Merge tag '6.6.beta5' into rings/complex_interval_acb

Sage version 6.6.beta5

.gitignore

@@ -29,7 +29,9 @@
 .\#*
 
 # Vim
-*.s[a-w][a-z]
+*.swp
+*.swo
+*.swn
 *.un~
 .netrwhist
 

COPYING.txt

@@ -30,10 +30,12 @@ SOFTWARE                    LICENSE
 -----------------------------------------------------------------------
 atlas                       Modified BSD
 boehm_gc                    MIT-like license (see below)
+backports_ssl_match_hostname  Python License
 boost_cropped               Boost Software License (see below)
 bzip2                       BSD-ish (see below)
 cddlib                      GPLv2+
 cephes                      "may be used freely" (see below)
+certifi                     ISC
 cliquer                     GPLv2+
 conway_polynomials          None (database)
 cvxopt                      GPLv2+
@@ -65,6 +67,7 @@ iml                         COPYING is GPLv2, source files state modified BSD
 ipython                     Modified BSD
 jinja2                      Modified BSD
 jmol                        LGPLv2.1+
+jsonschema                  MIT License
 lcalc                       GPLv2+
 libfplll                    LGPLv2.1+
 libgap                      GPLv3+
@@ -73,6 +76,7 @@ linbox                      LGPLv2.1+
 lrcalc                      GPLv2+
 m4ri                        GPLv2+
 m4rie                       GPLv2+
+mathjax                     Apache License 2.0
 matplotlib                  Matplotlib License (BSD compatible, see below)
 maxima                      See below
 mpc                         LGPLv3+

Makefile

@@ -59,6 +59,13 @@ doc: doc-html
 doc-html: build
 	$(PIPE) "./sage --docbuild --no-pdf-links all html $(SAGE_DOCBUILD_OPTS) 2>&1" "tee -a logs/dochtml.log"
 
+# 'doc-html-no-plot': build docs without building the graphics coming
+# from the '.. plot' directive, in case you want to save a few
+# megabytes of disk space. 'doc-clean' is a prerequisite because the
+# presence of graphics is cached in src/doc/output.
+doc-html-no-plot: build doc-clean
+	$(PIPE) "./sage --docbuild --no-pdf-links --no-plot all html $(SAGE_DOCBUILD_OPTS) 2>&1" "tee -a logs/dochtml.log"
+
 doc-html-mathjax: build
 	$(PIPE) "./sage --docbuild --no-pdf-links all html -j $(SAGE_DOCBUILD_OPTS) 2>&1" "tee -a logs/dochtml.log"
 

VERSION.txt

@@ -1 +1 @@
-Sage version 6.5.beta6, released 2015-01-24
+Sage version 6.6.beta5, released 2015-03-13

build/deps

@@ -23,10 +23,12 @@ all:
 # All targets except for the base packages
 all-sage: \
      $(INST)/$(ATLAS) \
+     $(INST)/$(BACKPORTS_SSL_MATCH_HOSTNAME) \
      $(INST)/$(BOEHM_GC) \
      $(INST)/$(BOOST_CROPPED) \
      $(INST)/$(CDDLIB) \
      $(INST)/$(CEPHES) \
+     $(INST)/$(CERTIFI) \
      $(INST)/$(CLIQUER) \
      $(INST)/$(COMBINATORIAL_DESIGNS) \
      $(INST)/$(CONWAY) \
@@ -58,13 +60,15 @@ all-sage: \
      $(INST)/$(IPYTHON) \
      $(INST)/$(JINJA2) \
      $(INST)/$(JMOL) \
+     $(INST)/$(JSONSCHEMA) \
      $(INST)/$(LCALC) \
      $(INST)/$(LRCALC) \
      $(INST)/$(LIBGAP) \
      $(INST)/$(LIBPNG) \
      $(INST)/$(LINBOX) \
      $(INST)/$(M4RI) \
      $(INST)/$(M4RIE) \
+     $(INST)/$(MATHJAX) \
      $(INST)/$(MATPLOTLIB) \
      $(INST)/$(MAXIMA) \
      $(INST)/$(MPC) \
@@ -308,6 +312,9 @@ $(INST)/$(GAP): $(INST)/$(NCURSES) $(INST)/$(READLINE) $(INST)/$(SAGE_MP_LIBRARY
 $(INST)/$(LIBGAP): $(INST)/$(GAP)
 	+$(PIPE) "$(SAGE_SPKG) $(LIBGAP) 2>&1" "tee -a $(SAGE_LOGS)/$(LIBGAP).log"
 
