Merge branch 'u/dkrenn/asy/one-times-zero' of trac.sagemath.org:sage …

…into t/19969/asy/SA-generator-log

* 'u/dkrenn/asy/one-times-zero' of trac.sagemath.org:sage: (549 commits)
  Trac #20043: add additional doctest to check parent
  move code of NotImplementedOZero to avoid merge-conflicts
  forbid asymptotic rings as base in growth groups
  fix O(0)-doctest
  correct other empty sums
  1*0 in asymptotic ring
  O(0) in asymptotic expansion
  remove old NotImplementedOZero and use new one
  new NotImplementedOZero in misc
  Updated Sage version to 7.1.beta3
  tornado depends on singledispatch
  Do not fiddle with SAGE_ROOT in the mac app start script
  Fix gamma_inc doctest
  made two doctests random pending #20028
  Fix a few more paths
  Upgrade PARI to latest master
  corrected typo infinite(ly) in a few places
  Broken seealso-link.
  Change function name.
  Pyparsing now depends on setuptools
  ...

Makefile

@@ -19,7 +19,7 @@ build: all-build
 
 # If configure was run before, rerun it with the old arguments.
 # Otherwise, run configure with argument $PREREQ_OPTIONS.
-build/make/Makefile: configure build/pkgs/*/*
+build/make/Makefile: configure build/make/deps build/pkgs/*/*
 	rm -f config.log
 	mkdir -p logs/pkgs
 	ln -s logs/pkgs/config.log config.log

README.txt

@@ -209,7 +209,7 @@ MORE DETAILED INSTRUCTIONS TO BUILD FROM SOURCE
 7. The HTML version of the documentation is built
    during the compilation process of Sage and resides in the directory:
 
-       $SAGE_ROOT/src/doc/output/html/
+       $SAGE_ROOT/local/share/doc/sage/html/
 
    OPTIONAL: If you want to build the PDF version (requires LaTeX) of
    the documentation, run:

VERSION.txt

@@ -1 +1 @@
-Sage version 7.0, released 2016-01-19
+Sage version 7.1.beta3, released 2016-02-11

build/make/deps

@@ -11,7 +11,8 @@ STARTED = $(SAGE_LOCAL)/etc/sage-started.txt
 .PHONY: all all-sage all-toolchain all-build start \
 	base toolchain toolchain-deps sagelib \
 	doc doc-html doc-html-jsmath doc-html-mathjax doc-pdf \
-	doc-clean clean sagelib-clean build-clean
+	doc-clean doc-src-clean doc-output-clean \
+	clean sagelib-clean build-clean
 
 # Build everything and start Sage.
 # Note that we put the "doc" target first in the rule below because
@@ -211,9 +212,14 @@ doc-html-jsmath: doc-html-mathjax
 doc-pdf: $(DOC_DEPENDENCIES)
 	cd ../.. && sage-logger './sage --docbuild all pdf $(SAGE_DOCBUILD_OPTS)' logs/docpdf.log
 
-doc-clean:
+doc-clean: doc-src-clean doc-output-clean
+
+doc-src-clean:
 	cd "$(SAGE_SRC)/doc" && $(MAKE) clean
 
+doc-output-clean:
+	rm -rf "$(SAGE_SHARE)/doc/sage"
+
 
 ###############################################################################
 # Cleaning up

build/make/install

@@ -5,23 +5,22 @@
 ########################################################################
 
 # Assume current directory is SAGE_ROOT/build/make
-SAGE_ROOT=`cd ../.. && pwd -P`
-SAGE_SRC="$SAGE_ROOT/src"
-SAGE_LOCAL="$SAGE_ROOT/local"
-SAGE_SHARE="$SAGE_LOCAL/share"
-SAGE_EXTCODE="$SAGE_SHARE/sage/ext"
-SAGE_LOGS="$SAGE_ROOT/logs/pkgs"
-SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed"
-SAGE_VERSION=`cat $SAGE_ROOT/VERSION.txt | sed 's+.*\ \(.*\),.*+\1+'`
+export SAGE_ROOT=`cd ../.. && pwd -P`
+export SAGE_SRC="$SAGE_ROOT/src"
+export SAGE_LOCAL="$SAGE_ROOT/local"
+export SAGE_SHARE="$SAGE_LOCAL/share"
+export SAGE_EXTCODE="$SAGE_SHARE/sage/ext"
+export SAGE_LOGS="$SAGE_ROOT/logs/pkgs"
+export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed"
+export SAGE_VERSION=`cat $SAGE_ROOT/VERSION.txt | sed 's+.*\ \(.*\),.*+\1+'`
 
