merged with sage 8.9beta6

sagemath · Aug 12, 2019 · 8085e8c · 8085e8c
2 parents 8c022dd + 213fe0b
commit 8085e8c
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diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-SageMath version 8.9.beta5, Release Date: 2019-08-03
+SageMath version 8.9.beta6, Release Date: 2019-08-10
diff --git a/build/pkgs/configure/checksums.ini b/build/pkgs/configure/checksums.ini
@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=997b7b8745c4b48954089e3607c0deb2f3de5fa1
-md5=7f2255d9146518296793f7f6183568c2
-cksum=2571648127
+sha1=e9fc4a6b98663c0f625707d699638017b65688ae
+md5=fe7bb18c282553543c98688e78dab7d0
+cksum=3711812649
diff --git a/build/pkgs/configure/package-version.txt b/build/pkgs/configure/package-version.txt
@@ -1 +1 @@
-73d2ad18c0e4fdd99f9cfbae99f726cdd70486f2
+442411009b7c99f34315b76fe35ad092aa3a6962
diff --git a/build/pkgs/dot2tex/SPKG.txt b/build/pkgs/dot2tex/SPKG.txt
@@ -22,6 +22,12 @@ example via the graphviz spkg).
 
 preview, a LaTeX package for extracting parts of a document.
 
+Self-tests dependencies:
+ * graphviz
+ * texlive-latex-base 
+ * texlive-pictures 
+ * texlive-pstricks
+
 == Patches ==
 
  * remove_test_semicolon.patch:

diff --git a/build/pkgs/gap_packages/dependencies b/build/pkgs/gap_packages/dependencies
@@ -1,4 +1,4 @@
-gap | $(SAGERUNTIME)
+gap libsemigroups planarity | $(SAGERUNTIME)
 
 ----------
 All lines of this file are ignored except the first.

diff --git a/build/pkgs/gap_packages/package-version.txt b/build/pkgs/gap_packages/package-version.txt
@@ -1 +1 @@
-4.10.2.p0
+4.10.2.p1
diff --git a/build/pkgs/gap_packages/spkg-install b/build/pkgs/gap_packages/spkg-install
@@ -19,6 +19,7 @@ sdh_install \
     crystcat \
     design-* \
     gbnp \
+    genss-* \
     Hap* \
     HAPcryst \
     hecke-* \
@@ -64,7 +65,7 @@ install_compiled_pkg()
 #
 # These packages have an old ./configure that take the GAP_ROOT as a positional
 # argument
-for pkg in cohomolo-* crypting-* grape-* guava-*
+for pkg in cohomolo-* crypting-* grape-* guava-* orb-*
 do
     echo "Building GAP package $pkg"
     cd "$PKG_SRC_DIR/$pkg"
@@ -77,10 +78,23 @@ done
 # These packages have a new-style autoconf ./configure
 # that takes --with-gaproot
 
-for pkg in nq-* io-*
+#############################################################################
+########## add extra parameters for packages' configures here ###############
+#
+# ng         : none
+# io         : none
+# semigroups needs to use external libsemigroups
+# digraphs   needs to use external planarity
+pararr=( " " " " "--with-external-planarity" "--with-external-libsemigroups" )
+##############################################################################
+
+parind=0
+for pkg in nq-* io-* digraphs-* semigroups-*
 do
+    echo "Building GAP package $pkg"
     cd "$PKG_SRC_DIR/$pkg"
-    sdh_configure --with-gaproot="$GAP_ROOT"
+    sdh_configure --with-gaproot="$GAP_ROOT" ${pararr[$parind]}
+    ((parind+=1))
     sdh_make -j1
     install_compiled_pkg "$pkg"
     cd "$PKG_SRC_DIR"

