Merge branch 'develop' into public/combinat/rigged_configurations/met…

…hods-15560

* develop: (58 commits)
  Updated Sage version to 6.2.beta2
  fix doctest error
  Limit the GAP command line history
  integrate better with Integer.is_prime
  Combine ECM-GMP with Baillie-PSW for prime factorization
  Cleaned up documentation and formatting.
  add doctesr
  Trac 15262: fix combine function
  trac #15810: The graph data structures may have a ._directed but no .directed
  ignore randomness in assertion
  trac #15810: Immutable directed graphs should know that they are directed
  Trac 15166: regression test
  Fix representation of RIF elements with large exponent
  docbuilding: suppress warnings during latex build
  workaround for the utf8 code points in the Sage banner
  Trac 15798: fix mwrank doctest for Solaris
  do not abbreviate 3.99999... to 3.99 with # abs tol 1e-2
  setuptools: export PYTHON_EGG_CACHE and silence a warning about it
  Remove .hgignore files
  PARI: fix pow, mod and shift operators
  ...

VERSION.txt

@@ -1 +1 @@
-Sage version 6.2.beta1, released 2014-02-07
+Sage version 6.2.beta2, released 2014-02-15

build/deps

@@ -224,9 +224,16 @@ $(INST)/$(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)

build/install

@@ -408,6 +408,8 @@ 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`

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=e0f0951560918d79141995852f276ac3e99a42f4
-md5=33b6cac80bafecc0ad880fd68cf258e6
-cksum=3483617699
+sha1=dc1ef3079014c19d7af48bf628a275b3dbcf2e11
+md5=1ab9d75a4babc66433730e4d95c24843
+cksum=4250141818

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-11
+12

build/pkgs/pari/SPKG.txt

@@ -14,8 +14,6 @@ Originally developed by Henri Cohen and his co-workers (Université
 Bordeaux I, France), PARI is now under the GPL and maintained by Karim
 Belabas with the help of many volunteer contributors.
 
-Website: http://pari.math.u-bordeaux.fr/
-
 == License ==
 
 GPL version 2+
@@ -27,42 +25,13 @@ GPL version 2+
  * Jeroen Demeyer
 
 == Upstream Contact ==
- * Karim Belabas, http://www.math.u-bordeaux.fr/~belabas/
- * [email protected]
+ * http://pari.math.u-bordeaux.fr/
 
 == Dependencies ==
  * MPIR (in place of GMP)
  * Readline
- * Termcap
  * GNU patch (shipped with Sage)
 
 == Special Update/Build Instructions ==
 
 See patches/README.txt for a list of patches.
-
-Most of the building of a new version of the PARI spkg is automated
-in the script spkg-src.  Normally, the following should work.  In case
-of doubt, have a look at the file spkg-src.
-
-  0) Edit the line "git checkout pari-2.5.5".
-
-  1) ./spkg-src
-     This will download the git sources to the directory parigit/
-     and will also download galdata.tgz and ellsea-small.tgz.
-     Then, a src/ directory will be created.
-     WARNING: This script will remove any existing src/ directory.
-     NOTES: The script ./spkg-src will actually compile PARI/GP, but
-     the compiled files are not used for the spkg.  We only need a few
-     files, in particular those created by bison.
-     Running spkg-src should be done on a reasonably standard machine
-     on which PARI/GP compiles out of the box.
-
-  2) Check that everything is okay somehow.  In particular, look at
-     patches/README.txt
-
-  3) rm -rf parigit
-     The directory parigit contains a git repository for the PARI sources.
-     When making this package just for testing, you can keep the parigit
-     directory.  However, it should not be there in a final version.
-
-  4) cd ..; sage --spkg pari-version-name

build/pkgs/pari/checksums.ini

@@ -1,4 +1,4 @@
 tarball=pari-VERSION.tar.bz2
-sha1=b58fe67c0c05416ae7de48bb990350056cc66a7d
-md5=3cd63f5ca9f7b37fbcb68e44c4c1f1b0
-cksum=2913087451
+sha1=3f0838940fcf1cb7748979fe16e4b5cab0d19080
+md5=4c54710f7e2d4de7b8781edb9d604c60
+cksum=2949888924

build/pkgs/pari/package-version.txt

@@ -1 +1 @@
-2.5.5.p2
+2.5.5b.p1

build/pkgs/pari/patches/README.txt

@@ -38,14 +38,6 @@ Patches to configuration files:
   - http://pari.math.u-bordeaux.fr/archives/pari-dev-1301/msg00000.html
 
