Merge tag '7.4.beta2' into t/20218/pip-install

SageMath version 7.4.beta2

Author: jdemeyer

COPYING.txt

@@ -801,7 +801,7 @@ at the notice in config.guess or ltmain.sh.)
 
 The atomic_ops library contains some code that is covered by the GNU General
 Public License, but is not needed by, nor linked into the collector library.
-It is included here only becuase the atomic_ops distribution is, for
+It is included here only because the atomic_ops distribution is, for
 simplicity, included in its entirety.
 
 ================================================================================

VERSION.txt

@@ -1 +1 @@
-SageMath version 7.4.beta0, Release Date: 2016-08-10
+SageMath version 7.4.beta2, Release Date: 2016-08-26

build/pkgs/bliss/dependencies

@@ -0,0 +1,5 @@
+# no dependencies
+
+----------
+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/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=60850f1ee56240b1a41aac70b3db92ddae396a55
-md5=f7b731a66537ef5db10207172ee94fd8
-cksum=66728830
+sha1=3d13a8f9dcaef6c048d0d21f91338b0b3d0fe125
+md5=63fc727ca070844c580b5a722d177cb1
+cksum=3010448970

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-177
+179

build/pkgs/ecm/package-version.txt

@@ -1 +1 @@
-6.4.4
+6.4.4.p0

build/pkgs/ecm/patches/cygwin.patch

@@ -0,0 +1,26 @@
+Make sure the assembly routines use the appropriate calling convention
+for Windows in Cygwin as well.  See https://trac.sagemath.org/ticket/21223
+diff -ruN a/configure.in b/configure.in
+--- a/configure.in	2016-08-11 13:51:46.869520300 +0200
++++ b/configure.in	2016-08-11 13:52:46.240830400 +0200
+@@ -256,7 +256,7 @@
+   GMP_ASM_TYPE 
+ 
+   case $host in
+-    *-*-mingw32) GMP_DEFINE([WINDOWS64_ABI], 1)
++    *-*-mingw32|*cygwin*) GMP_DEFINE([WINDOWS64_ABI], 1)
+                  AC_DEFINE([WINDOWS64_ABI], 1,[Define to 1 if x86_64 mulredc*() functions should be called with Windows ABI]);;
+     *) ;;
+   esac
+diff -ruN a/configure b/configure
+--- a/configure	2016-08-11 13:51:46.936572300 +0200
++++ b/configure	2016-08-11 13:53:31.281801500 +0200
+@@ -12957,7 +12957,7 @@
+ 
+ 
+   case $host in
+-    *-*-mingw32)
++    *-*-mingw32|*cygwin*)
+ echo 'define(<WINDOWS64_ABI>, <1>)' >>$gmp_tmpconfigm4
+ 
+ 

build/pkgs/flask_babel/dependencies

@@ -1,4 +1,4 @@
-$(PYTHON) | pip flask speaklater
+$(PYTHON) | pip flask speaklater babel
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/fricas/SPKG.txt

@@ -14,7 +14,8 @@ http://fricas.sourceforge.net/
 
 == Dependencies ==
 
-Put a bulleted list of dependencies here:
+ * ecl
 
-* ecl
+== Special Update/Build Instructions ==
 
+ * uffi.patch: see #21209 for details.

build/pkgs/fricas/checksums.ini

@@ -1,4 +1,4 @@
-tarball=fricas-VERSION.tar.bz2
-sha1=689b3e474579655b76686a56a1928ef411cb179b
-md5=ba4f3927d93f49b0d866e5e80fc5bf18
-cksum=2927195574
+tarball=fricas-VERSION-full.tar.bz2
+sha1=f476a535ba189658cbc6055a951867c0c23787e4
+md5=1850f25249ed238203b9519c522d1795
+cksum=2721391206

