Merge branch 'develop' into t/21996/factorization_in_iterated_extensi…

…ons_of_finite_fields

README.md

@@ -377,20 +377,10 @@ do.
 
          sage --sdist
 
-2. To make a binary distribution with your currently installed packages,  
-   type:
+   The result is placed in the directory "$SAGE_ROOT/dist/".
 
-         sage --bdist
-
-3. To make a binary that will run on the widest range of target  
-   machines, set the SAGE_FAT_BINARY environment variable to "yes"  
-   before building Sage:  
-
-         export SAGE_FAT_BINARY="yes"
-         make distclean && make
-         ./sage --bdist
-
-In all cases, the result is placed in the directory "$SAGE_ROOT/dist/".  
+2. To make a binary distribution with your currently installed packages,
+   visit https://github.com/sagemath/binary-pkg
 
 
 Changes to Included Software

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.0.beta2, Release Date: 2017-04-12
+SageMath version 8.0.beta9, Release Date: 2017-05-31

build/bin/sage-logger

@@ -60,14 +60,17 @@ else
     SED=cat
 fi
 
-# Store the current value of V, but do all logging of child processes
-# with V=1 to ensure that no information is lost.
-currentV=$V
-export V=1
-
 mkdir -p "$logdir"
 
-if [[ "$currentV" = 0 && $use_prefix = true ]]; then
+# Do all logging of child processes with V=1 to ensure that no
+# information is lost.
+export MAKEFLAGS="$MAKEFLAGS V=1"
+
+if [ "$V" = 0 ]; then
+    export SAGE_SILENT_BUILD=yes
+fi
+
+if [ -n "$SAGE_SILENT_BUILD" -a ${use_prefix} = true ]; then
     # Silent build.
     # Similar to https://www.gnu.org/software/automake/manual/html_node/Automake-Silent-Rules.html#Automake-Silent-Rules
     echo "[$logname] installing. Log file: $logfile"

build/bin/sage-pip-install

@@ -31,8 +31,18 @@ if [ "$1" != "." ]; then
     exit 1
 fi
 
+
+if [ "$SAGE_PYTHON3" = yes ]; then
+    PYTHON=python3
+    PIP=pip3
+else
+    PYTHON=python2
+    PIP=pip2
+fi
+
+
 # Find out the name of the package that we are installing
-name="$(python setup.py --name)"
+name="$($PYTHON setup.py --name)"
 
 if [ $? -ne 0 ]; then
     echo >&2 "Error: could not determine package name"
@@ -46,29 +56,36 @@ if [ $(echo "$name" | wc -l) -gt 1 ]; then
     echo >&2 "line as the package name: $name"
 fi
 
-# We should avoid running pip while uninstalling a package because that
+
+# We should avoid running pip2/3 while uninstalling a package because that
 # is prone to race conditions. Therefore, we use a lockfile while
-# running pip. This is implemented in the Python script pip-lock.
+# running pip. This is implemented in the Python script pip2/3-lock.
 
 # Keep uninstalling as long as it succeeds
 while true; do
-    out=$(pip-lock uninstall --disable-pip-version-check -y "$name" 2>&1)
+    out=$($PIP-lock uninstall --disable-pip-version-check -y "$name" 2>&1)
     if [ $? -ne 0 ]; then
         break
     fi
     echo "$out"
 done
 
 # Not ideal, but this is the easiest way to check if the package
-# was not installed to begin with (which pip treats as an error).
+# was not installed to begin with (which pip2/3 treats as an error).
 # If it wasn't, then we proceed quietly; if it was installed show the
 # uninstallation output and error out.
 if [[ "$out" != *"not installed" ]]; then
     echo >&2 "$out"
     exit 1
 fi
 
