Merge branch 'develop' into hermite_trac22841

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.0.beta9, Release Date: 2017-05-31
+SageMath version 8.0.beta10, Release Date: 2017-06-11

build/bin/sage-spkg

@@ -786,13 +786,16 @@ fi
 # Mark that the new package has been installed (and tested, if
 # applicable).
 PKG_NAME_INSTALLED="$SAGE_SPKG_INST/$PKG_NAME"
-echo "PACKAGE NAME: $PKG_NAME" > "$PKG_NAME_INSTALLED"
-echo "INSTALL DATE: `date`" >> "$PKG_NAME_INSTALLED"
-echo "UNAME: `uname -a`" >> "$PKG_NAME_INSTALLED"
-if [ -n "$TEST_SUITE_RESULT" ]; then
-    echo "TEST SUITE: $TEST_SUITE_RESULT" >> "$PKG_NAME_INSTALLED"
-fi
-cat "$SAGE_ROOT/VERSION.txt" >> "$PKG_NAME_INSTALLED"
+cat > "$PKG_NAME_INSTALLED" << __EOF__
+{
+    "package_name": "$PKG_BASE",
+    "package_version": "$PKG_VER",
+    "install_date": "$(date)",
+    "system_uname": "$(uname -a)",
+    "sage_version": "$(cat "${SAGE_ROOT}/VERSION.txt")",
+    "test_result": "$TEST_SUITE_RESULT"
+}
+__EOF__
 
 
 ##################################################################

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=1468ff678f41a3552bce2ba952af0795127d64d8
-md5=931c98793b007e28874089c17c40e53d
-cksum=1227610551
+sha1=4fa024947bd555ae00d155c022d52f5fddad045f
+md5=35c48d9ed0328cc92e2100a7721a996e
+cksum=2690821246

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-223
+224

build/pkgs/gf2x/package-version.txt

@@ -1 +1 @@
-1.1.p1
+1.1.p2

build/pkgs/gf2x/patches/0007-fix_tuning.patch

@@ -0,0 +1,13 @@
+diff --git a/src/mul9clk2.c b/src/mul9clk2.c
+index bf7ad4a..5c6b980 100644
+--- a/src/mul9clk2.c
++++ b/src/mul9clk2.c
+@@ -149,7 +149,7 @@ void gf2x_mul9 (unsigned long *c, const unsigned long *a, const unsigned long *b
+   e = p2e[1]; h=l; l=p2o[1];
+   _mm_storeu_si128((__v2di*)(c+14), e ^ _mm_slli_si128(l, 8) ^ _mm_srli_si128(h, 8));
+
+-  e = p2e[2];
++  e = p2e[2]; h=l;
+   _mm_storeu_si128((__v2di*)(c+16), e ^ _mm_srli_si128(h, 8));
+
+   /*

build/pkgs/mpir/spkg-install

@@ -166,12 +166,18 @@ fi
 # Workaround old GNU as version by disabling assembly use.
 if [ "$UNAME" = Linux ]; then
     as_version=`$AS --version | head -1 | awk 'NF>1{print $NF}'`
-    case "$as_version" in
-        1.*|2.1*|2.[0-2]*)
-        echo "Disable use of assembly because of GNU as < 2.23."
+    as_version_major=${as_version%%.*}
+    as_version_rest=${as_version#*.}
+    as_version_minor=${as_version_rest%%.*}
+    if [ $as_version_major -lt 2 ] || \
+       [ $as_version_major -eq 2 -a $as_version_minor -lt 24 ]; then
+        echo "Disable use of assembly because of GNU as <= 2.23."
         export MPN_PATH=generic
-        ;;
-    esac
+        if [ "$SAGE_FAT_BINARY" = "yes" ]; then
+            echo "Cannot build with SAGE_FAT_BINARY=yes."
+            exit 1
+        fi
+    fi
 fi
 
 # Work around a bug in GCC 4.7.0 which breaks the build on Itanium CPUs.

build/pkgs/sagenb/checksums.ini

@@ -1,4 +1,4 @@
 tarball=sagenb-VERSION.tar.bz2
-sha1=9fc8addff1c543521225acaf60a2336204e67d62
-md5=04ddd5a1ccf0764cd72dc0abcf322c1e
-cksum=1784359449
+sha1=cd46f50bf3f71a452735e7ad5573928ebc190f23
+md5=fea1225a9d630ac4a4f35fc6d936de0a
+cksum=1620865525

build/pkgs/sagenb/package-version.txt

@@ -1 +1 @@
-0.13
+1.0.1

build/pkgs/singular/spkg-install

@@ -61,17 +61,32 @@ remove_old_version()
     rm -f "$SAGE_LOCAL/include/omlimits.h" # 3.x only
     rm -rf "$SAGE_LOCAL/include/resources" #4.x only
     rm -rf "$SAGE_LOCAL/include/gfanlib" #4.x only
-    rm -f "$SAGE_LOCAL"/lib/libsingular* # 3.x with lower case
-    rm -f "$SAGE_LOCAL"/lib/libsingcf*.a # 3.x only additional archives
-    rm -f "$SAGE_LOCAL"/lib/libsingfac*.a # 3.x only additional archives
-    rm -f "$SAGE_LOCAL"/lib/libSingular* # 4.x with upper case
+
+    # Clean up all Singular-related libraries
+    libs=(
+        singular  # 3.x with lower case
+        singcf    # 3.x only additional archives
+        singfac   # 3.x only additional archives
+        Singular  # 4.x with upper case
+        polys
+        factory
+        omalloc
+        resources           # 3.x
+        singular_resources  # 4.x and up
+        gfan
+    )
+    if [ "$UNAME" = "CYGWIN" ]; then
+        for name in ${libs[*]}; do
+            rm -f "$SAGE_LOCAL"/bin/cyg${name}*.dll
+            rm -f "$SAGE_LOCAL"/lib/lib${name}*.a
+        done
+    else
+        for name in ${libs[*]}; do
+            rm -f "$SAGE_LOCAL"/lib/lib${name}*
+        done
+    fi
+
     rm -f "$SAGE_LOCAL"/lib/p_Procs_Field* # 3.x only
-    # a bunch of additional libraries for 4.x
-    rm -f "$SAGE_LOCAL"/lib/libpolys*
-    rm -f "$SAGE_LOCAL"/lib/libfactory*
-    rm -f "$SAGE_LOCAL"/lib/libomalloc*
-    rm -f "$SAGE_LOCAL"/lib/libresources*
-    rm -r "$SAGE_LOCAL"/lib/libgfan*
     rm -rf "$SAGE_LOCAL/share/singular"
     rm -f "$SAGE_LOCAL"/share/info/singular*
 }

