Merge branch 'ticket/9322-simon_two_descent_defaults' into ticket/10735-two_selmer_discrepancy

Conflicts:
	src/sage/schemes/elliptic_curves/ell_number_field.py
	src/sage/schemes/elliptic_curves/ell_rational_field.py

Author: pjbruin

COPYING.txt

@@ -38,6 +38,7 @@ cliquer                     GPLv2+
 conway_polynomials          None (database)
 cvxopt                      GPLv2+
 cython                      Apache, version 2.0
+dateutil                    Simplified BSD
 docutils                    Modified BSD
 ecl                         LGPLv2+
 eclib                       GPLv2+
@@ -72,7 +73,7 @@ libm4rie                    GPLv2+
 libpng                      Custom, very similar to zlib
 linbox                      LGPLv2.1+
 lrcalc                      GPLv2+
-matplotlib                  Python License
+matplotlib                  Matplotlib License (BSD compatible, see below)
 maxima                      See below
 mercurial                   GPLv2+
 mpc                         LGPLv3+
@@ -88,12 +89,15 @@ 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+
 pycrypto                    Public domain & Python License
 pygments                    Modified BSD
 pynac                       GPLv2+
+pyparsing                   MIT License
 python                      Python License (see below)
 R                           GPLv2+
 ratpoints                   GPLv2+
@@ -111,6 +115,7 @@ scipy                       Modified BSD
 scons                       MIT License
 setuptools                  Python License
 singular                    GPLv2 or GPLv3 (see below)
+six                         MIT License
 sphinx                      Modified BSD
 sqlalchemy                  MIT License
 sqlite                      Public Domain (see below)
@@ -119,6 +124,7 @@ sympow                      Modified BSD
 sympy                       Modified BSD
 tachyon                     Modified BSD
 termcap                     GPLv2+
+tornado                     Apache License
 zlib                        Custom (Modified BSD)
 zn_poly                     GPLv2 or GPLv3 (no later versions, see below)
 
@@ -1008,6 +1014,17 @@ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 ================================================================================
 
+matplotlib:
+(from http://matplotlib.sourceforge.net/users/license.html)
+
+Matplotlib only uses BSD compatible code, and its license is based on
+the PSF license. See the Open Source Initiative licenses page for
+details on individual licenses. Non-BSD compatible licenses (eg LGPL)
+are acceptable in matplotlib toolkits. For a discussion of the
+motivations behind the licencing choice, see Licenses.
+
+================================================================================
+
 maxima:
 (from http://maxima.sourceforge.net/authorization-letter.html)
 

VERSION.txt

@@ -1 +1 @@
-Sage version 6.2.beta1, released 2014-02-07
+Sage version 6.2.beta5, released 2014-03-23

build/deps

@@ -34,6 +34,7 @@ all-sage: \
      $(INST)/$(CONWAY) \
      $(INST)/$(CVXOPT) \
      $(INST)/$(CYTHON) \
+     $(INST)/$(DATEUTIL) \
      $(INST)/$(DOCUTILS) \
      $(INST)/$(ECL) \
      $(INST)/$(ECLIB) \
@@ -81,12 +82,15 @@ all-sage: \
      $(INST)/$(PARI) \
      $(INST)/$(PEXPECT) \
      $(INST)/$(PILLOW) \
+     $(INST)/$(PKGCONF) \
+     $(INST)/$(PKGCONFIG) \
      $(INST)/$(POLYBORI) \
      $(INST)/$(POLYTOPES_DB) \
      $(INST)/$(PPL) \
      $(INST)/$(PYCRYPTO) \
      $(INST)/$(PYGMENTS) \
      $(INST)/$(PYNAC) \
+     $(INST)/$(PYPARSING) \
      $(INST)/$(PYTHON) \
      $(INST)/$(RATPOINTS) \
      $(INST)/$(R) \
@@ -99,13 +103,15 @@ all-sage: \
      $(INST)/$(SCONS) \
      $(INST)/$(SETUPTOOLS) \
      $(INST)/$(SINGULAR) \
+     $(INST)/$(SIX) \
      $(INST)/$(SPHINX) \
      $(INST)/$(SQLALCHEMY) \
      $(INST)/$(SQLITE) \
      $(INST)/$(SYMMETRICA) \
      $(INST)/$(SYMPOW) \
      $(INST)/$(SYMPY) \
      $(INST)/$(TACHYON) \
+     $(INST)/$(TORNADO) \
      $(INST)/$(NCURSES) \
      $(INST)/$(ZLIB) \
      $(INST)/$(ZNPOLY) \
@@ -224,9 +230,16 @@ $(INST)/$(NTL): $(INST)/$(MPIR) $(INST)/$(GF2X)
 $(INST)/$(FPLLL): $(INST)/$(MPIR) $(INST)/$(MPFR)
 	+$(PIPE) "$(SAGE_SPKG) $(FPLLL) 2>&1" "tee -a $(SAGE_LOGS)/$(FPLLL).log"
 
-$(INST)/$(PARI): $(INST)/$(READLINE) $(INST)/$(MPIR)
+$(INST)/$(PARI): $(INST)/$(READLINE) $(INST)/$(MPIR) \
+    $(INST)/$(PARI_GALDATA) $(INST)/$(PARI_SEADATA_SMALL)
 	+$(PIPE) "$(SAGE_SPKG) $(PARI) 2>&1" "tee -a $(SAGE_LOGS)/$(PARI).log"
 