build/pkgs/fricas/package-version.txt

@@ -1 +1 @@
-1.2.4
+1.2.7

build/pkgs/fricas/patches/uffi.patch

@@ -0,0 +1,51 @@
+--- a/lisp/fricas-lisp.lisp
++++ b/lisp/fricas-lisp.lisp
+@@ -556,10 +556,10 @@ with this hack and will try to convince the GCL crowd to fix this.
+                     (dolist (el strs)
+                         (setf wrapper `(FFI:WITH-CSTRING ,el ,wrapper)))
+                     (setf wrapper `(defun ,name ,largs ,wrapper))
+-                    `(progn (uffi:def-function (,c-name ,sym)
++                    `(progn (ffi:def-function (,c-name ,sym)
+                                 ,fargs :returning ,l-ret)
+                             ,wrapper))
+-                `(uffi:def-function (,c-name ,name)
++                `(ffi:def-function (,c-name ,name)
+                      ,fargs :returning ,l-ret)))))
+ 
+ (defmacro fricas-foreign-call (name c-name return-type &rest arguments)
+@@ -788,14 +788,14 @@ with this hack and will try to convince the GCL crowd to fix this.
+ #+:ecl
+ (progn
+ 
+-(uffi:def-function ("sock_get_string_buf" sock_get_string_buf_wrapper)
++(ffi:def-function ("sock_get_string_buf" sock_get_string_buf_wrapper)
+                    ((purpose :int) (buf (:array :unsigned-char 10000)) (len :int))
+                    :returning :void)
+ 
+ (defun |sockGetStringFrom| (purpose)
+-    (uffi:with-foreign-object (buf '(:array :unsigned-char 10000))
++    (ffi:with-foreign-object (buf '(:array :unsigned-char 10000))
+         (sock_get_string_buf_wrapper purpose buf 10000)
+-        (uffi:convert-from-foreign-string buf)))
++        (ffi:convert-from-foreign-string buf)))
+ 
+ )
+ 
+@@ -825,7 +825,7 @@ with this hack and will try to convince the GCL crowd to fix this.
+   (LISP::defentry |makedir| (LISP::string)         (LISP::int "makedir")))
+ 
+ #+:ecl
+-(uffi:def-function ("directoryp" raw_file_kind)
++(ffi:def-function ("directoryp" raw_file_kind)
+                    ((arg :cstring))
+                    :returning :int)
+ #+:ecl
+@@ -834,7 +834,7 @@ with this hack and will try to convince the GCL crowd to fix this.
+            (raw_file_kind cname)))
+ 
+ #+:ecl
+-(uffi:def-function ("makedir" raw_makedir)
++(ffi:def-function ("makedir" raw_makedir)
+                    ((arg :cstring))
+                    :returning :int)
+ 

build/pkgs/fricas/spkg-install

@@ -2,6 +2,16 @@
 
 cd src
 
+cd src
+for patch in ../../patches/*.patch; do
+    patch -p1 <"$patch"
+    if [ $? -ne 0 ]; then
+        echo >&2 "Error applying '$patch'"
+        exit 1
+    fi
+done
+cd ..
+
 ./configure --prefix="$SAGE_LOCAL" \
             --libdir="$SAGE_LOCAL/lib" \
             --with-lisp=ecl

build/pkgs/linbox/spkg-install

@@ -48,7 +48,12 @@ if [ "$SAGE64" = yes ]; then
 fi
 
 # C++11 workaround https://trac.sagemath.org/ticket/20926
-CXXFLAGS="$CXXFLAGS -std=c++98"
+if [ "$UNAME" = CYGWIN ]; then
+    # Special case for Cygwin https://trac.sagemath.org/ticket/21185
+    CXXFLAGS="$CXXFLAGS -std=gnu++98"
+else
+    CXXFLAGS="$CXXFLAGS -std=c++98"
+fi
 
 ###############################################################################
 # Configure, build and install LinBox:

build/pkgs/matplotlib/SPKG.txt

@@ -53,7 +53,7 @@ The matplotlib mailing lists: see http://sourceforge.net/projects/matplotlib
    matplotlib versions 0.99.3 and 1.0.0.  Sage reads the version
    number VER by running
 
-      python -c 'import matplotlib; print matplotlib.__version__'
+      python -c 'import matplotlib; print(matplotlib.__version__)'
 
    Note that at the end of the install process for matplotlib, the
    spkg-install file prints a message showing what MPLCONFIGDIR will

build/pkgs/matplotlib/make-setup-config.py

@@ -1,4 +1,4 @@
-import ConfigParser
+from six.moves import configparser as ConfigParser
 import os
 
 config = ConfigParser.SafeConfigParser()
@@ -14,17 +14,17 @@
 # will not even try, even if we could.  See trac #5301.
 #####################################################################
 