src/bin/sage-banner

@@ -1,5 +1,5 @@
 ┌────────────────────────────────────────────────────────────────────┐
-│ SageMath version 8.0.beta9, Release Date: 2017-05-31               │
+│ SageMath version 8.0.beta10, Release Date: 2017-06-11              │
 │ Type "notebook()" for the browser-based notebook interface.        │
 │ Type "help()" for help.                                            │
 └────────────────────────────────────────────────────────────────────┘

src/bin/sage-version.sh

@@ -1,4 +1,4 @@
 # Sage version information for shell scripts
 # This file is auto-generated by the sage-update-version script, do not edit!
-SAGE_VERSION='8.0.beta9'
-SAGE_RELEASE_DATE='2017-05-31'
+SAGE_VERSION='8.0.beta10'
+SAGE_RELEASE_DATE='2017-06-11'

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

@@ -80,6 +80,7 @@ Non-associative algebras
 
    lie_algebras
    sage/algebras/jordan_algebra
+   sage/combinat/free_dendriform_algebra
    sage/combinat/free_prelie_algebra
    sage/algebras/shuffle_algebra
    sage/algebras/free_zinbiel_algebra

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

@@ -118,6 +118,7 @@ Comprehensive Module list
     sage/combinat/finite_state_machine
     sage/combinat/finite_state_machine_generators
     sage/combinat/free_module
+    sage/combinat/free_dendriform_algebra
     sage/combinat/free_prelie_algebra
     sage/combinat/fully_packed_loop
     sage/combinat/gelfand_tsetlin_patterns

src/doc/en/reference/plot3d/index.rst

@@ -4,7 +4,7 @@
 .. toctree::
    :maxdepth: 2
 
-   sage/plot/plot3d/examples
+   sage/plot/plot3d/introduction
 
 Function and Data Plots
 -----------------------

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

@@ -74,6 +74,7 @@ Utilities
 .. toctree::
    :maxdepth: 1
 
+   sage/structure/richcmp
    sage/structure/unique_representation
    sage/structure/factory
    sage/structure/dynamic_class

src/doc/en/thematic_tutorials/coercion_and_categories.rst

@@ -367,7 +367,7 @@ This gives rise to the following code::
     ....:     def _repr_(self):
     ....:         return "(%s):(%s)"%(self.n,self.d)
     ....:     def _richcmp_(self, other, op):
-    ....:         from sage.structure.sage_object import richcmp
+    ....:         from sage.structure.richcmp import richcmp
     ....:         return richcmp(self.n*other.denominator(), other.numerator()*self.d, op)
     ....:     def _add_(self, other):
     ....:         C = self.__class__
@@ -1858,7 +1858,7 @@ Appendix: The complete code
         # are allowed to use the denominator() and numerator() methods
         # on the second argument.
         def _richcmp_(self, other, op):
-            from sage.structure.sage_object import richcmp
+            from sage.structure.richcmp import richcmp
             return richcmp(self.n*other.denominator(), other.numerator()*self.d, op)
 
         # Arithmetic methods, single underscore. We can assume that both

src/doc/en/thematic_tutorials/numerical_sage/index.rst

@@ -5,19 +5,24 @@
 .. _numerical_computing:
 
 Numerical Computing with Sage
-==========================================
+=============================
+
+.. WARNING::
+
+    Beware that this document may be obsolete.
+
 This document is designed to introduce the reader to the tools in Sage
 that are useful for doing numerical computation. By numerical
 computation we essentially mean machine precision floating point
 computations.  In particular, things such as optimization, numerical
-linear algebra, solving ODE's/PDE's numerically, etc.  or the first
-part of this document the reader is only assumed to be familiar with
-Python/Sage. In the second section on using compiled code, the
-computational prerequisites increase and I assume the reader is
-comfortable with writing programs in C or Fortran. The third section
-is on mpi and parallel programming and only requires knowledge of
-Python,  though familiarity with mpi would be helpful.
-Finally the last section is about 3d visualization in Sage.
+linear algebra, solving ODE's or PDE's numerically, etc.
+
+In the first part of this document the reader is only assumed to be
+familiar with Python/Sage. In the second section on using compiled
+code, the computational prerequisites increase and I assume the reader
+is comfortable with writing programs in C or Fortran. The third
+section is on mpi and parallel programming and only requires knowledge
+of Python, though familiarity with mpi would be helpful.
 
 In the current version of this document the reader is assumed to be
 familiar with the techniques of numerical analysis. The goal of this
@@ -33,4 +38,3 @@ where they can find more information.
    numerical_tools
    using_compiled_code_iteractively
    parallel_computation
-   visualization