 if [ -z "${SAGE_ORIG_PATH_SET}" ]; then
     SAGE_ORIG_PATH=$PATH && export SAGE_ORIG_PATH
     SAGE_ORIG_PATH_SET=True && export SAGE_ORIG_PATH_SET
 fi
-PATH="$SAGE_ROOT/build/bin:$SAGE_SRC/bin:$SAGE_LOCAL/bin:$PATH"
+export PATH="$SAGE_ROOT/build/bin:$SAGE_SRC/bin:$SAGE_LOCAL/bin:$PATH"
 
-PYTHONPATH="$SAGE_LOCAL"
-export SAGE_ROOT SAGE_SRC SAGE_LOCAL SAGE_EXTCODE SAGE_LOGS SAGE_SPKG_INST SAGE_VERSION PATH PYTHONPATH
+export PYTHONPATH="$SAGE_LOCAL"
 
 # Storing the start time of the build process. The time is stored in
 # seconds since 1970-01-01 in a hidden file called

build/pkgs/backports_abc/SPKG.txt

@@ -0,0 +1,18 @@
+= backports_abc =
+
+== Description ==
+
+A backport of recent additions to the 'collections.abc' module.
+
+== License ==
+
+Python Software Foundation License
+
+== Upstream Contact ==
+
+Home page: https://pypi.python.org/pypi/backports_abc
+
+== Dependencies ==
+
+Python, Setuptools
+

build/pkgs/backports_abc/checksums.ini

@@ -0,0 +1,4 @@
+tarball=backports_abc-VERSION.tar.gz
+sha1=76060a68d14f9d1a4198e00c3bb3711467ecb1f4
+md5=0b65a216ce9dc9c1a7e20a729dd7c05b
+cksum=1989294907

build/pkgs/backports_abc/dependencies

@@ -0,0 +1,5 @@
+$(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
+
+----------
+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/backports_abc/package-version.txt

@@ -0,0 +1 @@
+0.4

build/pkgs/backports_abc/spkg-install

@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+
+if [ -z "$SAGE_LOCAL" ]; then
+    echo >&2 "SAGE_LOCAL undefined ... exiting"
+    echo >&2 "Maybe run 'sage --sh'?"
+    exit 1
+fi
+
+cd src
+
+python setup.py install
+if [ $? -ne 0 ]; then
+    echo "Error installing backports_abc ... exiting"
+    exit 1
+fi

build/pkgs/backports_abc/type

@@ -0,0 +1 @@
+standard

build/pkgs/backports_ssl_match_hostname/checksums.ini

@@ -1,4 +1,4 @@
 tarball=backports_ssl_match_hostname-VERSION.tar.gz
-sha1=194503d8b47066c2ce8d23cab707d19d6ada2eb9
-md5=5def436c23fa2bc09aedf221d61b7017
-cksum=132706006
+sha1=1d7500574eef84c826dfaf507722cd9249bf0672
+md5=c21f63bb4729eeab399932410a012934
+cksum=541176683

build/pkgs/backports_ssl_match_hostname/package-version.txt

@@ -1 +1 @@
-3.4.0.2
+3.5.0.1

build/pkgs/certifi/checksums.ini

@@ -1,4 +1,4 @@
 tarball=certifi-VERSION.tar.gz
-sha1=f53dc8f57aaf6d69c183ebadcec52ece0a55cc3f
-md5=315ea4e50673a16ab047099f816fd32a
-cksum=3559413705
+sha1=e31ab9b9bee02511d91758e73c8598a82a0b3c35
+md5=e04b512009401603f1485380ac879cf5
+cksum=3504777269

build/pkgs/certifi/package-version.txt

@@ -1 +1 @@
-14.05.14
+2015.11.20.1

build/pkgs/cliquer/SPKG.txt

@@ -16,7 +16,4 @@ http://users.tkk.fi/pat/cliquer.html
  * None
 
 == Patches ==
- * Makefile.patch: Patch the Makefile for Sage. Remove hardcoded
-   compiler and linker flags, allow flags to be set from spkg-install.
-   More importantly, we're building cliquer as a dynamic shared library,
-   instead of a stand-alone program.
+ * autotoolized - see https://github.com/dimpase/autocliquer

