Merge in sage-5.13.rc0

VERSION.txt

@@ -1 +1 @@
-Sage version 5.13.beta5, released 2013-12-05
+Sage version 5.13.rc0, released 2013-12-11

build/pkgs/gcc/SPKG.txt

@@ -30,6 +30,10 @@ http://gcc.gnu.org/
 
 == Changelog ==
 
+=== gcc-4.7.3.p1 (R. Andrew Ohana, 26 November 2013) ===
+ * Trac #15433: work around for incompatiblity between g++ and
+   an OS X 10.9 header
+
 === gcc-4.7.3.p0 (Jeroen Demeyer, 11 April 2013) ===
  * Trac #14441: upgrade to version 4.7.3.
 

build/pkgs/gcc/package-version.txt

@@ -1 +1 @@
-4.7.3.p0
+4.7.3.p1

build/pkgs/gcc/spkg-install

@@ -50,6 +50,12 @@ EOF
     export LD=ld
 fi
 
+# On OS X 10.9, g++ and the cdefs.h header are currently incompatible
+# Temporary workaround posted at http://trac.macports.org/ticket/41033
+if { uname -sr | grep 'Darwin 13\.' ;} &>/dev/null; then
+    mkdir -p "$SAGE_LOCAL/include/sys"
+    sed 's+defined(__GNUC_STDC_INLINE__)+& \&\& !defined(__cplusplus)+' /usr/include/sys/cdefs.h > "$SAGE_LOCAL/include/sys/cdefs.h"
+fi
 
 if [ "$SAGE_CHECK" = yes ]; then
     # Enable internal checks in GCC.  These checks do not affect the

build/pkgs/scipy/SPKG.txt

@@ -33,6 +33,9 @@ BSD terms. See http://www.scipy.org/License_Compatibility
 
 == Changelog ==
 
+=== scipy-0.12.0.p1 (R. Andrew Ohana, 26 November 2013) ===
+ * #15433: define __ACCELERATE__ on OSX
+
 === scipy-0.12.0.p0 (Jean-Pierre Flori, 20 May 2013) ===
  * #14617: update to version 0.12.0.
  * Removed default_dir.patch which is now upstream.

build/pkgs/scipy/package-version.txt

@@ -1 +1 @@
-0.12.0.p0
+0.12.0.p1

build/pkgs/scipy/spkg-install

@@ -17,6 +17,7 @@ if [ "$UNAME" = "Darwin" ]; then
     unset BLAS
     unset LAPACK
     export LDFLAGS="-bundle -undefined dynamic_lookup $LDFLAGS"
+    export CPPFLAGS="-D__ACCELERATE__ $CPPFLAGS"
 else
     export ATLAS="$SAGE_LOCAL"
     export BLAS="$SAGE_LOCAL"

build/pkgs/sqlite/SPKG.txt

@@ -23,6 +23,11 @@ None
 
 == Changelog ==
 
+=== sqlite-3.7.17.p1 (R. Andrew Ohana, 11 November 2013) ===
+ * #15433: don't build sqlite on OS X 10.9, as it can cause issues
+   for the system libraries that link against Apple's custom
+   version of sqlite
+
 === sqlite-3.7.17 (Jeroen Demeyer, 24 May 2013) ===
  * #14629: upgrade to version 3.7.17
  * Use standard template for SPKG.txt and spkg-install, use $MAKE instead of make

build/pkgs/sqlite/package-version.txt

@@ -1 +1 @@
-3.7.17
+3.7.17.p1

build/pkgs/sqlite/spkg-install

@@ -6,6 +6,19 @@ if [ -z "$SAGE_LOCAL" ]; then
     exit 1
 fi
 
+# OS X already has sqlite3 which includes some non-standard
+# modules to support their frameworks -- our own copy would
+# create issues since we set *_LIBRARY_PATH
+if { uname -sr | grep 'Darwin 1[3-9][.]' ;} &>/dev/null; then
+    ln -s /usr/bin/sqlite3 "$SAGE_LOCAL/bin"
+
+    # only exit if we actually linked it, otherwise we might
+    # break an upgrade
+    if [ -h "$SAGE_LOCAL/bin/sqlite3" ]; then
+        exit 0
+    fi
+fi
+
 cd src
 
