Merge branch 'u/dkrenn/sequences/k-regular-subseq' into u/dkrenn/sequences/rec-hash

* u/dkrenn/sequences/k-regular-subseq: (6376 commits)
  Updated SageMath version to 8.1
  Updated SageMath version to 8.1.rc4
  Updated tarball, add spkg-src and fix instructions
  fix for #24085 packaged as an update with non-official tarball
  Updated SageMath version to 8.1.rc3
  22851: make qepcad experimental
  sympy is needed by docbuild
  Updated SageMath version to 8.1.rc2
  Updated SageMath version to 8.1.rc1
  Added a comment with link to the relevant ticket
  Fixes https://trac.sagemath.org/ticket/24192
  Use correct format for nbserver_extensions
  Skip test on systems without RLIMIT_AS support
  Add patch fixing build errors in fpylll on Cygwin
  The path to lib/python/config does not contain the Python LD_VERSION on Python 2
  #24182 : update openssl package.
  increase tol
  Updated SageMath version to 8.1.rc0
  Add wikipedia link.
  Some reviewer comments.
  ...

Author: dkrenn

COPYING.txt

@@ -54,6 +54,7 @@ extcode                     GPLv2+
 fflas_ffpack                LGPLv2.1+
 flint                       GPLv2+
 flintqs                     GPLv2+
+fplll                       LGPLv2.1+
 freetype                    FreeType License (similar to BSD; see below)
 gap                         GPLv2+
 gcc                         GPLv3+
@@ -72,7 +73,6 @@ jinja2                      Modified BSD
 jmol                        LGPLv2.1+
 jsonschema                  MIT License
 lcalc                       GPLv2+
-libfplll                    LGPLv2.1+
 libgap                      GPLv3+
 libpng                      Custom, very similar to zlib
 linbox                      LGPLv2.1+

Makefile

@@ -71,6 +71,7 @@ distclean: build-clean
 	$(MAKE) misc-clean
 	@echo "Deleting all remaining output from build system ..."
 	rm -rf local
+	rm -f src/bin/sage-env-config
 
 # Delete all auto-generated files which are distributed as part of the
 # source tarball
@@ -129,14 +130,14 @@ ptestoptionallong: all
 configure: configure.ac src/bin/sage-version.sh m4/*.m4
 	./bootstrap -d
 
-install:
+install: all
 	@echo "******************************************************************"
-	@echo "The '$@' target is no longer supported:"
-	@echo "either build SageMath in-place or use the binary packaging scripts"
+	@echo "The '$@' target is a no-op; 'make' already does 'make install'"
+	@echo "You can change the install prefix from its default"
+	@echo "(the subdirectory 'local') by using ./configure --prefix=PREFIX"
+	@echo "You can also consider using the binary packaging scripts"
 	@echo "from https://github.com/sagemath/binary-pkg"
 	@echo "******************************************************************"
-	@exit 1
-
 
 .PHONY: default build install micro_release \
 	misc-clean bdist-clean distclean bootstrap-clean maintainer-clean \

README.md

@@ -3,7 +3,7 @@
 >   "Creating a Viable Open Source Alternative to
 >    Magma, Maple, Mathematica, and MATLAB"
 
->   Copyright (C) 2005-2016 The Sage Development Team
+>   Copyright (C) 2005-2017 The Sage Development Team
 
    http://www.sagemath.org
 
@@ -21,7 +21,8 @@ Getting Started
 ---------------
 
 This README.txt contains build instructions for Sage. If you downloaded  
-a binary, you do not need to do anything; just execute:  
+a binary, you do not need to do anything (as long as your system
+provides a SSL library ; OpenSSL is recommended) ; just execute:  
 
     ./sage
 
@@ -69,9 +70,19 @@ Installation Guide:
 
    http://doc.sagemath.org/html/en/installation
 
-__1. Make sure you have the dependencies and 5 GB of free disk space.__
+__1. Make sure your system has an SSL library and its development
+files installed.__
 
-   >* __All Linux versions:__ gcc, make, m4, perl, ranlib, and tar.  
+   >* Like Python, on which it is based, Sage uses the OpenSSL library
+   for added performance if made available by the operating system. It
+   has been shown that Sage can be successfully built against other
+   SSL libraries, with some of its features disabled.
+
+__2. Make sure you have the dependencies and 5 GB of free disk space.__
+
+   >* __All Linux versions:__ gcc, make, m4, perl, ranlib, and tar (a
+   matching set of gcc, gfortran and g++ will avoid the compilation
+   of Sage-specific compilers).__
 
    >* __Fedora or RedHat systems:__ the perl-ExtUtils-MakeMaker package.  
    (install these using your package manager)  
@@ -97,11 +108,11 @@ __1. Make sure you have the dependencies and 5 GB of free disk space.__
 
    >* Other platforms: See detailed instructions below.
 
