Merge remote-tracking branch 'trac/develop' into 28457

sagemath · Sep 5, 2019 · 3de1e64 · 3de1e64
2 parents ecf77d4 + bdf4b23
commit 3de1e64
Show file tree

Hide file tree

Showing 193 changed files with 7,872 additions and 1,744 deletions.
diff --git a/.ci/head-tail.sh b/.ci/head-tail.sh
@@ -33,6 +33,9 @@ stdbuf -i0 -o0 -e0 awk -v limit=$1 -v firstMissingNR=-1 -v offset=$OFFSET -v byt
     a[NR] = $0;
     delete a[NR-offset];
     printf "." > "/dev/stderr"
+    if (/^sage-logger/){
+      print > "/dev/stderr"
+    }
   }
 }
 END {

diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-SageMath version 8.9.beta7, Release Date: 2019-08-18
+SageMath version 8.9.beta9, Release Date: 2019-09-02
diff --git a/build/pkgs/configure/checksums.ini b/build/pkgs/configure/checksums.ini
@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=e1f5fb67f8895c261043e4203c654772c15011e9
-md5=cb0bcc975697113d75adad861af22570
-cksum=593852789
+sha1=63584e4da0b7b7c7a649da76c95dd60fec676adc
+md5=539bc61c8fc49db4e2d9b5555a87203a
+cksum=4072434824
diff --git a/build/pkgs/configure/package-version.txt b/build/pkgs/configure/package-version.txt
@@ -1 +1 @@
-8c985712aebdb887c2e66308af1d29907a6fc242
+c631202c123403af404116953fdb6b6a453dd69d
diff --git a/build/pkgs/cython/checksums.ini b/build/pkgs/cython/checksums.ini
@@ -1,4 +1,4 @@
 tarball=Cython-VERSION.tar.gz
-sha1=71ebfe5caafb44d0c37e5abbcf4c353cea120781
-md5=08939b99869f59007387aea0d1a86341
-cksum=2871245920
+sha1=1c0c6cb9ebb875e8769863e1720683b24a755a7c
+md5=f212574687a52706ff53738a64f91398
+cksum=1612385007
diff --git a/build/pkgs/cython/package-version.txt b/build/pkgs/cython/package-version.txt
@@ -1 +1 @@
-0.29.10.p0
+0.29.12.p0
diff --git a/build/pkgs/fflas_ffpack/spkg-install b/build/pkgs/fflas_ffpack/spkg-install
@@ -31,7 +31,7 @@ fi
 # http://trac.sagemath.org/ticket/17635#comment:67
 sdh_configure --with-default="$SAGE_LOCAL" --with-blas-libs="$LINBOX_BLAS" \
               "$LINBOX_BLAS_CFLAGS" --disable-static \
-              --enable-precompilation --disable-openmp $FFLAS_FFPACK_CONFIGURE
+              --enable-precompilation $FFLAS_FFPACK_CONFIGURE
 sdh_make
 