build/pkgs/cliquer/checksums.ini

@@ -1,4 +1,4 @@
-tarball=cliquer-VERSION.tar.bz2
-sha1=8239530eb14c1273c32ffcf3b671dd3766084374
-md5=32b97b6689318b58d9c099e2c7769521
-cksum=3641271864
+tarball=cliquer-VERSION.tar.gz
+sha1=930ec79f64facb8ac4035a3e3702ed2b1dabd092
+md5=1d985e0bed876cc69aed43953a814a6a
+cksum=766312376

build/pkgs/cliquer/package-version.txt

@@ -1 +1 @@
-1.21.p2
+1.21.p3

build/pkgs/cliquer/spkg-check

@@ -1,35 +1,18 @@
 #!/usr/bin/env bash
 
-if [ "$SAGE_LOCAL" = "" ]; then
-    echo "SAGE_LOCAL undefined ... exiting";
-    echo "Maybe run 'sage -sh'?"
+if [ -z "$SAGE_LOCAL" ]; then
+    echo >&2 "Error: SAGE_LOCAL undefined - exiting..."
+    echo >&2 "Maybe run 'sage -sh'?"
     exit 1
 fi
 
-OPTIMIZATION_FLAGS="-O3 -funroll-loops -fomit-frame-pointer"
-# Work around a bug in gcc 4.6.0: http://gcc.gnu.org/bugzilla/show_bug.cgi?id=48774
-if [ "`testcc.sh $CC`" = GCC ] ; then
-    if $CC -dumpversion 2>/dev/null |grep >/dev/null '^4\.6\.[01]' ; then
-        echo "Warning: Working around bug in gcc 4.6.0"
-        OPTIMIZATION_FLAGS="$OPTIMIZATION_FLAGS -fno-ivopts"
-    fi
-fi
-
-CFLAGS="$CFLAGS `testcflags.sh -g $OPTIMIZATION_FLAGS -fPIC -KPIC -Wall`"
-CPPFLAGS="$CPPFLAGS -I$SAGE_LOCAL/include"
-LDFLAGS="$LDFLAGS -L$SAGE_LOCAL/lib"
+cd src
 
-# Compile for 64-bit if SAGE64 is set to 'yes'.
-# On 64-bit hardware, we don't need to set this variable to true. A
-# 64-bit cliquer library would be built on such platform.
-if [ "$SAGE64" = yes ]; then
-    CFLAGS="$CFLAGS -m64 "
-    LDFLAGS="$LDFLAGS -m64 "
+echo "Now building and running cliquer's test suite..."
+$MAKE check
+if [ $? -ne 0 ]; then
+    echo >&2 "Error: The cliquer's test suite failed."
+    exit 1
 fi
 
-# Export everything
-export CFLAGS
-export CPPFLAGS
-export LDFLAGS
-
-cd src && $MAKE test
+echo "The cliquer's test suite passed successfully."

build/pkgs/cliquer/spkg-install

@@ -1,43 +1,14 @@
 #!/usr/bin/env bash
 
-OPTIMIZATION_FLAGS="-O3 -funroll-loops -fomit-frame-pointer"
-# Work around a bug in gcc 4.6.0: http://gcc.gnu.org/bugzilla/show_bug.cgi?id=48774
-if [ "`testcc.sh $CC`" = GCC ] ; then
-    if $CC -dumpversion 2>/dev/null |grep >/dev/null '^4\.6\.[01]' ; then
-        echo "Warning: Working around bug in gcc 4.6.0"
-        OPTIMIZATION_FLAGS="$OPTIMIZATION_FLAGS -fno-ivopts"
-    fi
-fi
-
-CFLAGS="$CFLAGS `testcflags.sh -g $OPTIMIZATION_FLAGS -fPIC -KPIC -Wall`"
-CPPFLAGS="$CPPFLAGS -I$SAGE_LOCAL/include"
-
-# Compile for 64-bit if SAGE64 is set to 'yes'.
-# On 64-bit hardware, we don't need to set this variable to true. A
-# 64-bit cliquer library would be built on such platform.
-if [ "$SAGE64" = yes ]; then
-    echo "Building a 64-bit version of cliquer"
-    CFLAGS="$CFLAGS -m64 "
-    LDFLAGS="$LDFLAGS -m64 "
-fi
-
-# Flags for building a dynamically linked shared object.
-if [ "$UNAME" = "Darwin" ]; then
-    SAGESOFLAGS="-dynamiclib -single_module -flat_namespace -undefined dynamic_lookup"
-elif [ "$UNAME" = "SunOS" ]; then
-    SAGESOFLAGS="-shared -Wl,-h,libcliquer.so -Wl,-ztext"
-else
-    SAGESOFLAGS="-shared -Wl,-soname,libcliquer.so"
+if [ -z "$SAGE_LOCAL" ]; then
+    echo >&2 "SAGE_LOCAL undefined - exiting..."
+    echo >&2 "Maybe run 'sage -sh'?"
+    exit 1
 fi
 
