Merge branch 'develop' into t/3624/ticket/3624

* develop: (1831 commits)
  Updated Sage version to 6.3
  mark all internet-using doctests as
  Updated Sage version to 6.3.rc1
  trac #16766: form -> from
  trac #16766: Git 101: How to create a conflict with 10 others patches in needs_review
  Typo
  Show the "please run make" message only if we actually installed something
  trac #16766: Broken doctest
  trac #16766: Broken doctests
  trac #16766: we don t want designs.deprecated_function_alias
  trac #16766: Improve the doc of combinat/designs/
  Treat the empty GAP list as list and not as string
  Move message about running 'make' to install() in src/bin/sage
  Stopgap for #16759: disable install_package
  Improve GAP String handling
  trac #16758: Use class of outer machine in composition
  trac #16758: Disallow composition with automaton
  Updated Sage version to 6.3.rc0
  trac #16758: Add failing doctests
  Samall correction in toc
  ...

.gitignore

@@ -37,6 +37,9 @@
 .idea
 .iml
 
+# XCode
+xcuserdata/
+
 # Eclipse
 *.pydevproject
 .project

VERSION.txt

@@ -1 +1 @@
-Sage version 6.3.beta0, released 2014-05-10
+Sage version 6.3, released 2014-08-10

build/deps

@@ -31,6 +31,7 @@ all-sage: \
      $(INST)/$(CDDLIB) \
      $(INST)/$(CEPHES) \
      $(INST)/$(CLIQUER) \
+     $(INST)/$(COMBINATORIAL_DESIGNS) \
      $(INST)/$(CONWAY) \
      $(INST)/$(CVXOPT) \
      $(INST)/$(CYTHON) \
@@ -158,12 +159,12 @@ $(INST)/prereq: ../configure
 	        echo "If you would like to try to build Sage anyway (to help porting),"; \
 	        echo "export the variable 'SAGE_PORT' to something non-empty."; \
 	        exit 1; \
-    	else \
+	    else \
 	        echo "Since 'SAGE_PORT' is set, we will try to build anyway."; \
-    	fi; )
+	    fi; )
 	touch $@
 
-$(INST)/$(BZIP2): $(INST)/prereq
+$(INST)/$(BZIP2): $(INST)/prereq $(INST)/$(PKGCONF)
 	+$(PIPE) "$(SAGE_SPKG) $(BZIP2) 2>&1" "tee -a $(SAGE_LOGS)/$(BZIP2).log"
 
 $(INST)/$(PATCH): $(INST)/$(BZIP2)
@@ -176,7 +177,7 @@ $(INST)/$(PATCH): $(INST)/$(BZIP2)
 $(INST)/$(ATLAS): $(INST)/$(PYTHON)
 	+$(PIPE) "$(SAGE_SPKG) $(ATLAS) 2>&1" "tee -a $(SAGE_LOGS)/$(ATLAS).log"
 
-$(INST)/$(BOEHM_GC):
+$(INST)/$(BOEHM_GC): $(INST)/$(PKGCONF)
 	+$(PIPE) "$(SAGE_SPKG) $(BOEHM_GC) 2>&1" "tee -a $(SAGE_LOGS)/$(BOEHM_GC).log"
 
 $(INST)/$(BOOST_CROPPED):
@@ -185,7 +186,10 @@ $(INST)/$(BOOST_CROPPED):
 $(INST)/$(CLIQUER):
 	+$(PIPE) "$(SAGE_SPKG) $(CLIQUER) 2>&1" "tee -a $(SAGE_LOGS)/$(CLIQUER).log"
 
-$(INST)/$(NCURSES):
+$(INST)/$(COMBINATORIAL_DESIGNS):
+	+$(PIPE) "$(SAGE_SPKG) $(COMBINATORIAL_DESIGNS) 2>&1" "tee -a $(SAGE_LOGS)/$(COMBINATORIAL_DESIGNS).log"
+
+$(INST)/$(NCURSES): $(INST)/$(PKGCONF)
 	+$(PIPE) "$(SAGE_SPKG) $(NCURSES) 2>&1" "tee -a $(SAGE_LOGS)/$(NCURSES).log"
 
