cc
+-
+-## Compiler flags:
+-
+-# GCC:  (also -march=pentium etc, for machine-dependent optimizing)
 -CFLAGS=-Wall -O3 -fomit-frame-pointer -funroll-loops
-+#CFLAGS=-Wall -O3 -fomit-frame-pointer -funroll-loops
-
- # GCC w/ debugging:
- #CFLAGS=-Wall -g -DINLINE=
-@@ -29,14 +32,14 @@
+-
+-# GCC w/ debugging:
+-#CFLAGS=-Wall -g -DINLINE=
+-
+-# Compaq C / Digital C:
+-#CFLAGS=-arch=host -fast
+-
+-# SunOS:
+-#CFLAGS=-fast
+-
+ ## Program options:
+
+ # Enable long options for cl (eg. "cl --help"), comment out to disable.
+@@ -29,14 +8,14 @@
  ##### End of configurable options
 
 

diff --git a/build/pkgs/cliquer/spkg-check b/build/pkgs/cliquer/spkg-check
@@ -0,0 +1,35 @@
+#!/usr/bin/env bash
+
+if [ "$SAGE_LOCAL" = "" ]; then
+    echo "SAGE_LOCAL undefined ... exiting";
+    echo "Maybe run 'sage -sh'?"
+    exit 1
+fi
+
+OPTIMIZATION_FLAGS="-O3 -funroll-loops -fomit-frame-pointer"
+# Work around a bug in gcc 4.6.0: http://gcc.gnu.org/bugzilla/show_bug.cgi?id=48774
+if [ "`testcc.sh $CC`" = GCC ] ; then
+    if $CC -dumpversion 2>/dev/null |grep >/dev/null '^4\.6\.[01]' ; then
+        echo "Warning: Working around bug in gcc 4.6.0"
+        OPTIMIZATION_FLAGS="$OPTIMIZATION_FLAGS -fno-ivopts"
+    fi
+fi
+
+CFLAGS="$CFLAGS `testcflags.sh -g $OPTIMIZATION_FLAGS -fPIC -KPIC -Wall`"
+CPPFLAGS="$CPPFLAGS -I$SAGE_LOCAL/include"
+LDFLAGS="$LDFLAGS -L$SAGE_LOCAL/lib"
+
+# Compile for 64-bit if SAGE64 is set to 'yes'.
+# On 64-bit hardware, we don't need to set this variable to true. A
+# 64-bit cliquer library would be built on such platform.
+if [ "$SAGE64" = yes ]; then
+    CFLAGS="$CFLAGS -m64 "
+    LDFLAGS="$LDFLAGS -m64 "
+fi
+
+# Export everything
+export CFLAGS
+export CPPFLAGS
+export LDFLAGS
+
+cd src && $MAKE test