+$(INST)/$(JSONSCHEMA): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
+	+$(PIPE) "$(SAGE_SPKG) $(JSONSCHEMA) 2>&1" "tee -a $(SAGE_LOGS)/$(JSONSCHEMA).log"
+
 $(INST)/$(IPYTHON): $(INST)/$(PYTHON) $(INST)/$(JINJA2) $(INST)/$(TORNADO) $(INST)/$(PYZMQ)
 	+$(PIPE) "$(SAGE_SPKG) $(IPYTHON) 2>&1" "tee -a $(SAGE_LOGS)/$(IPYTHON).log"
 
@@ -379,9 +386,19 @@ $(INST)/$(PYPARSING): $(INST)/$(PYTHON)
 $(INST)/$(PYZMQ): $(INST)/$(PYTHON) $(INST)/$(ZEROMQ) $(INST)/$(SETUPTOOLS)
 	+$(PIPE) "$(SAGE_SPKG) $(PYZMQ) 2>&1" "tee -a $(SAGE_LOGS)/$(PYZMQ).log"
 
-$(INST)/$(TORNADO): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
+$(INST)/$(CERTIFI):  $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
+	+$(PIPE) "$(SAGE_SPKG) $(CERTIFI) 2>&1" "tee -a $(SAGE_LOGS)/$(CERTIFI).log"
+
+$(INST)/$(BACKPORTS_SSL_MATCH_HOSTNAME): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
+	+$(PIPE) "$(SAGE_SPKG) $(BACKPORTS_SSL_MATCH_HOSTNAME) 2>&1" "tee -a $(SAGE_LOGS)/$(BACKPORTS_SSL_MATCH_HOSTNAME).log"
+
+$(INST)/$(TORNADO): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS) \
+                    $(INST)/$(BACKPORTS_SSL_MATCH_HOSTNAME) $(INST)/$(CERTIFI)
 	+$(PIPE) "$(SAGE_SPKG) $(TORNADO) 2>&1" "tee -a $(SAGE_LOGS)/$(TORNADO).log"
 
+$(INST)/$(MATHJAX):
+	+$(PIPE) "$(SAGE_SPKG) $(MATHJAX) 2>&1" "tee -a $(SAGE_LOGS)/$(MATHJAX).log"
+
 $(INST)/$(MATPLOTLIB): $(INST)/$(PYTHON) $(INST)/$(NUMPY) \
                        $(INST)/$(FREETYPE) $(INST)/$(LIBPNG) \
                        $(INST)/$(GDMODULE) $(INST)/$(DATEUTIL) \
@@ -510,7 +527,8 @@ $(INST)/csage: $(INST)/$(SCONS) \
        $(INST)/$(SAGE_MP_LIBRARY) \
        $(INST)/$(NTL) \
        $(INST)/$(PARI) \
-       $(INST)/$(PYTHON)
+       $(INST)/$(PYTHON) \
+       $(CSAGE_SOURCES)
 	if [ -z "$$SAGE_INSTALL_FETCH_ONLY" ]; then \
 		cd $(SAGE_SRC) && source bin/sage-env && cd c_lib && \
 		$(PIPE) 'time scons -Q install 2>&1' 'tee -a $(SAGE_LOGS)/csage-$(SAGE_VERSION).log' && \

build/install

@@ -296,11 +296,13 @@ newest_version() {
 cat >&5 <<EOF
 # Standard packages
 ATLAS=`newest_version atlas`
+BACKPORTS_SSL_MATCH_HOSTNAME=`newest_version backports_ssl_match_hostname`
 BOEHM_GC=`newest_version boehm_gc`
 BOOST_CROPPED=`newest_version boost_cropped`
 BZIP2=`newest_version bzip2`
 CDDLIB=`newest_version cddlib`
 CEPHES=`newest_version cephes`
+CERTIFI=`newest_version certifi`
 CLIQUER=`newest_version cliquer`
 COMBINATORIAL_DESIGNS=`newest_version combinatorial_designs`
 CONWAY=`newest_version conway_polynomials`
@@ -333,13 +335,15 @@ IML=`newest_version iml`
 IPYTHON=`newest_version ipython`
 JINJA2=`newest_version jinja2`
 JMOL=`newest_version jmol`
+JSONSCHEMA=`newest_version jsonschema`
 LCALC=`newest_version lcalc`
 LRCALC=`newest_version lrcalc`
 LIBGAP=`newest_version libgap`
 LIBPNG=`newest_version libpng`
 LINBOX=`newest_version linbox`
 M4RI=`newest_version m4ri`
 M4RIE=`newest_version m4rie`
+MATHJAX=`newest_version mathjax`
 MATPLOTLIB=`newest_version matplotlib`
 MAXIMA=`newest_version maxima`
 MPC=`newest_version mpc`
@@ -418,6 +422,11 @@ if [ "$need_to_install_gcc" = yes ]; then
 fi
 echo >&5
 