 $MAKE autotune

diff --git a/build/pkgs/givaro/spkg-configure.m4 b/build/pkgs/givaro/spkg-configure.m4
@@ -0,0 +1,17 @@
+SAGE_SPKG_CONFIGURE([givaro], [
+    m4_pushdef([SAGE_GIVARO_MINVER],["40101"])
+    SAGE_SPKG_DEPCHECK([gmp mpir], [
+        AC_PATH_PROG([GIVAROCONFIG], [givaro-config])
+        AS_IF([test x$GIVAROCONFIG = x], [
+           AC_MSG_NOTICE([givaro-config not found. Installing givaro])
+           sage_spkg_install_givaro=yes], [
+           AC_MSG_CHECKING([is givaro's version good enough? ])
+           givaro_ver=`$GIVAROCONFIG --decimal-version 2>> config.log`
+           AX_COMPARE_VERSION([$givaro_ver], [ge], [$SAGE_GIVARO_MINVER], [
+               AC_MSG_RESULT([yes. Use system's givaro])], [
+               AC_MSG_RESULT([no. Install givaro])
+               sage_spkg_install_givaro=yes])
+        ])
+    ])
+    m4_popdef([SAGE_GIVARO_MINVER])
+])
diff --git a/build/pkgs/jupymake/dependencies b/build/pkgs/jupymake/dependencies
@@ -0,0 +1,5 @@
+$(PYTHON) polymake | pip
+
+----------
+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/m4ri/spkg-configure.m4 b/build/pkgs/m4ri/spkg-configure.m4
@@ -0,0 +1,6 @@
+SAGE_SPKG_CONFIGURE([m4ri], [
+    SAGE_SPKG_DEPCHECK([libpng], [
+        PKG_CHECK_MODULES([M4RI], [m4ri >= 20140914], [], [
+           sage_spkg_install_m4ri=yes])
+    ])
+])
diff --git a/build/pkgs/m4rie/spkg-configure.m4 b/build/pkgs/m4rie/spkg-configure.m4
@@ -0,0 +1,8 @@
+SAGE_SPKG_CONFIGURE([m4rie], [
+    SAGE_SPKG_DEPCHECK([m4ri], [
+       AC_CHECK_HEADER([m4rie/m4rie.h], [
+        AC_SEARCH_LIBS([gf2e_init], [m4rie], [
+        ], [sage_spkg_install_m4rie=yes])
+       ], [sage_spkg_install_m4rie=yes])
+    ])
+])
diff --git a/build/pkgs/polymake/spkg-check b/build/pkgs/polymake/spkg-check
@@ -0,0 +1,2 @@
+cd src/
+sdh_make test
diff --git a/build/pkgs/pynac/checksums.ini b/build/pkgs/pynac/checksums.ini
@@ -1,4 +1,4 @@
 tarball=pynac-VERSION.tar.bz2
-sha1=fc7c792fc4646cccea5ef0e24dd5a269f2589e5c
-md5=edd4e2cf1f3f6c3269d57fd89790b52a
-cksum=2239304387
+sha1=895950af30f818d4bbd55d6695c33ec63515fd5f
+md5=44f1f0a2c5feff7b3e30fa763ff7e2c0
+cksum=3238748787
diff --git a/build/pkgs/pynac/package-version.txt b/build/pkgs/pynac/package-version.txt
@@ -1 +1 @@
-0.7.24.p0
+0.7.26
diff --git a/build/pkgs/pynac/patches/0001-Fix-compliation-error-with-GMP-long-long-limbs.patch b/build/pkgs/pynac/patches/0001-Fix-compliation-error-with-GMP-long-long-limbs.patch
diff --git a/build/pkgs/scipy/patches/4a8a35f2c27be9f209cfc6f347e7a57a4a62e693.patch b/build/pkgs/scipy/patches/4a8a35f2c27be9f209cfc6f347e7a57a4a62e693.patch
@@ -0,0 +1,48 @@
+From 4a8a35f2c27be9f209cfc6f347e7a57a4a62e693 Mon Sep 17 00:00:00 2001
+From: Eric Larson <larson.eric.d@gmail.com>
+Date: Wed, 19 Dec 2018 10:50:47 -0500
+Subject: [PATCH] FIX: Fix encoding lines
+
+---
+ scipy/io/__init__.py                | 2 +-
+ scipy/stats/_continuous_distns.py   | 1 +
+ scipy/stats/_stats_mstats_common.py | 3 +++
+ 3 files changed, 5 insertions(+), 1 deletion(-)
+
+diff --git a/scipy/io/__init__.py b/scipy/io/__init__.py
+index 64a7aa55d39..056c742687b 100644
+--- a/scipy/io/__init__.py
++++ b/scipy/io/__init__.py
+@@ -1,4 +1,4 @@
+-# -*- encoding:utf-8 -*-
++# -*- coding: utf-8 -*-
+ """
+ ==================================
+ Input and output (:mod:`scipy.io`)
+diff --git a/scipy/stats/_continuous_distns.py b/scipy/stats/_continuous_distns.py
+index 44c05bb7d67..b48d7e7af32 100644
+--- a/scipy/stats/_continuous_distns.py
++++ b/scipy/stats/_continuous_distns.py
+@@ -1,3 +1,4 @@
++# -*- coding: utf-8 -*-
+ #
+ # Author:  Travis Oliphant  2002-2011 with contributions from
+ #          SciPy Developers 2004-2011
+diff --git a/scipy/stats/_stats_mstats_common.py b/scipy/stats/_stats_mstats_common.py
+index e86c8287b48..be478da1f2a 100644
+--- a/scipy/stats/_stats_mstats_common.py
++++ b/scipy/stats/_stats_mstats_common.py
+@@ -1,3 +1,5 @@
++# -*- coding: utf-8 -*-
++
+ from collections import namedtuple
+
+ import numpy as np
+@@ -11,6 +13,7 @@
+                                                    'rvalue', 'pvalue',
+                                                    'stderr'))
+
++
+ def linregress(x, y=None):
+     """
+     Calculate a linear least-squares regression for two sets of measurements.
diff --git a/docker/README.md b/docker/README.md
@@ -6,7 +6,7 @@
 * `x.x` — all stable releases of Sage are tagged with their version number.
 * `x.x.{beta,rc}x` - betas and release candidates of Sage as [tagged in our git repository](https://github.com/sagemath/sage/tags).
 * `develop` — the current development version of Sage which gets merged into the `master` branch when a new version of Sage is released [![GitHub last commit (branch)](https://img.shields.io/github/last-commit/sagemath/sage/develop.svg)](https://github.com/sagemath/sage/commits/develop) [![GitLab CI](https://gitlab.com/sagemath/sage/badges/develop/pipeline.svg)](https://gitlab.com/sagemath/sage/commits/develop)
-
+* all the above tags can be complemented by `-py3` for Python 3 based images
 