 $(INST)/$(READLINE): $(INST)/$(NCURSES)
@@ -211,7 +215,7 @@ $(INST)/$(GRAPHS):
 $(INST)/$(GLPK): $(INST)/$(MPIR) $(INST)/$(ZLIB)
 	+$(PIPE) "$(SAGE_SPKG) $(GLPK) 2>&1" "tee -a $(SAGE_LOGS)/$(GLPK).log"
 
-$(INST)/$(PYTHON): $(INST)/$(ZLIB) $(INST)/$(BZIP2) \
+$(INST)/$(PYTHON): $(INST)/$(ZLIB) $(INST)/$(BZIP2) $(INST)/$(PKGCONF) \
 		   $(INST)/$(READLINE) $(INST)/$(SQLITE) $(INST)/$(LIBPNG)
 	+$(PIPE) "$(SAGE_SPKG) $(PYTHON) 2>&1" "tee -a $(SAGE_LOGS)/$(PYTHON).log"
 
@@ -336,7 +340,7 @@ $(INST)/$(SAGETEX): $(INST)/$(PYTHON) \
 $(INST)/$(SETUPTOOLS): $(INST)/$(PYTHON)
 	+$(PIPE) "$(SAGE_SPKG) $(SETUPTOOLS) 2>&1" "tee -a $(SAGE_LOGS)/$(SETUPTOOLS).log"
 
-$(INST)/$(SINGULAR): $(INST)/$(MPIR) $(INST)/$(NTL) \
+$(INST)/$(SINGULAR): $(INST)/$(MPIR) $(INST)/$(NTL) $(INST)/$(FLINT) \
 		     $(INST)/$(READLINE) $(INST)/$(MPFR)
 	+$(PIPE) "$(SAGE_SPKG) $(SINGULAR) 2>&1" "tee -a $(SAGE_LOGS)/$(SINGULAR).log"
 
@@ -401,7 +405,7 @@ $(INST)/$(ECL): $(INST)/$(MPIR) $(INST)/$(READLINE) $(INST)/$(BOEHM_GC)
 $(INST)/$(MAXIMA): $(INST)/$(ECL)
 	+$(PIPE) "$(SAGE_SPKG) $(MAXIMA) 2>&1" "tee -a $(SAGE_LOGS)/$(MAXIMA).log"
 
-$(INST)/$(R): $(INST)/$(ATLAS) $(INST)/$(ICONV) $(INST)/$(READLINE)
+$(INST)/$(R): $(INST)/$(ATLAS) $(INST)/$(ICONV) $(INST)/$(READLINE) $(INST)/$(PKGCONF)
 	+$(PIPE) "$(SAGE_SPKG) $(R) 2>&1" "tee -a $(SAGE_LOGS)/$(R).log"
 
 $(INST)/$(RPY): $(INST)/$(PYTHON) $(INST)/$(R)
@@ -422,7 +426,7 @@ $(INST)/$(FLINT): $(INST)/$(MPIR) $(INST)/$(MPFR) $(INST)/$(NTL)
 $(INST)/$(ECLIB): $(INST)/$(PARI) $(INST)/$(NTL) $(INST)/$(FLINT)
 	+$(PIPE) "$(SAGE_SPKG) $(ECLIB) 2>&1" "tee -a $(SAGE_LOGS)/$(ECLIB).log"
 
-$(INST)/$(M4RI): $(INST)/$(LIBPNG)
+$(INST)/$(M4RI): $(INST)/$(LIBPNG) $(INST)/$(PKGCONF)
 	+$(PIPE) "$(SAGE_SPKG) $(M4RI) 2>&1" "tee -a $(SAGE_LOGS)/$(M4RI).log"
 
 $(INST)/$(M4RIE): $(INST)/$(M4RI) $(INST)/$(GIVARO) $(INST)/$(NTL)
@@ -527,7 +531,7 @@ $(INST)/$(PKGCONF):
 $(INST)/$(PKGCONFIG): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
 	+$(PIPE) "$(SAGE_SPKG) $(PKGCONFIG) 2>&1" "tee -a $(SAGE_LOGS)/$(PKGCONFIG).log"
 
-$(INST)/$(NUMPY): $(INST)/$(PYTHON) $(INST)/$(ATLAS)
+$(INST)/$(NUMPY): $(INST)/$(PYTHON) $(INST)/$(ATLAS) $(INST)/$(PKGCONF)
 	+$(PIPE) "$(SAGE_SPKG) $(NUMPY) 2>&1" "tee -a $(SAGE_LOGS)/$(NUMPY).log"
 