 # Apply patches.  See SPKG.txt for information about what each patch

src/bin/sage-banner

@@ -1,5 +1,5 @@
 ┌────────────────────────────────────────────────────────────────────┐
-│ Sage Version 5.13.beta5, Release Date: 2013-12-05                  │
+│ Sage Version 5.13.rc0, Release Date: 2013-12-11                    │
 │ Type "notebook()" for the browser-based notebook interface.        │
 │ Type "help()" for help.                                            │
 └────────────────────────────────────────────────────────────────────┘

src/doc/en/reference/combinat/index.rst

@@ -71,6 +71,7 @@ Combinatorics
    tableaux
    symmetric_functions
    ncsf_qsym
+   ncsym
    root_systems
 
    sage/combinat/kazhdan_lusztig

src/doc/en/reference/combinat/ncsym.rst

@@ -0,0 +1,10 @@
+Symmetric Functions in Non-Commuting Variables
+==============================================
+
+.. toctree::
+   :maxdepth: 2
+
+   ../sage/combinat/ncsym/bases
+   ../sage/combinat/ncsym/dual
+   ../sage/combinat/ncsym/ncsym
+

src/doc/en/website/templates/index.html

@@ -163,7 +163,7 @@ <h1>{{ docstitle|e }}</h1>
         <a class="biglink" href="prep/index.html">
           PREP Tutorials
         </a>
-        <a title="Download PDF" class="pdf" href="../../pdf/en/prep/prep_tutorial.pdf">
+        <a title="Download PDF" class="pdf" href="../../pdf/en/prep/prep_tutorials.pdf">
           <img class="icon" src="_static/pdf.png"></img>
         </a>
         <br>

src/module_list.py

@@ -22,7 +22,7 @@
 elif os.path.exists('/usr/lib/libcblas.dylib') or \
      os.path.exists('/usr/lib/libcblas.so'):
     BLAS='cblas'
-    BLAS2='atlas'
+    BLAS2='cblas'
 elif os.path.exists('/usr/lib/libblas.dll.a'):
     BLAS='gslcblas'
     BLAS2='gslcblas'

src/sage/coding/binary_code.pyx

@@ -73,7 +73,6 @@ cdef int *hamming_weights():
         ham_wts[i] = ham_wts[i & 255] + ham_wts[(i>>8) & 255]
     return ham_wts
 
-include 'sage/misc/bitset_pxd.pxi'
 include 'sage/misc/bitset.pxi'
 def weight_dist(M):
     """

src/sage/combinat/all.py

@@ -123,6 +123,7 @@
 from root_system.all import *
 from sf.all import *
 from ncsf_qsym.all import *
+from ncsym.all import *
 from matrices.all import *
 # Posets
 from posets.all import *

src/sage/combinat/ncsf_qsym/ncsf.py

@@ -493,6 +493,71 @@ def to_symmetric_function(self):
                 codomain = on_basis(self.one_basis()).parent()
                 return self.module_morphism(on_basis=on_basis, codomain=codomain)
 