-# Finally actually do the installation (the "SHARED" tells pip-lock
+# Finally actually do the installation (the "SHARED" tells pip2/3-lock
 # to apply a shared lock)
-echo "Installing package $name using pip"
-exec pip-lock SHARED install $pip_install_flags .
+echo "Installing package $name using $PIP"
+
+$PIP-lock SHARED install $pip_install_flags .
+if [ $? -ne 0 ]; then
+    echo >&2 "Error: installing with $PIP failed"
+    exit 3
+fi
+

build/bin/sage-python23

@@ -0,0 +1,21 @@
+#!/usr/bin/env bash
+
+
+# Run the Python interpreter that we are currently building Sage with
+#
+# An existing Python is a build-time dependency for Sage, but
+# sometimes packages need to specifically run the one in Sage and not
+# just any Python interpreter.
+#
+# This is similar to the sage-pip-install script, which you should be
+# using for installing Python packages if at all possible.
+
+
+if [ "$SAGE_PYTHON3" = yes ]; then
+   PYTHON="$SAGE_LOCAL/bin/python3"
+else
+   PYTHON="$SAGE_LOCAL/bin/python2"
+fi
+
+
+exec $PYTHON "$@"

build/bin/sage-spkg

@@ -749,6 +749,13 @@ else
     fi
 fi
 
+if [ "$UNAME" = "CYGWIN" ]; then
+    # Rebase after installing each package--in case any packages load this
+    # package at build time we need to ensure during the build that no binaries
+    # have conflicting address spaces
+    sage-rebase.sh "$SAGE_LOCAL" 2>/dev/null
+fi
+
 echo "Successfully installed $PKG_NAME"
 
 if [ "$SAGE_CHECK" = "yes" ]; then

build/make/deps

@@ -118,6 +118,7 @@ sagelib: \
 		$(inst_brial) \
 		$(inst_cephes) \
 		$(inst_cliquer) \
+		$(inst_cypari) \
 		$(inst_cysignals) \
 		$(inst_cython) \
 		$(inst_ecl) \

build/pkgs/brial/spkg-install

@@ -7,7 +7,7 @@ if [ "$SAGE_LOCAL" = "" ]; then
 fi
 
 echo "Cleaning out old PolyBoRi and BRiAl installations"
-rm -rf "$SAGE_LOCAL"/lib/python/site-packages/{polybori,brial}
+rm -rf "$SAGE_LOCAL"/lib/python*/site-packages/{polybori,brial}
 rm -f "$SAGE_LOCAL"/lib/lib{polybori,brial}*
 rm -rf "$SAGE_LOCAL"/include/polybori*
 rm -rf "$SAGE_LOCAL"/share/polybori
@@ -17,6 +17,8 @@ cd src
 # C++11 workaround https://trac.sagemath.org/ticket/20926
 export CXXFLAGS="$CXXFLAGS -std=c++98"
 
+export PYTHON=sage-python23
+
 ./configure \
     --prefix="$SAGE_LOCAL" \
     --libdir="$SAGE_LOCAL/lib" \

build/pkgs/cmake/SPKG.txt

@@ -25,5 +25,8 @@ CMake is distributed under the OSI-approved BSD 3-clause License.
 
 == Dependencies ==
 
+* curl
 * zlib
 * bzip2
+* xz
+

build/pkgs/cmake/checksums.ini

@@ -1,4 +1,4 @@
 tarball=cmake-VERSION.tar.gz
-sha1=fa176cc5b1ccf2e98196b50908432d0268323501
-md5=d51c92bf66b1e9d4fe2b7aaedd51377c
-cksum=3408528151
+sha1=4e4bf2e2f3443325f2abaec5e96819840d832427
+md5=e8ef820ddf7a650845252bca846696e7
+cksum=3021330276

build/pkgs/cmake/dependencies

@@ -0,0 +1,5 @@
+curl zlib bzip2 xz
+
+----------
+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.

build/pkgs/cmake/package-version.txt

@@ -1 +1 @@
-3.2.3
+3.8.1

build/pkgs/cmake/patches/osx10.10.patch

@@ -6,39 +6,52 @@ dispatch/dispatch.h. Since CoreFoundation/CFStream.h is not needed for CMake,
 specific headers needed are included to replace CoreFoundation/CoreFoundation.h
 
 diff -dru src/Source/cmFindProgramCommand.cxx new/Source/cmFindProgramCommand.cxx
---- src/Source/cmFindProgramCommand.cxx 2015-03-10 20:08:44.000000000 +0530
-+++ new/Source/cmFindProgramCommand.cxx 2015-06-17 13:26:32.543667394 +0530
-@@ -14,7 +14,7 @@
- #include <stdlib.h>
+--- src/Source/cmFindProgramCommand.cxx	2017-05-02 14:59:43.000000000 +0200
++++ new/Source/cmFindProgramCommand.cxx	2017-05-18 15:56:09.094011660 +0200
+@@ -9,7 +9,7 @@
+ class cmExecutionStatus;
 