 # What is SageMath
 

diff --git a/m4/sage_spkg_configure.m4 b/m4/sage_spkg_configure.m4
@@ -103,3 +103,25 @@ m4_popdef([SPKG_NAME])
 AC_DEFUN([SAGE_SPKG_CONFIGURE], [
     SAGE_SPKG_CONFIGURE_BASE([$1], [$2], [$3], [$4], [$5], [AC_REQUIRE([SAGE_SPKG_CONFIGURE_GCC])])
 ])
+
+# SYNOPSIS
+#
+#   SAGE_SPKG_DEPCHECK(PACKAGE-DEPENDENCIES, FURTHER-CHECK)
+#                                 $1              $2
+#
+# DESCRIPTION
+#     *** to be called from SAGE_SPKG_CONFIGURE* ***
+#     check for space-separated list of package dependencies $1 of package SPKG_NAME
+#     do $2 if successful
+#
+AC_DEFUN([SAGE_SPKG_DEPCHECK], [
+    m4_foreach_w([DEP], $1, [
+       AC_REQUIRE([SAGE_SPKG_CONFIGURE_]m4_toupper(DEP))])
+    AC_MSG_CHECKING([installing any of $1? ])
+    AS_IF([test x = y m4_foreach_w([DEP], $1, [ -o [x$sage_spkg_install_]DEP = xyes])], [
+        AC_MSG_RESULT([yes; install SPKG_NAME as well])
+        [sage_spkg_install_]SPKG_NAME=yes], [
+        AC_MSG_RESULT([no])
+        $2
+        ])
+])
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.beta7'
-SAGE_RELEASE_DATE='2019-08-18'
-SAGE_VERSION_BANNER='SageMath version 8.9.beta7, Release Date: 2019-08-18'
+SAGE_VERSION='8.9.beta9'
+SAGE_RELEASE_DATE='2019-09-02'
+SAGE_VERSION_BANNER='SageMath version 8.9.beta9, Release Date: 2019-09-02'
diff --git a/src/doc/en/faq/faq-usage.rst b/src/doc/en/faq/faq-usage.rst
@@ -167,15 +167,12 @@ every change applied to the file simple.py will be automatically updated in Sage
 Can I use SageMath with Python 3.x?
 """""""""""""""""""""""""""""""""""
 