+            def to_ncsym_on_basis(self, I):
+                r"""
+                The image of the basis element indexed by ``I`` under the
+                map `\kappa` to the symmetric functions in non-commuting
+                variables such that for the natural maps `\chi : NCSym \to Sym`
+                and `\rho : NSym \to Sym`, we have `\chi \circ \kappa = \rho`.
+
+                This default implementation does a change of basis and
+                computes the image in the complete basis.
+
+                INPUT:
+
+                - ``I`` -- a composition
+
+                EXAMPLES::
+
+                    sage: S = NonCommutativeSymmetricFunctions(QQ).S()
+                    sage: S.to_ncsym(S[2,1])
+                    1/2*m{{1}, {2}, {3}} + 1/2*m{{1}, {2, 3}} + m{{1, 2}, {3}}
+                     + m{{1, 2, 3}} + 1/2*m{{1, 3}, {2}}
+                    sage: R = NonCommutativeSymmetricFunctions(QQ).R()
+                    sage: R.to_ncsym_on_basis(Composition([2,1]))
+                    1/3*m{{1}, {2}, {3}} + 1/6*m{{1}, {2, 3}} + 2/3*m{{1, 2}, {3}} + 1/6*m{{1, 3}, {2}}
+                """
+                S = self.realization_of().complete()
+                return S.to_ncsym(S(self[I]))
+
+            @lazy_attribute
+            def to_ncsym(self):
+                r"""
+                Morphism `\kappa` of ``self`` to the algebra of symmetric
+                functions in non-commuting variables that for the natural
+                maps `\chi : NCSym \to Sym` and `\rho : NSym \to Sym`, we
+                have `\chi \circ \kappa = \rho`.
+
+                This is constructed by extending the method
+                :meth:`to_ncsym_on_basis` linearly.
+
+                EXAMPLES::
+
+                    sage: N = NonCommutativeSymmetricFunctions(QQ)
+                    sage: R = N.ribbon()
+                    sage: x = R.an_element(); x
+                    2*R[] + 2*R[1] + 3*R[1, 1]
+                    sage: R.to_ncsym(x)
+                    2*m{} + 2*m{{1}} + 3/2*m{{1}, {2}}
+                    sage: S = N.complete()
+                    sage: S.to_ncsym(S[1,2])
+                    1/2*m{{1}, {2}, {3}} + m{{1}, {2, 3}} + 1/2*m{{1, 2}, {3}}
+                     + m{{1, 2, 3}} + 1/2*m{{1, 3}, {2}}
+                    sage: Phi = N.Phi()
+                    sage: Phi.to_ncsym(Phi[1,3])
+                    -1/4*m{{1}, {2}, {3, 4}} - 1/4*m{{1}, {2, 3}, {4}} + m{{1}, {2, 3, 4}}
+                     + 1/2*m{{1}, {2, 4}, {3}} - 1/4*m{{1, 2}, {3, 4}} - 1/4*m{{1, 2, 3}, {4}}
+                     + m{{1, 2, 3, 4}} + 1/2*m{{1, 2, 4}, {3}} + 1/2*m{{1, 3}, {2, 4}}
+                     - 1/4*m{{1, 3, 4}, {2}} - 1/4*m{{1, 4}, {2, 3}}
+                    sage: R.to_ncsym
+                    Generic morphism:
+                      From: Non-Commutative Symmetric Functions over the Rational Field in the Ribbon basis
+                      To:   Symmetric functions in non-commuting variables over the Rational Field in the monomial basis
+                """
+                from sage.combinat.ncsym.ncsym import SymmetricFunctionsNonCommutingVariables
+                codomain = SymmetricFunctionsNonCommutingVariables(self.base_ring()).monomial()
+                return self.module_morphism(self.to_ncsym_on_basis, codomain=codomain)
+
         class ElementMethods:
 
             def verschiebung(self, n):
@@ -729,6 +794,26 @@ def to_symmetric_function(self):
 
             chi = to_symmetric_function
 
+            def to_ncsym(self):
+                r"""
+                Return the image of ``self`` in the symmetric functions in
+                non-commuting variables under the map that fixes the usual
+                symmetric functions.
+
+                EXAMPLES::
+
+                    sage: N = NonCommutativeSymmetricFunctions(QQ)
+                    sage: R = N.ribbon()
+                    sage: x = R.an_element(); x
+                    2*R[] + 2*R[1] + 3*R[1, 1]
+                    sage: x.to_ncsym()
+                    2*m{} + 2*m{{1}} + 3/2*m{{1}, {2}}
+                    sage: y = N.Phi()[1,2]
+                    sage: y.to_ncsym()
+                    m{{1}, {2, 3}} + m{{1, 2, 3}}
+                """
+                return self.parent().to_ncsym(self)
+
     class MultiplicativeBases(Category_realization_of_parent):
         """
         Category of multiplicative bases of non-commutative symmetric functions.
@@ -1353,7 +1438,6 @@ def __init__(self, NCSF):
 
                 sage: S = NonCommutativeSymmetricFunctions(QQ).complete()
                 sage: TestSuite(S).run()
-
             """
             CombinatorialFreeModule.__init__(self, NCSF.base_ring(), Compositions(),
                                              prefix='S', bracket=False,
@@ -1497,6 +1581,66 @@ def _to_symmetric_group_algebra_on_basis(self, I):
                     x += sga(p)
             return x
 