  #if defined(__APPLE__)
 -#include <CoreFoundation/CoreFoundation.h>
 +#include <CoreFoundation/CFBundle.h>
  #endif
 
- // cmFindProgramCommand
+ struct cmFindProgramHelper
 diff -dru src/Source/cmXCodeObject.cxx new/Source/cmXCodeObject.cxx
---- src/Source/cmXCodeObject.cxx        2015-03-10 20:08:44.000000000 +0530
-+++ new/Source/cmXCodeObject.cxx        2015-06-17 13:26:37.191667311 +0530
-@@ -12,7 +12,7 @@
+--- src/Source/cmXCodeObject.cxx	2017-05-02 14:59:43.000000000 +0200
++++ new/Source/cmXCodeObject.cxx	2017-05-18 15:57:35.222438748 +0200
+@@ -2,7 +2,7 @@
+    file Copyright.txt or https://cmake.org/licensing for details.  */
  #include "cmXCodeObject.h"
+
+-#include <CoreFoundation/CoreFoundation.h>
++#include <CoreFoundation/CFUUID.h>
+ #include <ostream>
+
  #include "cmSystemTools.h"
+diff -dru src/Source/CPack/cmCPackDragNDropGenerator.cxx new/Source/CPack/cmCPackDragNDropGenerator.cxx
+--- src/Source/CPack/cmCPackDragNDropGenerator.cxx	2017-05-02 14:59:43.000000000 +0200
++++ new/Source/CPack/cmCPackDragNDropGenerator.cxx	2017-05-18 22:00:35.917646538 +0200
+@@ -12,8 +12,9 @@
+ #include <iomanip>
+ #include <map>
+ #include <stdlib.h>
++#include <algorithm>
 
--#include <CoreFoundation/CoreFoundation.h> // CFUUIDCreate
-+#include <CoreFoundation/CFUUID.h> // CFUUIDCreate
+-#include <CoreFoundation/CoreFoundation.h>
++#include <CoreFoundation/CFString.h>
 
- //----------------------------------------------------------------------------
- const char* cmXCodeObject::PBXTypeNames[] = {
+ #ifdef HAVE_CoreServices
+ // For the old LocaleStringToLangAndRegionCodes() function, to convert
 diff -dru src/Source/CPack/OSXScriptLauncher.cxx new/Source/CPack/OSXScriptLauncher.cxx
---- src/Source/CPack/OSXScriptLauncher.cxx      2015-03-10 20:08:44.000000000 +0530
-+++ new/Source/CPack/OSXScriptLauncher.cxx      2015-06-17 13:26:21.575667590 +0530
-@@ -14,7 +14,7 @@
- #include <cmsys/ios/iostream>
- #include <cmsys/FStream.hxx>
+--- src/Source/CPack/OSXScriptLauncher.cxx	2017-05-02 14:59:43.000000000 +0200
++++ new/Source/CPack/OSXScriptLauncher.cxx	2017-05-18 16:00:45.179380694 +0200
+@@ -8,7 +8,7 @@
+ #include <string>
+ #include <vector>
 
 -#include <CoreFoundation/CoreFoundation.h>
 +#include <CoreFoundation/CFBundle.h>
 