 $(INST)/$(SCIPY): $(INST)/$(ATLAS) $(INST)/$(NUMPY)

build/install

@@ -324,6 +324,7 @@ BZIP2=`newest_version bzip2`
 CDDLIB=`newest_version cddlib`
 CEPHES=`newest_version cephes`
 CLIQUER=`newest_version cliquer`
+COMBINATORIAL_DESIGNS=`newest_version combinatorial_designs`
 CONWAY=`newest_version conway_polynomials`
 CVXOPT=`newest_version cvxopt`
 CYTHON=`newest_version cython`

build/pkgs/atlas/spkg-install

@@ -329,7 +329,7 @@ def configure(arch=None, isa_ext=None):
 
     # use hard floats on ARM
     if conf['ARM?']:
-        cmd += '-D c -DATL_ARM_HARDFP=1'
+        cmd += ' -D c -DATL_ARM_HARDFP=1'
 
     # set machine architecture
     if arch is not None:

build/pkgs/cddlib/patches/lib-src-gmp_Makefile.am.patch

@@ -12,3 +12,10 @@ index b3ab11a..a9673b8 100644
 
  include_HEADERS = \
  cdd.h \
+@@ -24,5 +25,5 @@
+ cddtypes_f.h \
+ setoper.h
+
+-AM_CPPFLAGS = -I$(gmpincludedir) -DGMPRATIONAL
++AM_CPPFLAGS = -DGMPRATIONAL
+ AM_LDFLAGS = -version-info 0:0:0

build/pkgs/cddlib/patches/lib-src-gmp_Makefile.in.patch

@@ -2,7 +2,7 @@ diff --git a/src.bak/lib-src-gmp/Makefile.in b/src/lib-src-gmp/Makefile.in
 index 4ab9342..93ff335 100644
 --- a/src.bak/lib-src-gmp/Makefile.in
 +++ b/src/lib-src-gmp/Makefile.in
-@@ -54,7 +54,7 @@ LTLIBRARIES = $(lib_LTLIBRARIES)
+@@ -54,7 +54,7 @@
  libcddgmp_la_LIBADD =
  am_libcddgmp_la_OBJECTS = cddcore.lo cddlp.lo cddmp.lo cddio.lo \
  	cddlib.lo cddproj.lo cddcore_f.lo cddlp_f.lo cddmp_f.lo \
@@ -11,7 +11,7 @@ index 4ab9342..93ff335 100644
  libcddgmp_la_OBJECTS = $(am_libcddgmp_la_OBJECTS)
  DEFAULT_INCLUDES = -I.@am__isrc@
  depcomp = $(SHELL) $(top_srcdir)/depcomp
-@@ -199,7 +199,8 @@ cddmp_f.c \
+@@ -199,7 +199,8 @@
  cddio_f.c \
  cddlib_f.c \
  cddproj_f.c \
@@ -21,7 +21,16 @@ index 4ab9342..93ff335 100644
 
  include_HEADERS = \
  cdd.h \
-@@ -293,6 +294,7 @@ distclean-compile:
+@@ -210,7 +211,7 @@
+ cddtypes_f.h \
+ setoper.h
+
+-AM_CPPFLAGS = -I$(gmpincludedir) -DGMPRATIONAL
++AM_CPPFLAGS = -DGMPRATIONAL
+ AM_LDFLAGS = -version-info 0:0:0
+ all: all-am
+
+@@ -293,6 +294,7 @@
  @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cddmp_f.Plo@am__quote@
  @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cddproj.Plo@am__quote@
  @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cddproj_f.Plo@am__quote@

build/pkgs/cddlib/patches/src-gmp_Makefile.am.patch

@@ -2,7 +2,7 @@ diff --git a/src.bak/src-gmp/Makefile.am b/src/src-gmp/Makefile.am
 index e4dbb86..e579d71 100644
 --- a/src.bak/src-gmp/Makefile.am
 +++ b/src/src-gmp/Makefile.am
-@@ -11,7 +11,8 @@ testcdd1_gmp \
+@@ -11,7 +11,8 @@
  testcdd2_gmp \
  testlp1_gmp \
  testlp2_gmp \
@@ -12,11 +12,15 @@ index e4dbb86..e579d71 100644
  #cddmathlink
 
  scdd_gmp_SOURCES                   = simplecdd.c
-@@ -27,6 +28,7 @@ testcdd2_gmp_SOURCES               = testcdd2.c
+@@ -27,10 +28,9 @@
  testlp1_gmp_SOURCES                = testlp1.c
  testlp2_gmp_SOURCES                = testlp2.c
  testlp3_gmp_SOURCES                = testlp3.c
 +cdd_both_reps_gmp_SOURCES          = cdd_both_reps.c
  # cddmathlink_SOURCES                = cddmathlink.c cddmlio.h cddmlio.c
 