+        def to_ncsym_on_basis(self, I):
+            r"""
+            Return the image of the complete non-commutative symmetric function
+            in the symmetric functions in non-commuting variables under the
+            embedding `\mathcal{I}` which fixes the symmetric functions.
+
+            This map is defined by
+
+            .. MATH::
+
+                S_n \mapsto \sum_{A \vdash [n]}
+                \frac{\lambda(A)! \lambda(A)^!}{n!} \mathbf{m}_A
+
+            and extended as an algebra homomorphism.
+
+            EXAMPLES::
+
+                sage: S = NonCommutativeSymmetricFunctions(QQ).S()
+                sage: S.to_ncsym_on_basis(Composition([2]))
+                1/2*m{{1}, {2}} + m{{1, 2}}
+                sage: S.to_ncsym_on_basis(Composition([1,2,1]))
+                1/2*m{{1}, {2}, {3}, {4}} + 1/2*m{{1}, {2}, {3, 4}} + m{{1}, {2, 3}, {4}}
+                 + m{{1}, {2, 3, 4}} + 1/2*m{{1}, {2, 4}, {3}} + 1/2*m{{1, 2}, {3}, {4}}
+                 + 1/2*m{{1, 2}, {3, 4}} + m{{1, 2, 3}, {4}} + m{{1, 2, 3, 4}}
+                 + 1/2*m{{1, 2, 4}, {3}} + 1/2*m{{1, 3}, {2}, {4}} + 1/2*m{{1, 3}, {2, 4}}
+                 + 1/2*m{{1, 3, 4}, {2}} + 1/2*m{{1, 4}, {2}, {3}} + m{{1, 4}, {2, 3}}
+                sage: S.to_ncsym_on_basis(Composition([]))
+                m{}
+
+            TESTS:
+
+            Check that the image under `\mathcal{I}` fixes the
+            symmetric functions::
+
+                sage: S = NonCommutativeSymmetricFunctions(QQ).S()
+                sage: m = SymmetricFunctionsNonCommutingVariables(QQ).monomial()
+                sage: mon = SymmetricFunctions(QQ).monomial()
+                sage: all(S[c].to_ncsym().to_symmetric_function() == S[c].to_symmetric_function()
+                ....:     for i in range(5) for c in Compositions(i))
+                True
+
+            We also check that the `NCSym` monomials agree on the homogeneous
+            and complete basis::
+
+                sage: h = SymmetricFunctions(QQ).h()
+                sage: all(m.from_symmetric_function(h[i]) == S[i].to_ncsym() for i in range(6))
+                True
+            """
+            from sage.combinat.ncsym.ncsym import SymmetricFunctionsNonCommutingVariables
+            m = SymmetricFunctionsNonCommutingVariables(self.base_ring()).m()
+            if I == []:
+                return m.one()
+
+            from sage.combinat.set_partition import SetPartitions
+            R = self.base_ring()
+            P = SetPartitions()
+            c_num = lambda A: prod([factorial(i) for i in A.shape()], R.one())
+            return prod(m.sum_of_terms([(P(A), R(c_num(A) / factorial(n))) for A in SetPartitions(n)], distinct=True)
+                        for n in I)
+
     S = complete = Complete
 
     class Elementary(CombinatorialFreeModule, BindableClass):

src/sage/combinat/ncsym/all.py

@@ -0,0 +1,3 @@
+from ncsym import SymmetricFunctionsNonCommutingVariables
+from dual import SymmetricFunctionsNonCommutingVariablesDual
+