-Currently, (September 2018) you can build the source code of SageMath with
-Python 3 using the instructions at the bottom of
-https://wiki.sagemath.org/Python3-compatible%20code
+As of August 2019, most of SageMath works fine with Python 3. However, we still
+consider Python 3 support to be experimental and no official Python 3 release
+has been made yet.
 
-Beware that this is still at an experimental stage.
-
-Work in progress aims to allow usage of Python 3 in the not-so-far
-future. Until this task is completed, SageMath will continue to use
-Python 2.x.
+You can build the source code of SageMath with Python 3 using the instructions
+at the bottom of https://wiki.sagemath.org/Python3-compatible%20code
 
 See :trac:`15530` and :trac:`26212` for tracking the current progress.
 

diff --git a/src/doc/en/installation/source.rst b/src/doc/en/installation/source.rst
@@ -223,20 +223,24 @@ distribution, but on a `Debian <https://www.debian.org/>`_ based system (e.g.
 you would use
 `apt-get <https://en.wikipedia.org/wiki/Advanced_Packaging_Tool>`_::
 
-     # debian (Stretch or newer) / ubuntu
+     # debian (Buster or newer) / ubuntu
      $ sudo apt-get install binutils pixz gcc g++ gfortran make m4 perl tar \
        git patch openssl libssl-dev libz-dev bc libbz2-dev liblzma-dev libgmp-dev \
        libffi-dev libgf2x-dev libcurl4-openssl-dev libzmq3-dev curl yasm \
        pkg-config libntl-dev libmpfr-dev libmpc-dev libflint-dev \
        libpcre3-dev libgd-dev libflint-dev libflint-arb-dev \
-       libsymmetrica2-dev gmp-ecm libecm-dev
+       libsymmetrica2-dev gmp-ecm libecm-dev libisl-dev libgivaro-dev \
+       libpari-dev pari-gp2c libec-dev liblrcalc-dev \
+       libm4ri-dev libm4rie-dev liblfunction-dev lcalc
 
      # redhat / fedora / centos
      $ sudo yum install binutils xz gcc gcc-c++ gcc-gfortran make m4 perl \
        tar git patch perl-ExtUtils-MakeMaker openssl openssl-devel zlib-devel \
        bzip2 bzip2-devel xz-devel gmp gmp-devel libcurl-devel curl yasm \
        pkg-config ntl-devel mpfr-devel libmpc-devel libsymmetrica-devel \
-       gmp-ecm-devel
+       eclib-devel gmp-ecm-devel lrcalc-devel isl-devel givaro-devel \
+       pari-devel pari-elldata pari-seadata pari-galdata pari-galpol \
+       m4ri-devel m4rie-devel L-function-devel
 
 (These examples suppose that you choose to use a systemwide OpenSSL library.)
 In addition, if you don't want Sage to build other packages that might be available from
@@ -467,7 +471,7 @@ or similar commands.
 If you installed Sage first, all is not lost. You just need to rebuild
 Sage's Python and any part of Sage relying on it::
 
-    $ sage -f python2  # rebuild Python
+    $ sage -f python2  # rebuild Python2
     $ make             # rebuild components of Sage depending on Python
 
 after installing the Tcl/Tk development libraries as above.
@@ -622,11 +626,10 @@ Running Sage from a directory with spaces in its name will also fail.
    You should see the Sage prompt, which will look something like this::
 
        $ sage
-       ----------------------------------------------------------------------
-       | Sage Version 5.8, Release Date: 2013-03-15                         |
-       | Type "notebook()" for the browser-based notebook interface.        |
-       | Type "help()" for help.                                            |
-       ----------------------------------------------------------------------
+       ┌────────────────────────────────────────────────────────────────────┐
+       │ SageMath version 8.8, Release Date: 2019-06-26                     │
+       │ Using Python 2.7.15. Type "help()" for help.                       │
+       └────────────────────────────────────────────────────────────────────┘
        sage:
 
    Note that Sage should take well under a minute when it starts for the first
@@ -1428,4 +1431,4 @@ the directory where you want to install Sage.
 