 C files:
-* src/kernel/gmp/mp.c (Leif Leonhardy):
-  Do not override GMP's memory functions.
-  In addition, let PARI use "GMP internals" (access members of GMP
-  structures directly) *conditionally*. (We *don't* disable that by
-  default, since at least currently this is compatible with both GMP
-  *and* MPIR. To disable the use, add "-DPARI_DONT_USE_GMP_INTERNALS"
-  to CFLAGS. This is a trivial patch to mp.c only; see also the comment
-  there.):
 * GCC_PR49330.patch (Jeroen Demeyer): in pari_init_functions(), reorder
   code to work around a GCC bug concerning pointer arithmetic:
   http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49330

build/pkgs/pari_galdata/SPKG.txt

@@ -0,0 +1,22 @@
+= pari_galdata =
+
+== Description ==
+
+PARI package "galdata": Needed by polgalois to compute Galois group in
+degrees 8 through 11. 
+
+== License ==
+
+GPL version 2+
+
+== SPKG Maintainers ==
+
+* Jeroen Demeyer
+
+== Upstream Contact ==
+
+http://pari.math.u-bordeaux.fr/
+
+== Dependencies ==
+
+None (package contains data files only)

build/pkgs/pari_galdata/checksums.ini

@@ -0,0 +1,4 @@
+tarball=pari_galdata-VERSION.tar.bz2
+sha1=4ae710687cb711c49645314c28d53ab3b3a38706
+md5=b661c455bb1b2028b3b957d3bc8595de
+cksum=3937576682

build/pkgs/pari_galdata/package-version.txt

@@ -0,0 +1 @@
+20080411

build/pkgs/pari_galdata/spkg-install

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+mkdir -p "$SAGE_SHARE/pari"
+cd data && cp -R * "$SAGE_SHARE/pari"

build/pkgs/pari_seadata_small/SPKG.txt

@@ -0,0 +1,24 @@
+= pari_seadata_small =
+
+== Description ==
+
+PARI package "seadata_small": Needed by ellap for large primes. This
+"small" one is a much smaller version that should be suitable for
+primes up to 350 bits. These polynomials were extracted from the ECHIDNA
+databases and computed by David R. Kohel. 
+
+== License ==
+
+GPL version 2+
+
+== SPKG Maintainers ==
+
+* Jeroen Demeyer
+
+== Upstream Contact ==
+
+http://pari.math.u-bordeaux.fr/
+
+== Dependencies ==
+
+None (package contains data files only)

build/pkgs/pari_seadata_small/checksums.ini

@@ -0,0 +1,4 @@
+tarball=pari_seadata_small-VERSION.tar.bz2
+sha1=9df70728bfae81fad4ff66a3c7f57d99bbe70732
+md5=5a9a6200e4536d2c6b4020c4313721f5
+cksum=3561726107

build/pkgs/pari_seadata_small/package-version.txt

@@ -0,0 +1 @@
+20090618

build/pkgs/pari_seadata_small/spkg-install

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+mkdir -p "$SAGE_SHARE/pari"
+cd data && cp -R * "$SAGE_SHARE/pari"

build/pkgs/python/SPKG.txt

@@ -75,9 +75,13 @@ http://www.python.org/community/
  * inc_lib_dirs-issue_17990.patch: Only modify include and library search
    paths when cross-compiling.
  * node-issue_3871.patch: fix _PyNode_Sizeof declaration.
+ * tinfo.patch: make sure tinfo is correctly linked in when needed on Cygwin.
 
 == Changelog ==
 
+=== python-2.7.5.p2 (Jean-Pierre Flori, 5 January 2014) ===
+ * Trac #15317: Make sure tinfo is correctly linked in when needed on Cygwin.
+
 === python-2.7.5.p1 (Jean-Pierre Flori, 3 June 2013) ===
  * Trac #14600: give patches more talkative names.
  * Fix hashlibfallbacks patch.

build/pkgs/python/package-version.txt

@@ -1 +1 @@
-2.7.5.p1
+2.7.5.p2