Merge branch 't/21325/sequences/k-regular-subseq' into t/21319/sequen…

…ces/rec-hash

* t/21325/sequences/k-regular-subseq: (2027 commits)
  Python3: xrange
  Python3: absolut import
  Python3: absolute import
  Python3: izip
  Python3: __nonzero__
  Trac #21295: fix typos
  Trac #21295: fix ReST error
  Updated SageMath version to 7.5
  Updated SageMath version to 7.5.rc3
  Use a deterministic sorting key for number fields
  Updated SageMath version to 7.5.rc2
  22136: pkg version/chksum
  Upgrade to Python 2.7.13
  Updated SageMath version to 7.5.rc1
  amending coment and message in setup.py
  Move autogen to a more appropriate location.
  22095: better doctest
  run tests only in spkg-check. Also run spkg-check with the same options as spkg-install
  SAGERUNTIME requires psutil
  22095: zero should be zero
  ...

.dir-locals.el

@@ -0,0 +1,9 @@
+;;; Directory Local Variables
+;;; For more information see (info "(emacs) Directory Variables")
+
+((nil
+  ;; Use space instead of tabs for indentation
+  (indent-tabs-mode . nil))
+ (makefile-mode
+  ;; But use tabs in Makefiles
+  (indent-tabs-mode . t)))

COPYING.txt

@@ -8,6 +8,9 @@ free open source license as defined at http://www.opensource.org/.
 The whole Sage software distribution is licensed under the General
 Public License, version 3 (no other versions!).
 
+All Sage documentation is licensed under Creative Commons 3.0 BY-SA
+License.
+
 Some of the code available in *optional* Sage packages (not included
 in sage-*.tar) are licensed under more restrictive conditions.
 

VERSION.txt

@@ -1 +1 @@
-SageMath version 7.4.beta2, Release Date: 2016-08-26
+SageMath version 7.5, Release Date: 2017-01-11

bootstrap

@@ -26,6 +26,8 @@ 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

build/README.txt

@@ -0,0 +1,15 @@
+This directory contains the build system of Sage, the distribution.
+
+Subdirectories:
+
+ - bin: Various scripts needed at build time.  Not installed.
+
+ - make: Makefiles and related scripts.
+
+ - pkgs: New-style sage packages.
+
+ - sage_bootstrap: Python utility library for dealing with
+   third-party tarballs and building Sage. See its README for
+   more information.  Not installed.
+
+ - test: Test suite for sage_bootstrap.

build/bin/sage-apply-patches

@@ -0,0 +1,78 @@
+#!/usr/bin/env bash
+#
+# sage-apply-patches [-p<num>] [-d patch-subdir] [patch-dir] -- [...]
+#
+# Apply any patches to original spkg sources.  Patch files must have
+# the .patch extension.
+#
+# By default the patches are applied from ../patches/ using the -p1
+# option, and it is assumed that the patches are being applied from
+# the root of the package source.
+#
+# An optional patch subdirectory may be specified with the -d flag.
+# For example `sage-apply-patches -d cygwin` applies only those
+# patches under <patch-dir>/cygwin.
+#
+# The -p<num> arg is the argument accepted by the `patch` command,
+# and overrides the default -p1
+#
+# Any additional arguments following " -- " are passed directly
+# to the `patch` command.
+#
+#***************************************************************************
+#
+#  Distributed under the terms of the GNU General Public License (GPL)
+#  as published by the Free Software Foundation; either version 2 of
+#  the License, or (at your option) any later version.
+#                  http://www.gnu.org/licenses/
+#***************************************************************************
+
+patchdir="../patches"
+patch_subdir=""
+patch_strip="-p1"
+patch_args_sep=""
+patch_args="--no-backup-if-mismatch"
+
+while [[ $# > 0 ]]; do
+    if [[ -z "$patch_args_sep" ]]; then
+        case $1 in
+            -d)
+                patch_subdir="${2%/}"
+                shift
+                ;;
+            -p[0-9])
+                patch_strip="$1"
+                ;;
+            --)
+                patch_args_sep="$1"
+                ;;
+            *)
+                patchdir="${1%/}"
+                ;;
+        esac
+    else
+        patch_args="$patch_args $1"
+    fi
+
+    shift
+done
+
+patchdir="${patchdir}/${patch_subdir}"
+patchdir="${patchdir%/}"
+patches=( "${patchdir}"/*.patch )
+
+if [[ -r "${patches[0]}" ]]; then
+    echo "Applying patches from ${patchdir}..."
+    for patch in ${patches[@]}; do
+        # Skip non-existing or non-readable patches
+        [ -r "$patch" ] || continue
+        echo "Applying $patch"
+        patch $patch_strip $patch_args < "$patch"
+        if [ $? -ne 0 ]; then
+            echo >&2 "Error applying '$patch'"
+            exit 1
+        fi
+    done
+else
+    >&2 echo "No patch files found in $patchdir"
+fi