diff --git a/build/pkgs/libsemigroups/SPKG.txt b/build/pkgs/libsemigroups/SPKG.txt
@@ -0,0 +1,15 @@
+= libffi =
+
+== Description ==
+
+C++ library for semigroups and monoids;
+used in GAP's package Semigroups.
+
+== License ==
+
+GPL-3.0
+
+== Upstream Contact ==
+
+http://james-d-mitchell.github.io/libsemigroups
+https://github.com/james-d-mitchell/libsemigroups
diff --git a/build/pkgs/libsemigroups/checksums.ini b/build/pkgs/libsemigroups/checksums.ini
@@ -0,0 +1,4 @@
+tarball=libsemigroups-VERSION.tar.gz
+sha1=d1be401d098fc36b096f8b5a89a556892a471385
+md5=788856c7cf162474580e48094ff5de29
+cksum=2423299159
diff --git a/build/pkgs/libsemigroups/dependencies b/build/pkgs/libsemigroups/dependencies
@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/libsemigroups/package-version.txt b/build/pkgs/libsemigroups/package-version.txt
@@ -0,0 +1 @@
+0.6.7
diff --git a/build/pkgs/libsemigroups/spkg-check b/build/pkgs/libsemigroups/spkg-check
@@ -0,0 +1,2 @@
+cd src
+$MAKE check
diff --git a/build/pkgs/libsemigroups/spkg-configure.m4 b/build/pkgs/libsemigroups/spkg-configure.m4
@@ -0,0 +1,4 @@
+SAGE_SPKG_CONFIGURE([libsemigroups], [
+    dnl  checking with pkg-config
+    PKG_CHECK_MODULES([LIBSEMIGROUPS], [libsemigroups >= 0.6.7], [], [sage_spkg_install_libsemigroups=yes])
+])
diff --git a/build/pkgs/libsemigroups/spkg-install b/build/pkgs/libsemigroups/spkg-install
@@ -0,0 +1,4 @@
+cd src
+sdh_configure
+sdh_make
+sdh_make_install
diff --git a/build/pkgs/libsemigroups/type b/build/pkgs/libsemigroups/type
@@ -0,0 +1 @@
+optional
diff --git a/build/pkgs/lrcalc/spkg-configure.m4 b/build/pkgs/lrcalc/spkg-configure.m4
@@ -0,0 +1,9 @@
+SAGE_SPKG_CONFIGURE([lrcalc], [
+    AC_CHECK_HEADERS([lrcalc/schublib.h], [
+          AC_SEARCH_LIBS([mult_poly_schubert], [lrcalc], [], [sage_spkg_install_lrcalc=yes])
+    ], [sage_spkg_install_lrcalc=yes],
+    [[#ifndef _HASHTAB_H
+      #include <lrcalc/hashtab.h>
+      #include <lrcalc/vector.h>
+      #endif]])
+])
diff --git a/build/pkgs/mpfi/spkg-configure.m4 b/build/pkgs/mpfi/spkg-configure.m4
@@ -0,0 +1,38 @@
+SAGE_SPKG_CONFIGURE([mpfi], [
+    AC_REQUIRE([SAGE_SPKG_CONFIGURE_MPFR])
+    AC_MSG_CHECKING([installing mpfr? ])
+    if test x$sage_spkg_install_mpfr = xyes; then
+        AC_MSG_RESULT([yes; install mpfi as well])
+        sage_spkg_install_mpfi=yes
+    else
+        AC_MSG_RESULT([no])
+    fi
+
+    m4_pushdef(SAGE_MPFI_VERSION_MAJOR, [1])
+    m4_pushdef(SAGE_MPFI_VERSION_MINOR, [5])
+
+    if test x$sage_spkg_install_mpfi != xyes; then
+        AC_CHECK_HEADER([mpfi.h], [], [sage_spkg_install_mpfi=yes])
+        AC_SEARCH_LIBS([mpfi_diam_abs], [mpfi], [
+          AC_LANG_PUSH(C)
+          AC_MSG_CHECKING([MPFI version >= ]SAGE_MPFI_VERSION_MAJOR[.]SAGE_MPFI_VERSION_MINOR)
+          AC_RUN_IFELSE([
+            AC_LANG_PROGRAM(
+            [[#include <mpfi.h>
+              #include <stdio.h>
+            ]], [[
+              printf("%s\n", MPFI_VERSION_STRING);
+              if (MPFI_VERSION_MAJOR >]] SAGE_MPFI_VERSION_MAJOR[[) return 0;
+              else if (MPFI_VERSION_MAJOR ==]] SAGE_MPFI_VERSION_MAJOR[[ &&
+                       MPFI_VERSION_MINOR >=]] SAGE_MPFI_VERSION_MINOR[[) return 0;
+              else return 1;
+            ]])], [AC_MSG_RESULT([.. yes])], [
+                   AC_MSG_RESULT([.. no])
+                   sage_spkg_install_mpfi=yes])
+        AC_LANG_POP(C)], [sage_spkg_install_mpfi=yes])
+    fi
+
+    m4_popdef([SAGE_MPFI_VERSION_MAJOR])
+    m4_popdef([SAGE_MPFI_VERSION_MINOR])
+])
+
diff --git a/src/bin/sage-version.sh b/src/bin/sage-version.sh
@@ -1,5 +1,5 @@
 # Sage version information for shell scripts
 # This file is auto-generated by the sage-update-version script, do not edit!
-SAGE_VERSION='8.9.beta5'
-SAGE_RELEASE_DATE='2019-08-03'
-SAGE_VERSION_BANNER='SageMath version 8.9.beta5, Release Date: 2019-08-03'
+SAGE_VERSION='8.9.beta6'
+SAGE_RELEASE_DATE='2019-08-10'
+SAGE_VERSION_BANNER='SageMath version 8.9.beta6, Release Date: 2019-08-10'
diff --git a/src/doc/en/installation/source.rst b/src/doc/en/installation/source.rst
@@ -156,7 +156,8 @@ In any case, you always need at least a C/C++ compiler to build the GCC
 package and its prerequisites before the compilers it provides can be used.
 