-__2. Extract the tarball:__
+__3. Extract the tarball:__
 
          tar xvf sage-*.tar
 
-__3. cd into the Sage directory and type make:__
+__4. cd into the Sage directory and type make:__
 
          cd sage-*/
          make
@@ -316,7 +327,7 @@ SAGE_ROOT                 Root directory (sage-x.y.z in Sage tarball)
 |       ...
 |       └── zn_poly-0.9.p11.log
 ├── Makefile              Running "make" uses this file
-├── README.txt            This file
+├── README.md             This file
 ├── sage                  Script to start Sage
 ├── src                   All of Sage source (not third-party packages)
 |   ├── bin               Scripts that Sage uses internally
@@ -366,20 +377,10 @@ do.
 
          sage --sdist
 
-2. To make a binary distribution with your currently installed packages,  
-   type:
-
-         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
+   The result is placed in the directory "$SAGE_ROOT/dist/".
 
-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 7.5, Release Date: 2017-01-11
+SageMath version 8.1, Release Date: 2017-12-07

bootstrap

@@ -25,9 +25,8 @@ PKG=build/pkgs/configure
 MAKE="${MAKE:-make}"
 CONFVERSION=`cat $PKG/package-version.txt`
 
+
 bootstrap () {
-    # Get autotools from our own package into PATH (Trac #21214)
-    source src/bin/sage-env
     aclocal -I m4 && \
     automake --add-missing --copy build/make/Makefile-auto && \
     autoconf
@@ -57,8 +56,7 @@ bootstrap () {
 
 # Bootstrap by downloading the auto-generated files
 bootstrap-download () {
-    source src/bin/sage-env
-    sage-download-file configure-$CONFVERSION.tar.gz
+    build/bin/sage-download-file configure-$CONFVERSION.tar.gz
     if [ $? -ne 0 ]; then
         echo >&2 "Error: downloading configure-$CONFVERSION.tar.gz failed"
         exit 1
@@ -127,6 +125,12 @@ fi
 $MAKE bootstrap-clean 2>/dev/null
 mkdir config 2>/dev/null
 
+# Get autotools from our own package into PATH (Trac #21214).
+# If Sage has not been built yet, this will fail due to a missing
+# sage-env-config. We just ignore that error.
+source src/bin/sage-env 2>/dev/null
+
+
 if [ $ALWAYSDOWNLOAD = yes ]; then
     bootstrap-download || exit $?
 else

build/bin/sage-logger

@@ -62,12 +62,18 @@ fi
 
 mkdir -p "$logdir"
 
-if [[ "$V" = 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"
-    # Use verbose mode for output to logfiles.
-    export V=1
     ( exec>> $logfile 2>&1 ; eval "$cmd" )
     status=$?
     if [[ $status != 0 ]]; then

build/bin/sage-pip-install

@@ -15,7 +15,9 @@
 # --no-deps          : Don't install runtime dependencies from PyPI.
 # --no-index         : Don't look at the package index.
 #                      This also disables pip's version self-check.
-pip_install_flags="--ignore-installed --verbose --no-deps --no-index"
+# --isolated         : Don't read configuration files such as
+#                      ~/.pydistutils.cfg
+pip_install_flags="--ignore-installed --verbose --no-deps --no-index --isolated"
 
 # Consume any additional pip install arguments except the last one
 while [ $# -gt 1 ]; do
@@ -29,8 +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"
@@ -44,29 +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 +1,31 @@
+#!/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="$SAGE_LOCAL/bin/python2"
+fi
+
+# Check that Python is actually installed and issue an error message if not--in
+# particular if this was run from an spkg-install before Python is installed
+# this indicates that Python should be a dependency of that package.
+if [ ! -x "$PYTHON" ]; then
+     echo >&2 "Error: Tried to use Sage's Python which was not yet installed."
+     echo >&2 'If this was called from an spkg-install script for another '
+     echo >&2 'package you should add $(PYTHON) as a dependency in '
+     echo >&2 'build/pkgs/<pkg>/dependencies'
+     exit 1
+fi
+
+exec $PYTHON "$@"