build/bin/sage-logger

@@ -44,26 +44,50 @@ fi
 # Use sed option to reduce buffering, to make the output appear more
 # smoothly. For GNU sed, this is the --unbuffered option.
 # For BSD sed (which is also on OS X), this is the -l option.
-if sed </dev/null 2>/dev/null --unbuffered ""; then
-    SED="sed --unbuffered"
-elif sed </dev/null 2>/dev/null -l ""; then
-    SED="sed -l"
+if [ -n "$prefix" ]; then
+    if sed </dev/null 2>/dev/null --unbuffered ""; then
+        SED="sed --unbuffered"
+    elif sed </dev/null 2>/dev/null -l ""; then
+        SED="sed -l"
+    else
+        SED="sed"
+    fi
+
+    # eval needed to get the quoting around the regexp right
+    SED="eval $SED 's/^/$prefix/'"
 else
-    SED="sed"
+    # Make SED a useless use of cat
+    SED=cat
 fi
 
 mkdir -p "$logdir"
 
-# Redirect stdout and stderr to a subprocess running tee.
-# We trap SIGINT such that SIGINT interrupts the main process being
-# run, not the logging.
-( exec 2>&1; eval "$cmd" ) | \
-    ( trap '' SIGINT; tee -a "$logfile" | $SED "s/^/$prefix/" )
+if [[ "$V" = 0 && $use_prefix = true ]]; then
+    # Silent build.
+    # Similar to https://www.gnu.org/software/automake/manual/html_node/Automake-Silent-Rules.html#Automake-Silent-Rules
+    echo "[$logname] installing. Log file: $logfile"
+    # Use verbose mode for output to logfiles.
+    export V=1
+    ( exec>> $logfile 2>&1 ; eval "$cmd" )
+    status=$?
+    if [[ $status != 0 ]]; then
+        echo "  [$logname] error installing, exit status $status. Log file: $logfile"
+    else
+        echo "  [$logname] successfully installed."
+    fi
+    exit $status
+else
+    # Redirect stdout and stderr to a subprocess running tee.
+    # We trap SIGINT such that SIGINT interrupts the main process being
+    # run, not the logging.
+    ( exec 2>&1; eval "$cmd" ) | \
+        ( trap '' SIGINT; tee -a "$logfile" | $SED )
 
-pipestatus=(${PIPESTATUS[*]})
+    pipestatus=(${PIPESTATUS[*]})
 
-if [ ${pipestatus[1]} -ne 0 ]; then
-    exit ${pipestatus[1]}
-else
-    exit ${pipestatus[0]}
+    if [ ${pipestatus[1]} -ne 0 ]; then
+        exit ${pipestatus[1]}
+    else
+        exit ${pipestatus[0]}
+    fi
 fi

build/bin/sage-pip-install

@@ -0,0 +1,72 @@
+#!/usr/bin/env bash
+# This command is specifically for pip-installing from a local
+# source directory, as opposed to from a package index via package
+# name.  That is, it is for pip-installing Sage spkgs from their
+# extracted upstream sources.
+#
+# This ensures that any previous installations of the same package
+# are uninstalled first.
+
+# Default arguments for all packages installed with `pip install`
+# --ignore-installed : Force pip to re-install package even if it thinks it's
+#                      already installed (for which it sometimes gets false
+#                      positives for partially-installed packages).
+# --verbose          : Display the output when running setup.py.
+# --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"
+
+# Consume any additional pip install arguments except the last one
+while [ $# -gt 1 ]; do
+    pip_install_flags="$pip_install_flags $1"
+    shift
+done
+
+# Last argument must be "." and will be ignored
+if [ "$1" != "." ]; then
+    echo >&2 "$0 requires . as final argument"
+    exit 1
+fi
+
+# Find out the name of the package that we are installing
+name="$(python setup.py --name)"
+
+if [ $? -ne 0 ]; then
+    echo >&2 "Error: could not determine package name"
+    exit 1
+fi
+
+if [ $(echo "$name" | wc -l) -gt 1 ]; then
+    name="$(echo "$name" | tail -1)"
+    echo >&2 "Warning: This package has a badly-behaved setup.py which outputs"
+    echo >&2 "more than the package name for 'setup.py --name'; using the last"
+    echo >&2 "line as the package name: $name"
+fi
+
+# We should avoid running pip while uninstalling a package because that
+# is prone to race conditions. Therefore, we use a lockfile while
+# running pip. This is implemented in the Python script pip-lock.
+
+# Keep uninstalling as long as it succeeds
+while true; do
+    out=$(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).
+# 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
+# to apply a shared lock)
+echo "Installing package $name using pip"
+exec pip-lock SHARED install $pip_install_flags .