  LDADD        = ../lib-src-gmp/libcddgmp.la
+-AM_LDFLAGS   = -L$(gmplibdir)
+ INCLUDES     = -I../lib-src-gmp
+-INCLUDES    += -I$(gmpincludedir)
+ AM_CPPFLAGS  = -DGMPRATIONAL

build/pkgs/cddlib/patches/src-gmp_Makefile.in.patch

@@ -2,7 +2,7 @@ diff --git a/src.bak/src-gmp/Makefile.in b/src/src-gmp/Makefile.in
 index f88c83f..3470dc9 100644
 --- a/src.bak/src-gmp/Makefile.in
 +++ b/src/src-gmp/Makefile.in
-@@ -37,7 +37,8 @@ bin_PROGRAMS = scdd_gmp$(EXEEXT) lcdd_gmp$(EXEEXT) \
+@@ -37,7 +37,8 @@
  	projection_gmp$(EXEEXT) adjacency_gmp$(EXEEXT) \
  	allfaces_gmp$(EXEEXT) testshoot_gmp$(EXEEXT) \
  	testcdd1_gmp$(EXEEXT) testcdd2_gmp$(EXEEXT) \
@@ -12,7 +12,7 @@ index f88c83f..3470dc9 100644
  subdir = src-gmp
  DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
  ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-@@ -57,6 +58,10 @@ am_allfaces_gmp_OBJECTS = allfaces.$(OBJEXT)
+@@ -57,6 +58,10 @@
  allfaces_gmp_OBJECTS = $(am_allfaces_gmp_OBJECTS)
  allfaces_gmp_LDADD = $(LDADD)
  allfaces_gmp_DEPENDENCIES = ../lib-src-gmp/libcddgmp.la
@@ -23,7 +23,7 @@ index f88c83f..3470dc9 100644
  am_fourier_gmp_OBJECTS = fourier.$(OBJEXT)
  fourier_gmp_OBJECTS = $(am_fourier_gmp_OBJECTS)
  fourier_gmp_LDADD = $(LDADD)
-@@ -114,19 +119,19 @@ LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+@@ -114,19 +119,19 @@
  	--mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) \
  	$(LDFLAGS) -o $@
  SOURCES = $(adjacency_gmp_SOURCES) $(allfaces_gmp_SOURCES) \
@@ -55,15 +55,20 @@ index f88c83f..3470dc9 100644
  ETAGS = etags
  CTAGS = ctags
  DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-@@ -254,6 +259,7 @@ testcdd2_gmp_SOURCES = testcdd2.c
+@@ -254,10 +259,10 @@
  testlp1_gmp_SOURCES = testlp1.c
  testlp2_gmp_SOURCES = testlp2.c
  testlp3_gmp_SOURCES = testlp3.c
 +cdd_both_reps_gmp_SOURCES = cdd_both_reps.c
  # cddmathlink_SOURCES                = cddmathlink.c cddmlio.h cddmlio.c
  LDADD = ../lib-src-gmp/libcddgmp.la
- AM_LDFLAGS = -L$(gmplibdir)
-@@ -326,6 +332,9 @@ adjacency_gmp$(EXEEXT): $(adjacency_gmp_OBJECTS) $(adjacency_gmp_DEPENDENCIES)
+-AM_LDFLAGS = -L$(gmplibdir)
+-INCLUDES = -I../lib-src-gmp -I$(gmpincludedir)
++INCLUDES = -I../lib-src-gmp
+ AM_CPPFLAGS = -DGMPRATIONAL
+ all: all-am
+
+@@ -326,6 +331,9 @@
  allfaces_gmp$(EXEEXT): $(allfaces_gmp_OBJECTS) $(allfaces_gmp_DEPENDENCIES) 
  	@rm -f allfaces_gmp$(EXEEXT)
  	$(LINK) $(allfaces_gmp_OBJECTS) $(allfaces_gmp_LDADD) $(LIBS)
@@ -73,7 +78,7 @@ index f88c83f..3470dc9 100644
  fourier_gmp$(EXEEXT): $(fourier_gmp_OBJECTS) $(fourier_gmp_DEPENDENCIES) 
  	@rm -f fourier_gmp$(EXEEXT)
  	$(LINK) $(fourier_gmp_OBJECTS) $(fourier_gmp_LDADD) $(LIBS)
-@@ -368,6 +377,7 @@ distclean-compile:
+@@ -368,6 +376,7 @@
 