+$(INST)/$(PARI_GALDATA):
+	+$(PIPE) "$(SAGE_SPKG) $(PARI_GALDATA) 2>&1" "tee -a $(SAGE_LOGS)/$(PARI_GALDATA).log"
+
+$(INST)/$(PARI_SEADATA_SMALL):
+	+$(PIPE) "$(SAGE_SPKG) $(PARI_SEADATA_SMALL) 2>&1" "tee -a $(SAGE_LOGS)/$(PARI_SEADATA_SMALL).log"
+
 $(INST)/$(POLYBORI): $(INST)/$(PYTHON) $(INST)/$(IPYTHON) \
          $(INST)/$(SCONS) $(INST)/$(BOOST_CROPPED) \
          $(INST)/$(M4RI) $(INST)/$(GD)
@@ -348,9 +361,23 @@ $(INST)/$(FREETYPE): $(INST)/$(LIBPNG)
 $(INST)/$(LIBPNG): $(INST)/$(ZLIB)
 	+$(PIPE) "$(SAGE_SPKG) $(LIBPNG) 2>&1" "tee -a $(SAGE_LOGS)/$(LIBPNG).log"
 
+$(INST)/$(SIX): $(INST)/$(PYTHON)
+	+$(PIPE) "$(SAGE_SPKG) $(SIX) 2>&1" "tee -a $(SAGE_LOGS)/$(SIX).log"
+
+$(INST)/$(DATEUTIL): $(INST)/$(PYTHON) $(INST)/$(SIX)
+	+$(PIPE) "$(SAGE_SPKG) $(DATEUTIL) 2>&1" "tee -a $(SAGE_LOGS)/$(DATEUTIL).log"
+
+$(INST)/$(PYPARSING): $(INST)/$(PYTHON)
+	+$(PIPE) "$(SAGE_SPKG) $(PYPARSING) 2>&1" "tee -a $(SAGE_LOGS)/$(PYPARSING).log"
+
+$(INST)/$(TORNADO): $(INST)/$(PYTHON)
+	+$(PIPE) "$(SAGE_SPKG) $(TORNADO) 2>&1" "tee -a $(SAGE_LOGS)/$(TORNADO).log"
+
 $(INST)/$(MATPLOTLIB): $(INST)/$(PYTHON) $(INST)/$(NUMPY) \
 		       $(INST)/$(FREETYPE) $(INST)/$(LIBPNG) \
-		       $(INST)/$(GDMODULE)
+		       $(INST)/$(GDMODULE) $(INST)/$(DATEUTIL) \
+		       $(INST)/$(PKGCONFIG) $(INST)/$(PYPARSING) \
+                       $(INST)/$(SETUPTOOLS)
 	+$(PIPE) "$(SAGE_SPKG) $(MATPLOTLIB) 2>&1" "tee -a $(SAGE_LOGS)/$(MATPLOTLIB).log"
 
 $(INST)/$(CDDLIB): $(INST)/$(MPIR)
@@ -494,6 +521,12 @@ $(INST)/$(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"
 
@@ -509,13 +542,3 @@ $(INST)/$(CVXOPT): $(INST)/$(NUMPY) \
 $(INST)/$(CEPHES):
 	+$(PIPE) "$(SAGE_SPKG) $(CEPHES) 2>&1" "tee -a $(SAGE_LOGS)/$(CEPHES).log"
 
-###############################################################################
-
-# setuptools forgets to update easy-install.pth during parallel
-# builds, so we build the relevant packages serially.
-
-$(INST)/$(SQLALCHEMY): $(INST)/$(PILLOW)
-$(INST)/$(PYGMENTS): $(INST)/$(SQLALCHEMY)
-$(INST)/$(JINJA2): $(INST)/$(PYGMENTS)
-$(INST)/$(SPHINX): $(INST)/$(JINJA2)
-$(INST)/$(SAGENB): $(INST)/$(SPHINX)

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
 ###############################################################################
@@ -362,6 +328,7 @@ CLIQUER=`newest_version cliquer`
 CONWAY=`newest_version conway_polynomials`
 CVXOPT=`newest_version cvxopt`
 CYTHON=`newest_version cython`
+DATEUTIL=`newest_version dateutil`
 DOCUTILS=`newest_version docutils`
 ECL=`newest_version ecl`
 ECLIB=`newest_version eclib`
@@ -408,15 +375,20 @@ NTL=`newest_version ntl`
 NUMPY=`newest_version numpy`
 PALP=`newest_version palp`
 PARI=`newest_version pari`
+PARI_GALDATA=`newest_version pari_galdata`
+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`
 PYCRYPTO=`newest_version pycrypto`
 PYGMENTS=`newest_version pygments`
 PYNAC=`newest_version pynac`
+PYPARSING=`newest_version pyparsing`
 PYTHON=`newest_version python`
 R=`newest_version r`
 RPY=`newest_version rpy2`
@@ -429,13 +401,15 @@ SCIPY=`newest_version scipy`
 SCONS=`newest_version scons`
 SETUPTOOLS=`newest_version setuptools`
 SINGULAR=`newest_version singular`
+SIX=`newest_version six`
 SPHINX=`newest_version sphinx`
 SQLALCHEMY=`newest_version sqlalchemy`
 SQLITE=`newest_version sqlite`
 SYMMETRICA=`newest_version symmetrica`
 SYMPOW=`newest_version sympow`
 SYMPY=`newest_version sympy`
 TACHYON=`newest_version tachyon`
+TORNADO=`newest_version tornado`
 NCURSES=`newest_version ncurses`
 ZLIB=`newest_version zlib`
 ZNPOLY=`newest_version zn_poly`

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')