Merge branch 'develop (7.1.beta3)' into 18836

.gitignore

@@ -75,4 +75,10 @@ $RECYCLE.BIN/
 #################
 *.sage-chat
 *.sage-history
-*.syncdoc*
+*.syncdoc*
+
+###########
+# Jupyter #
+###########
+.ipynb_checkpoints
+Untitled*.ipynb

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 6.10, released 2015-12-18
+Sage version 7.1.beta3, released 2016-02-11

bootstrap

@@ -72,6 +72,14 @@ bootstrap-download () {
 save () {
     set -e
 
+    # Check that config.guess is sufficiently recent
+    if ! grep '^timestamp=.*201[5-9]' config/config.guess >/dev/null; then
+        echo >&2 "Error: config.guess is outdated:"
+        grep >&2 '^timestamp=' config/config.guess
+        echo >&2 "You should update the 'gnuconfig' or 'automake' package and try again"
+        exit 63
+    fi
+
     # Create configure tarball
     echo "Creating $CONFBALL..."
     mkdir -p upstream

build/bin/sage-spkg

@@ -453,11 +453,23 @@ fi
 # Handle --info
 ##################################################################
 
+# Usage: zip_to_tar $PKG_FILE_NAME
+# Outputs (to stdout) a .tar version of a .zip archive
+zip_to_tar()
+{
+    tmpdir="$(mktemp -d)"       &&
+	tmpfile="$(mktemp).tar" &&
+	cd "$tmpdir"            &&
+	sage-unzip "$1"         &&
+	tar -cf "$tmpfile" *    &&
+	cat "$tmpfile"
+}
+
 # Usage: uncompress_spkg $PKG_FILE_NAME
 # Uncompresses a spkg to stdout.
 uncompress_spkg()
 {
-    lbzip2 -d -c "$1" 2>/dev/null || bzip2 -d -c "$1" 2>/dev/null || gzip -d -c "$1" 2>/dev/null || cat "$1"
+    lbzip2 -d -c "$1" 2>/dev/null || bzip2 -d -c "$1" 2>/dev/null || gzip -d -c "$1" 2>/dev/null || zip_to_tar "$1" || cat "$1"
 }
 
 if [ $INFO -ne 0 -a -z "$USE_LOCAL_SCRIPTS" ]; then
@@ -543,7 +555,16 @@ fi
 
 if [ "$USE_LOCAL_SCRIPTS" = yes ]; then
     shopt -s nocaseglob      # see trac:16415
-    mv "${PKG_NAME_UPSTREAM%.tar*}"* src
+    # Strip file extension from the archive file and hope (as per
+    # automake standards) that this is the same as the directory name
+    # inside; move the directory to "src".  (This goes wrong for
+    # upstream package archives that have been renamed to appease some
+    # other Sage script, such as "latte-int", whose archive is renamed
+    # to "latte_int".)
+    mv "$(echo "$PKG_NAME_UPSTREAM" | sed 's/\.zip$//g;s/\.tgz$//g;s/\.tar\.gz$//g;s/\.tar\.xz$//g;s/\.tar\.lz$//g;s/\.tar\.bz2$//g;s/\.tar$//g')"* src
+    # Do not check for errors here; the "mv" fails in the situation
+    # mentioned above, and the package-specific script needs to do
+    # this work itself.
     shopt -u nocaseglob
     echo "Finished set up"
 else

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
@@ -65,7 +66,6 @@ toolchain-deps:
 	$(MAKE) $(INST)/$(SAGE_MP_LIBRARY)
 	$(MAKE) $(INST)/$(MPFR)
 	$(MAKE) $(INST)/$(MPC)
-	$(MAKE) $(INST)/$(PPL)
 
 # Everything needed to start up Sage using "./sage".  Of course, not
 # every part of Sage will work.  It does not include Maxima for example.
@@ -212,9 +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/4ti2/checksums.ini

@@ -1,4 +1,4 @@
 tarball=4ti2-VERSION.tar.gz
-sha1=afd61b1479f61bfbb1996ab833c43996c401385a
-md5=289d50cf7932488adc24c9c308bbafcf
-cksum=1124458672
+sha1=9a9a6913bcd52b667355a7df7fa954ca101054cb
+md5=90def0d6b01a0247e439356777467497
+cksum=439147307

build/pkgs/4ti2/package-version.txt

@@ -1 +1 @@
-1.6.5
+1.6.7

build/pkgs/4ti2/type

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

build/pkgs/arb/package-version.txt

@@ -1 +1 @@
-2.7.0.p0
+2.7.0.p1

build/pkgs/arb/patches/flint_includes.patch

@@ -1,5 +1,7 @@
 Fix FLINT include paths
 
+See https://github.com/fredrik-johansson/arb/pull/55
+
 diff -ru a/acb/test/t-rising2_ui_bs.c b/acb/test/t-rising2_ui_bs.c
 --- a/acb/test/t-rising2_ui_bs.c	2015-07-14 15:59:03.000000000 +0200
 +++ b/acb/test/t-rising2_ui_bs.c	2015-11-28 20:14:34.089305460 +0100