-# Export everything
-export CFLAGS
-export CPPFLAGS
-export LDFLAGS
-export SAGESOFLAGS
-
 cd src
 
+echo "Applying patches..."
 # Apply all patches
 for patch in ../patches/*.patch; do
     [ -r "$patch" ] || continue  # Skip non-existing or non-readable patches
@@ -49,22 +20,16 @@ for patch in ../patches/*.patch; do
     fi
 done
 
-$MAKE
+echo "Configuring..."
+./configure --prefix="$SAGE_LOCAL" --disable-static --libdir="$SAGE_LOCAL/lib"
 if [ $? -ne 0 ]; then
-    echo >&2 "Failed to compile cliquer"
-    exit 1
+   echo >&2 "Error configuring cliquer"
+   exit 1
 fi
 
-rm -rf "$SAGE_LOCAL/include/cliquer/"
-mkdir -p "$SAGE_LOCAL/include/cliquer/"
-cp *.h "$SAGE_LOCAL/include/cliquer/"
-
-if [ "$UNAME" = "Darwin" ]; then
-    cp -f libcliquer.so "$SAGE_LOCAL/lib/libcliquer.dylib"
-    install_name_tool -id "${SAGE_LOCAL}"/lib/libcliquer.dylib "${SAGE_LOCAL}"/lib/libcliquer.dylib
-elif [ "$UNAME" = "CYGWIN" ]; then
-    cp -f libcliquer.so "$SAGE_LOCAL/lib/libcliquer.dll"
+echo "Building and installing ..."
+$MAKE install
+if [ $? -ne 0 ]; then
+    echo >&2 "Error installing cliquer"
+    exit 1
 fi
-
-# Copy this in all cases, in any case it doesn't hurt.
-cp -f libcliquer.so "$SAGE_LOCAL/lib/libcliquer.so"

build/pkgs/cliquer/spkg-src

@@ -0,0 +1,23 @@
+#!/bin/sh
+#
+# creates the tarball in the current dir, to be moved to ../../../upstream
+
+#PATCHLEVEL=".p0"
+PATCHLEVEL=
+
+rm -rf autocliquer/
+git clone https://github.com/dimpase/autocliquer.git
+cd autocliquer/
+
+VERSION=`autoconf --trace='AC_INIT:$2'`
+autoreconf -fi
+automake --add-missing --copy
+./configure
+
+rm -f cliquer-$VERSION.tar.gz
+make dist
+mv cliquer-$VERSION.tar.gz ../
+cd ..
+rm -rf autocliquer/ 
+
+

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=631a348f0ac864b3ec37dfcb1d7fab79e213a075
-md5=5759d84c96102aee89c7eaea0aadf842
-cksum=2510923339
+sha1=603a0399bf37b613bda1b82cd2bc05058a009104
+md5=15a9898dbcb629850559d7a520ed141f
+cksum=3386674131

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-140
+144

build/pkgs/cython/checksums.ini

@@ -1,4 +1,4 @@
 tarball=Cython-VERSION.tar.gz
-sha1=d5592dc3d529c55a5ef95346caccf11c556993bd
-md5=813df20f7ce5f00e60568e0371fbd07c
-cksum=365027876
+sha1=fc574c5050cd5a8e34435432e2a4a693353ed807
+md5=157df1f69bcec6b56fd97e0f2e057f6e
+cksum=346066359

build/pkgs/cython/package-version.txt

@@ -1 +1 @@
-0.23.3
+0.23.4