+echo >&5 'CSAGE_SOURCES = \'
+for file in "$SAGE_SRC/c_lib/src/"*.c "$SAGE_SRC/c_lib/src/"*.cpp "$SAGE_SRC/c_lib/include"/*.h; do
+    echo >&5 "                \$(SAGE_SRC)${file#$SAGE_SRC} \\"
+done
+echo >&5
 echo >&5 'SCRIPT_SOURCES = \'
 for file in "$SAGE_SRC/bin/"*; do
     echo >&5 "                 \$(SAGE_SRC)${file#$SAGE_SRC} \\"

build/pkgs/arb/patches/dedekind_sum.patch

@@ -0,0 +1,28 @@
+Patch tests of arb-2.5 to be compatible with flint-2.4.4
+
+Arb's testsuite, src/acb_modular/test/t-epsilon_arg.c, calls
+fmpq_dedekind_sum. However, this function does not exist in
+flint-2.4.4.
+
+fmpq_dedekind_sum was introduced in
+https://github.com/wbhart/flint2/commit/64f656fb8db591ea11db606c7905de9f47b05e84
+and arith_dedekind_sum is now an alias to fmpq_dedekind_sum.
+
+So I patch src/acb_modular/test/t-epsilon_arg.c to call
+arith_dedekind_sum instead of fmpq_dedekind_sum.
+
+See also http://trac.sagemath.org/ticket/17688#comment:8 .
+
+diff -r -u src/acb_modular/test/t-epsilon_arg.c new/acb_modular/test/t-epsilon_arg.c
+--- src/acb_modular/test/t-epsilon_arg.c	2015-01-28 19:20:07.000000000 +0200
++++ new/acb_modular/test/t-epsilon_arg.c	2015-02-11 14:07:30.947675579 +0200
+@@ -49,7 +49,7 @@
+         fmpz_mul_ui(fmpq_denref(arg), c, 12);
+         fmpq_canonicalise(arg);
+
+-        fmpq_dedekind_sum(t, d, c);
++        arith_dedekind_sum(t, d, c);
+         fmpq_sub(arg, arg, t);
+
+         fmpq_clear(t);
+Only in new/acb_modular/test: t-epsilon_arg.c~

build/pkgs/arb/spkg-install

@@ -2,6 +2,15 @@
 
 cd src
 
+for patch in ../patches/*.patch; do
+    [ -r "$patch" ] || continue  # Skip non-existing or non-readable patches
+    patch -p1 <"$patch"
+    if [ $? -ne 0 ]; then
+        echo >&2 "Error applying '$patch'"
+        exit 1
+    fi
+done
+
 ./configure --prefix="$SAGE_LOCAL" --with-flint="$SAGE_LOCAL" \
     --with-gmp="$SAGE_LOCAL" --with-mpfr="$SAGE_LOCAL"
 if [ $? -ne 0 ]; then

build/pkgs/atlas/spkg-install

@@ -367,6 +367,9 @@ def configure_fast():
     elif conf['IA64?']:
         print('Fast configuration on Itanium.')
         arch = 'IA64Itan2'
+    elif conf['ARM?']:
+        print('Fast configuration on ARM.')
+        arch='ARMv7'
     else:
         raise NotImplementedError('I don\'t know a "fast" configuration for your cpu.')
     return (arch, isa_ext, thread_limit)
@@ -392,6 +395,9 @@ def configure_base():
     elif conf['IA64?']:
         print('Base configuration on Itanium.')
         arch = 'IA64Itan'
+    elif conf['ARM?']:
+        print('Base configuration on ARM.')
+        arch = 'ARMv6'
     else:
         raise NotImplementedError('I don\'t know a "base" configuration for your cpu.')
     return (arch, isa_ext, thread_limit)

build/pkgs/backports_ssl_match_hostname/SPKG.txt

@@ -0,0 +1,24 @@
+= backports.ssl_match_hostname =
+
+== Description ==
+
+This backport brings match_hostname() to users of
+Python 2.x
+
+== License ==
+
+Python Software Foundation License
+
+== Upstream Contact ==
+
+Home page: https://pypi.python.org/pypi/backports.ssl_match_hostname
+
+== Dependencies ==
+
+Python, Setuptools
+
+== Special Update/Build Instructions ==
+
+* Unpack the tarball
+* rename backports.ssl_match_hostname -> backports_ssl_match_hostname
+* Tar as backports_ssl_match_hostname.VERSION.tar.gz