build/pkgs/arb/patches/mpn_mul_vars.patch

@@ -0,0 +1,27 @@
+Use variable names which do not conflict with FLINT
+
+See https://github.com/fredrik-johansson/arb/pull/78
+
+diff --git a/arf.h b/arf.h
+index 6f67834..b8e1927 100644
+--- a/arf.h
++++ b/arf.h
+@@ -870,12 +870,12 @@ void arf_randtest_special(arf_t x, flint_rand_t state, slong bits, slong mag_bit
+         } \
+         else if ((_xn) == 2) \
+         { \
+-            mp_limb_t __x1, __x0, __y1, __y0; \
+-            __x0 = (_x)[0]; \
+-            __x1 = (_x)[1]; \
+-            __y0 = (_y)[0]; \
+-            __y1 = (_y)[1]; \
+-            nn_mul_2x2((_z)[3], (_z)[2], (_z)[1], (_z)[0], __x1, __x0, __y1, __y0); \
++            mp_limb_t __arb_x1, __arb_x0, __arb_y1, __arb_y0; \
++            __arb_x0 = (_x)[0]; \
++            __arb_x1 = (_x)[1]; \
++            __arb_y0 = (_y)[0]; \
++            __arb_y1 = (_y)[1]; \
++            nn_mul_2x2((_z)[3], (_z)[2], (_z)[1], (_z)[0], __arb_x1, __arb_x0, __arb_y1, __arb_y0); \
+         } \
+         else if ((_x) == (_y)) \
+         { \

build/pkgs/atlas/configuration.py

@@ -161,6 +161,8 @@ def close(self):
 
 conf['generic_binary?'] = (os.environ.get('SAGE_FAT_BINARY', 'no') == 'yes')
 
+conf['user'] = os.environ.get('ATLAS_CONFIGURE', '')
+
 ######################################################################
 ### bit width
 ######################################################################
@@ -253,9 +255,5 @@ def close(self):
 ######################################################################
 
 print("Configuration:")
-for key, value in conf.items():
-    print('    '+str(key)+': '+str(value))
-
-
-
-
+for k in sorted(conf, key=str.lower):
+    print('    {}: {}'.format(k, conf[k]))

build/pkgs/atlas/spkg-install

@@ -60,7 +60,7 @@ def assert_success(rc, good=None, bad=None):
     traceback.print_stack(file=sys.stdout)
     print('-'*60)
     if bad is not None:
-        print('Error: ', bad)
+        print('Error:', bad)
     sys.exit(rc)
 
 
@@ -247,13 +247,18 @@ def configure(arch=None, isa_ext=None):
     - ``arch`` -- ``None`` or one of ``ATLAS_MACHTYPE``
 
     - ``isa_ext`` -- ``None`` or a sublist of ``ATLAS_ISAEXT``
+
+    OUTPUT: 0 if ``configure`` was successful, 1 if it failed.
     """
-    if arch is None:
-        arch, isa_ext, thread_limit = configure_options_from_environment()
-    if arch=='fast':
-        arch, isa_ext, thread_limit = configure_fast()
-    if arch=='generic' or arch=='base':
-        arch, isa_ext, thread_limit = configure_base()
+    try:
+        if arch is None:
+            arch, isa_ext, thread_limit = configure_options_from_environment()
+        if arch == 'fast':
+            arch, isa_ext, thread_limit = configure_fast()
+        if arch == 'generic' or arch == 'base':
+            arch, isa_ext, thread_limit = configure_base()
+    except NotImplementedError:
+        return 1
 
     print('Running configure with arch = '+str(arch)+ \
         ', isa extensions '+str(isa_ext), ' thread limit '+str(thread_limit))
@@ -292,8 +297,9 @@ def configure(arch=None, isa_ext=None):
     ## typically adds 3-4 hours of install time
     cmd += ' -Si latune 0'
 
-    # -Fa alg -fPIC: set flags so we can build dynamic libraries
-    cmd += ' -Fa alg -fPIC'
+    # Set flags for all compilers so we can build dynamic libraries
+    ALLFLAGS = "-fPIC " + os.environ["LDFLAGS"]
+    cmd += ' -Fa alg "{}"'.format(ALLFLAGS)
 
     # set number of threads limit: 0 = off, -1 = unlimited
     if thread_limit is not None:
@@ -340,6 +346,10 @@ def configure(arch=None, isa_ext=None):
         isa_extension = sum(1 << ATLAS_ISAEXT.index(x) for x in isa_ext)
         cmd += ' -V '+str(isa_extension)
 
+    # Custom configure options
+    if conf['user']:
+        cmd += " " + conf['user']
+
     rc = system_with_flush(cmd)
     make_check_enums()
     return rc
@@ -452,7 +462,10 @@ def build(arch=None, isa_ext=None):
     Return ``0`` if successfull.
     """
     rc = configure(arch, isa_ext)
-    assert_success(rc, bad='Configure failed.', good='Finished configuring ATLAS.')
+    if rc:
+        print("Configure failed.")
+        return rc
+    print("Finished configuring ATLAS.")
     return make_atlas()
 
 def build_tuning():

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_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/bliss/checksums.ini

@@ -1,4 +1,4 @@
-tarball=bliss-VERSION.tar.gz
-sha1=46322da1a03750e199e156d8967d88b89ebad5de
-md5=b936d5d54b618a77ed59dfeeced3fa58
-cksum=76340303
+tarball=bliss-VERSION.zip
+sha1=ca86a10c674a5b3ec9fa163edf6ffde002699628
+md5=72f2e310786923b5c398ba0fc40b42ce
+cksum=1722393284