  // For the PATH_MAX constant
  #include <sys/syslimits.h>
-

build/pkgs/cmake/spkg-check

@@ -1,4 +1,26 @@
 #!/usr/bin/env bash
 
+if [ "$UNAME" = Darwin ]; then
+    CC=clang
+    CXX=clang++
+fi
+
 cd src
-ctest -E CTestTestStopTime
+unset MACOSX_DEPLOYMENT_TARGET
+# Supress tests failing for reason out of our controls
+FAILING_TESTS="CTestTestStopTime|TestUpload|ctest_submit"
+# gui interface may pull dependency conflicting with
+# sage libraries
+# (1) QT libraries
+FAILING_TESTS="${FAILING_TESTS}|Qt5Autogen|Qt4Autogen|Qt4Targets|Qt4And5AutomocReverse"
+# (2) GTK2
+FAILING_TESTS="${FAILING_TESTS}|GTK2Components|GTK2Targets"
+# BundleUtilities test is failing on some platforms, skipped in Gentoo for that reason
+FAILING_TESTS="${FAILING_TESTS}|BundleUtilities"
+# Test failing on freeBSD. Upstream acknoledged the test is faulty
+# on that platform https://gitlab.kitware.com/cmake/cmake/issues/16887
+if [ "$UNAME" = "FreeBSD" ]; then
+    FAILING_TESTS="${FAILING_TESTS}|RunCMake.GNUInstallDirs"
+fi
+ctest --extra-verbose --output-on-failure -E "(${FAILING_TESTS})"
+

build/pkgs/cmake/spkg-install

@@ -1,18 +1,17 @@
 #!/usr/bin/env bash
 
-cd src
-
-system_curl=""
-
-if [ "$UNAME" = "Darwin" ]; then
-    system_curl="--system-curl"
-    unset MACOSX_DEPLOYMENT_TARGET
+if [ "$UNAME" = Darwin ]; then
+    CC=clang
+    CXX=clang++
 fi
 
+cd src
+
 ./bootstrap --prefix=$SAGE_LOCAL \
     --system-bzip2 \
     --system-zlib \
-    $system_curl \
+    --system-liblzma \
+    --system-curl \
     -- \
     -DCMAKE_PREFIX_PATH=$SAGE_LOCAL \
     -DCMAKE_TESTS_CDASH_SERVER=NOTFOUND

build/pkgs/cmake/type

@@ -1 +1 @@
-experimental
+optional

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=8bdfb4b87a803b90d6b9a937d961835955723a09
-md5=1f1aa69a7ac98e4443e82611a3bbea23
-cksum=4121821509
+sha1=1468ff678f41a3552bce2ba952af0795127d64d8
+md5=931c98793b007e28874089c17c40e53d
+cksum=1227610551

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-216
+223

build/pkgs/conway_polynomials/checksums.ini

@@ -1,4 +1,4 @@
 tarball=conway_polynomials-VERSION.tar.bz2
-sha1=25b7abe5c935d20c3ebcde943308652c412d14dc
-md5=17f061204b3a6133abb21e17b3abea19
-cksum=3204784255
+sha1=d4d89bda60ac54e73121f84635e774766e19a8b6
+md5=a2725ba21f44554196781424d957f68a
+cksum=1387933493

build/pkgs/conway_polynomials/dependencies

@@ -1,7 +1,4 @@
-| $(SAGERUNTIME)
-
-CONWAY_POLYNOMIALS depends on SAGERUNTIME because it runs Sage code to
-generate a Sage object (.sobj).
+$(PYTHON) $(inst_six)
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/conway_polynomials/package-version.txt

@@ -1 +1 @@
-0.4.p0
+0.5

build/pkgs/conway_polynomials/spkg-install

@@ -1,21 +1,21 @@
-#!/usr/bin/env python
-
+#!/usr/bin/env sage-python23
 import os
-from sage.structure.sage_object import save
-from sage.env import SAGE_SHARE
+from six.moves import cPickle as pickle
 
+SAGE_SHARE = os.getenv('SAGE_SHARE')
 install_root = os.path.join(SAGE_SHARE, 'conway_polynomials')
 
 def create_db():
     db = {}
     from src import conway_polynomials
-    for p,n,v in conway_polynomials:
+    for p, n, v in conway_polynomials:
         if not p in db:
             db[p] = {}
         db[p][n] = v
     if not os.path.exists(install_root):
         os.makedirs(install_root)
-    save(db, os.path.join(install_root, 'conway_polynomials.sobj'))
+    with open(os.path.join(install_root, 'conway_polynomials.p'), 'wb') as f:
+        pickle.dump(db, f)
 
 if __name__ == '__main__':
     create_db()

build/pkgs/coxeter3/patches/test.output.expected

@@ -1,4 +1,4 @@
-This is Coxeter version 3.0_beta2.
+This is Coxeter version 3.1.sage.
 Enter help if you need assistance, carriage return to start the program.
 
 coxeter :