 
 
-**This page was last updated in September 2017 (Sage 8.1).**
+**This page was last updated in August 2019 (Sage 8.8).**
diff --git a/src/doc/en/reference/coercion/index.rst b/src/doc/en/reference/coercion/index.rst
@@ -63,9 +63,9 @@ either parents or have a parent. Typically whenever one sees the word
     (1 + O(5^20))*t^3 + 4*5 + 4*5^2 + 4*5^3 + 4*5^4 + 4*5^5 + 4*5^6 + 4*5^7 + 4*5^8 + 4*5^9 + 4*5^10 + 4*5^11 + 4*5^12 + 4*5^13 + 4*5^14 + 4*5^15 + 4*5^16 + 4*5^17 + 4*5^18 + 4*5^19 + 4*5^20 + O(5^21)
     sage: parent(f)
     Univariate Polynomial Ring in t over 5-adic Field with capped relative precision 20
-    sage: f = EllipticCurve('37a').lseries().taylor_series(10); f
-    0.990010459847588 + 0.0191338632530789*z - 0.0197489006172923*z^2 + 0.0137240085327618*z^3 - 0.00703880791607153*z^4 + 0.00280906165766519*z^5 + O(z^6)           # 32-bit
-    0.997997869801216 + 0.00140712894524925*z - 0.000498127610960097*z^2 + 0.000118835596665956*z^3 - 0.0000215906522442707*z^4 + (3.20363155418419e-6)*z^5 + O(z^6)  # 64-bit
+    sage: f = EllipticCurve('37a').lseries().taylor_series(10); f  # abs tol 1e-14
+    0.997997869801216 + 0.00140712894524925*z - 0.000498127610960097*z^2 + 0.000118835596665956*z^3 - 0.0000215906522442708*z^4 + (3.20363155418421e-6)*z^5 + O(z^6)  # 32-bit
+    0.997997869801216 + 0.00140712894524925*z - 0.000498127610960097*z^2 + 0.000118835596665956*z^3 - 0.0000215906522442708*z^4 + (3.20363155418427e-6)*z^5 + O(z^6)  # 64-bit
     sage: parent(f)
     Power Series Ring in z over Complex Field with 53 bits of precision
 
@@ -84,7 +84,7 @@ There is an important distinction between Parents and types::
     sage: parent(a) == parent(b)
     False
 
-However, non-Sage objects don't really have parents, but we still want
+However, non-Sage objects do not really have parents, but we still want
 to be able to reason with them, so their type is used instead::
 
     sage: a = int(10)

diff --git a/src/doc/en/reference/combinat/module_list.rst b/src/doc/en/reference/combinat/module_list.rst
@@ -346,6 +346,7 @@ Comprehensive Module list
     sage/combinat/subsets_pairwise
     sage/combinat/subword
     sage/combinat/subword_complex
+    sage/combinat/super_tableau
     sage/combinat/superpartition
     sage/combinat/symmetric_group_algebra
     sage/combinat/symmetric_group_representations

diff --git a/src/doc/en/reference/cryptography/index.rst b/src/doc/en/reference/cryptography/index.rst
@@ -13,6 +13,7 @@ Cryptography
 
    sage/crypto/block_cipher/sdes
    sage/crypto/block_cipher/miniaes
+   sage/crypto/block_cipher/present
 
    sage/crypto/public_key/blum_goldwasser