build/pkgs/backports_ssl_match_hostname/checksums.ini

@@ -0,0 +1,4 @@
+tarball=backports_ssl_match_hostname-VERSION.tar.gz
+sha1=194503d8b47066c2ce8d23cab707d19d6ada2eb9
+md5=5def436c23fa2bc09aedf221d61b7017
+cksum=132706006

build/pkgs/backports_ssl_match_hostname/package-version.txt

@@ -0,0 +1 @@
+3.4.0.2

build/pkgs/backports_ssl_match_hostname/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.ssl_match_hostname ... exiting"
+    exit 1
+fi

build/pkgs/certifi/SPKG.txt

@@ -0,0 +1,18 @@
+= Certifi =
+
+== Description ==
+
+Python package for providing Mozilla's CA Bundle.
+
+== License ==
+
+ISC
+
+== Upstream Contact ==
+
+Home page: https://pypi.python.org/pypi/certifi
+
+== Dependencies ==
+
+Python, Setuptools
+

build/pkgs/certifi/checksums.ini

@@ -0,0 +1,4 @@
+tarball=certifi-VERSION.tar.gz
+sha1=f53dc8f57aaf6d69c183ebadcec52ece0a55cc3f
+md5=315ea4e50673a16ab047099f816fd32a
+cksum=3559413705

build/pkgs/certifi/package-version.txt

@@ -0,0 +1 @@
+14.05.14

build/pkgs/certifi/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 certifi ... exiting"
+    exit 1
+fi

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=99eab7d6d7eabfb85e3efe2ce4b2096c836681ce
-md5=9823a583c3663035cdb47fdb6f334173
-cksum=2606347674
+sha1=12e8d35579711c8bf8beddb890aaebd6b2c51db1
+md5=dbb592c16e66f4f2e3345071fb115abf
+cksum=693230472

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-64
+75

build/pkgs/cython/checksums.ini

@@ -1,4 +1,4 @@
-tarball=cython-VERSION.tar.gz
-sha1=02c6f25025923e5a5647e7876670a4cc7759371e
-md5=c59163d7c72c0a0ee5eb84edd17935ed
-cksum=3555036300
+tarball=cython-VERSION.tar.bz2
+sha1=89cf4f3d9a840e593da066a9f723b31a27d7c6a6
+md5=6fe7c9d93970ce602d60defd903188d8
+cksum=1851959595

build/pkgs/cython/package-version.txt

@@ -1 +1 @@
-0.21.1
+0.22

build/pkgs/database_gap/checksums.ini

@@ -1,4 +1,4 @@
 tarball=database_gap-VERSION.tar.bz2
-sha1=0e81cd017dc0542fc5faf923324eb1fffb61cdeb
-md5=879fc85f53fa9ff9f12dc7ebd621a528
-cksum=3437971482
+sha1=14f99d80583928d373b053cb346d21effd17d53e
+md5=1fe8a7e5e0eddf8c7de46b1485fb491f
+cksum=2596097681

build/pkgs/database_gap/package-version.txt

@@ -1 +1 @@
-4.7.5
+4.7.7

build/pkgs/database_odlyzko_zeta/SPKG.txt

@@ -0,0 +1,12 @@
+= Zeros of the Riemann zeta function =
+
+== Description ==
+
+Table of zeros of the Riemann zeta function by Andrew Odlyzko.
+
+This package contains the file 'zeros6' with the first 2,001,052 zeros
+of the Riemann zeta function, accurate to within 4*10^(-9).
+
+== Dependencies ==
+
+ * Sage library

build/pkgs/database_odlyzko_zeta/checksums.ini

@@ -0,0 +1,4 @@
+tarball=database_odlyzko_zeta-VERSION.tar.bz2
+sha1=97f586307d2f67a0a8594bd010602e2c4d5e0b4d
+md5=c93f63760540d5a787728a7a89ca2d9c
+cksum=3293740202

build/pkgs/database_odlyzko_zeta/package-version.txt

@@ -0,0 +1 @@
+20061209

build/pkgs/database_odlyzko_zeta/spkg-install

@@ -0,0 +1,15 @@
+#!/usr/bin/env python
+
+import os
+from sage.all import save
+from sage.env import SAGE_SHARE
+from sage.misc.misc import sage_makedirs
+
+install_root = os.path.join(SAGE_SHARE, 'odlyzko')
+target = os.path.join(install_root, 'zeros.sobj')
+
+if __name__ == '__main__':
+    sage_makedirs(install_root)
+    print("Creating Odlyzko database.")
+    F = [float(x) for x in open("src/zeros6").readlines()]
+    save(F, target)