  @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/adjacency.Po@am__quote@
  @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/allfaces.Po@am__quote@

build/pkgs/combinatorial_designs/SPKG.txt

@@ -0,0 +1,29 @@
+= Combinatorial Designs =
+
+== Description ==
+
+Data for Combinatorial Designs. Current content:
+
+- The table of MOLS (10 000 integers) from the Handbook of Combinatorial
+  Designs, 2ed.
+
+== SPKG Maintainers ==
+
+ * Nathann Cohen
+
+== License ==
+
+Public domain.
+
+== Upstream Contact ==
+
+ None
+
+== Dependencies ==
+
+N/A
+
+== Changelog ==
+
+== designs-20140630 (Nathann Cohen, 2014-06-30) ==
+ * #16541: Table of MOLS

build/pkgs/combinatorial_designs/checksums.ini

@@ -0,0 +1,4 @@
+tarball=combinatorial_designs-VERSION.tar.bz2
+sha1=353ba24217f9b7920890a784fd75dc59175f7196
+md5=f345a6918b1bcf34fcd71c2f26d10de0
+cksum=131472289

build/pkgs/combinatorial_designs/package-version.txt

@@ -0,0 +1 @@
+20140630

build/pkgs/combinatorial_designs/spkg-install

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+mkdir -p "$SAGE_SHARE"/combinatorial_designs
+mv src/* "$SAGE_SHARE"/combinatorial_designs

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=f84edfe5ea286c69e40c8be16fdff2bede9a2050
-md5=e6b56c8709cbdad74a5254d357c3060f
-cksum=3422919565
+sha1=66707652c9fc87fa6d0fdc92a305a3844e4299ea
+md5=ab1dcf6477ff8b1a65e2f5c6abc97a16
+cksum=615729644

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-27
+43

build/pkgs/d3js/SPKG.txt

@@ -0,0 +1,33 @@
+= d3js =
+
+== Description ==
+
+D3.js is a JavaScript library for manipulating documents based on data.
+The file d3.min.js will be placed into the ${SAGE_SHARE}/d3js/ directory.
+
+== License ==
+
+BSD 3-Clause License
+
+== SPKG Maintainers ==
+
+* Thierry Monteil
+
+== Upstream Contact ==
+
+Author: Mike Bostock (http://bost.ocks.org/mike/)
+Home page: http://d3js.org/
+
+== Dependencies ==
+
+None.
+
+== Special Update/Build Instructions ==
+
+Two kind of archives can be downloaded from d3.js website: one with all source
+code and tests that weights 2,9M (both in zip and tar.gz formats) and one with
+the final javascript scripts which weights 121K (zip format only). Since
+testing requires node.js that is not shipped with Sage, we currenlty ship the
+final js only. Hence we have to transform it from zip to tar.gz format.
+Running sage-src should do all the repackaging job.
+

build/pkgs/d3js/checksums.ini

@@ -0,0 +1,4 @@
+tarball=d3js-VERSION.tar.gz
+sha1=2fd4da34ca9e645cf81bf914d289c21c7bb8c166
+md5=d859a120f1eaebb8b563f4598868c564
+cksum=527881311

build/pkgs/d3js/package-version.txt

@@ -0,0 +1 @@
+3.4.8

build/pkgs/d3js/spkg-install

@@ -0,0 +1,15 @@
+#!/bin/sh
+
+if [ -z "$SAGE_SHARE" ]; then
+    echo >&2 "SAGE_SHARE undefined ... exiting"
+    echo >&2 "Maybe run 'sage --sh'?"
+    exit 1
+fi
+
+TARGET="${SAGE_SHARE}/d3js"
+if [ ! -d "${TARGET}" ]; then
+   mkdir "${TARGET}"
+fi
+
+cp 'src/d3.min.js' "${TARGET}/"
+