 Note that you can always override this behavior through the configure
-options `--without-system-gcc` and `--with-system-gcc`, see :ref:`section_compilers`.
+options ``--without-system-gcc`` and ``--with-system-gcc``, see
+:ref:`section_compilers`.
 
 Other notes
 ^^^^^^^^^^^

diff --git a/src/doc/en/reference/coding/index.rst b/src/doc/en/reference/coding/index.rst
@@ -3,54 +3,51 @@
 Coding Theory
 =============
 
-Basic Coding Theory objects
----------------------------
+Coding theory is the mathematical theory for algebraic and combinatorial codes
+used for forward error correction in communications theory. Sage provides an
+extensive library of objects and algorithms in coding theory.
 
+Basic objects in coding theory are channels, linear codes, encoders, and
+decoders. The following modules provide the base classes defining them.
 
 .. toctree::
    :maxdepth: 1
 
    sage/coding/linear_code
-   sage/coding/channel_constructions
-   sage/coding/decoder
+   sage/coding/channel
    sage/coding/encoder
+   sage/coding/decoder
 
-Catalogs
---------
+Catalogs for available constructions of the basic objects and for bounds on
+the parameters of linear codes are provided.
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
 
    sage/coding/channels_catalog
    sage/coding/codes_catalog
    sage/coding/decoders_catalog
    sage/coding/encoders_catalog
    sage/coding/bounds_catalog
-   sage/coding/databases
-   sage/coding/two_weight_db
 
-Code constructions
-------------------
+Families of Codes
+-----------------
 
-.. toctree::
-   :maxdepth: 1
-
-   sage/coding/linear_code
-
-The named code families below are represented in Sage by their own classes,
-allowing specialised implementations of e.g. decoding or computation of properties:
+Famous families of codes, listed below, are represented in Sage by their own
+classes. For some of them, implementations of special decoding algorithms or
+computations for structural invariants are available.
 
 .. toctree::
    :maxdepth: 2
 
-   sage/coding/grs
+   sage/coding/parity_check_code
    sage/coding/hamming_code
+   sage/coding/cyclic_code
+   sage/coding/bch_code
    sage/coding/golay_code
-   sage/coding/parity_check_code
    sage/coding/reed_muller_code
-   sage/coding/cyclic_code
-   sage/coding/bch
-   sage/coding/goppa
+   sage/coding/grs_code
+   sage/coding/goppa_code
 
 In contrast, for some code families Sage can only construct their generator
 matrix and has no other a priori knowledge on them:
@@ -67,8 +64,8 @@ Derived Code Constructions
 --------------------------
 
 Sage supports the following derived code constructions. If the constituent code
-is from a special code family, the derived codes inherit e.g. decoding or
-minimum distance capabilities:
+is from a special code family, the derived codes inherit structural properties
+like decoding radius or minimum distance:
 
 .. toctree::
    :maxdepth: 2
@@ -80,37 +77,67 @@ minimum distance capabilities:
 Other derived constructions that simply produce the modified generator matrix
 can be found among the methods of a constructed code.
 
-Methods and Operations related to Linear Codes
-----------------------------------------------
+Decoding
+--------
+
+Information-set decoding for linear codes:
+
+.. toctree::
+   :maxdepth: 1
+
+   sage/coding/information_set_decoder
 
+Guruswami-Sudan interpolation-based list decoding for Reed-Solomon codes:
+
+.. toctree::
+   :maxdepth: 1
+
+   sage/coding/guruswami_sudan/gs_decoder
+   sage/coding/guruswami_sudan/interpolation
+   sage/coding/guruswami_sudan/utils
+
+Automorphism Groups of Linear Codes
+-----------------------------------
 
 .. toctree::
    :maxdepth: 2
 
    sage/coding/codecan/codecan
    sage/coding/codecan/autgroup_can_label
 
-Source coding
--------------
+Bounds for Parameters of Linear Codes
+-------------------------------------
+
+.. toctree::
+   :maxdepth: 2
+
+   sage/coding/code_bounds
+   sage/coding/delsarte_bounds
+
+Databases for Coding Theory
+---------------------------
+
+.. toctree::
+   :maxdepth: 2
+
+   sage/coding/databases
+   sage/coding/two_weight_db
+
+Miscellaneous Modules
+---------------------
+
+There is at least one module in Sage for source coding in communications theory:
 
 .. toctree::
    :maxdepth: 1
 
    sage/coding/source_coding/huffman
 
-Other modules
--------------
+Finally an experimental module used for code constructions:
 
 .. toctree::
    :maxdepth: 1
 
    sage/coding/relative_finite_field_extension
-   sage/coding/guruswami_sudan/gs_decoder
-   sage/coding/guruswami_sudan/interpolation
-   sage/coding/guruswami_sudan/utils
-   sage/coding/information_set_decoder
-   sage/coding/code_bounds
-   sage/coding/delsarte_bounds
-
 
 .. include:: ../footer.txt