-print "NOTE: Set SAGE_MATPLOTLIB_GUI to anything but 'no' to try to build the Matplotlib GUI."
+print("NOTE: Set SAGE_MATPLOTLIB_GUI to anything but 'no' to try to build the Matplotlib GUI.")
 
 graphical_backend='False'
 if os.environ.get('SAGE_MATPLOTLIB_GUI', 'no').lower() != 'no':
     graphical_backend = 'auto'
 
-if graphical_backend=='auto':
-    print "Building graphical backends.  WARNING: This may causing some annoying and confusing behavior"
-    print "when using Sage + pylab, at least on OS X."
+if graphical_backend == 'auto':
+    print("Building graphical backends.  WARNING: This may causing some annoying and confusing behavior")
+    print("when using Sage + pylab, at least on OS X.")
 else:
-    print "Not building any matplotlib graphical backends."
+    print("Not building any matplotlib graphical backends.")
 
 config.add_section('gui_support')
 for backend in ('gtk', 'gtkagg', 'tkagg', 'wxagg', 'macosx', 'windowing'):

build/pkgs/matplotlib/spkg-install

@@ -36,7 +36,7 @@ if [ $? -ne 0 ]; then
 fi
 
 # Print value of MPLCONFIGDIR
-VERSION=`python -c 'import pkg_resources; print pkg_resources.get_distribution("matplotlib").version'`
+VERSION=`python -c 'import pkg_resources; print(pkg_resources.get_distribution("matplotlib").version)'`
 echo
 echo "When Sage runs, MPLCONFIGDIR will be set to '\$DOT_SAGE/matplotlib-$VERSION'."
 echo

build/pkgs/pari/checksums.ini

@@ -1,4 +1,4 @@
 tarball=pari-VERSION.tar.gz
-sha1=a936e0ed661c8e453578f3c129c3a454e2039e3e
-md5=59f2e4c3c51f7652182400489cd76e6a
-cksum=1366291737
+sha1=efd1eb6b8d87066b2b9f3b2c38ecb30bbfdb48d2
+md5=f3f3342913a3b3b306970b3462f4d47d
+cksum=1553747906

build/pkgs/pari/package-version.txt

@@ -1 +1 @@
-2.8-2771-gb70b447.p0
+2.8.0.alpha.p0

build/pkgs/polymake/SPKG.txt

@@ -0,0 +1,62 @@
+= Polymake =
+
+== Description ==
+
+polymake is open source software for research in polyhedral
+geometry. It deals with polytopes, polyhedra and fans as
+well as simplicial complexes, matroids, graphs, tropical
+hypersurfaces, and other objects. Supported platforms
+include various flavors of Linux, Free BSD and Mac OS.
+
+== License ==
+
+ * GPL v3
+
+== Upstream Contact ==
+
+ * https://polymake.org/
+
+== Dependencies ==
+
+Polymake needs a working installation of Perl, including its shared
+library and some modules (XML::Writer XML::LibXML XML::LibXSLT).
+These are not provided by a Sage package.  Sage does install the
+Term::Readline::Gnu module, however, when you install polymake.
+
+On Ubuntu, use:
+ sudo apt-get install libxml-libxslt-perl libxml-writer-perl libxml2-dev libperl-dev libncurses-dev
+
+On Fedora 23, use:
+ sudo yum install perl-ExtUtils-Embed
+
+On Mac OS X, all modules (except for Term::Readline::Gnu) appear to be
+standard.
+
+
+Several Sage packages should be installed before installing the
+polymake package to give a more featureful Polymake installation:
+ sage -i 4ti2 latte_int topcom
+
+Also this old-style Sage package can be installed for a more
+featureful Polymake installation:
+ sage -p qhull
+
+Software that would need to be installed manually (no Sage package
+ available) for a more featureful Polymake installation:
+ azove,
+ porta,
+ vinci,
+ SplitsTree4,
+ bliss (needs Debian patches; can't use the existing old-style Sage package)
+
+Information on missing Polymake prerequisites after installing
+polymake:
+ $ sage -sh
+ (sage-sh) $ polymake
+ polytope> show_unconfigured;
+
+== Debugging polymake install problems ==
+
+# apt-get install libdevel-trace-perl
+$ cd src
+$ perl -d:Trace support/configure.pl

build/pkgs/polymake/checksums.ini

@@ -0,0 +1,4 @@
+tarball=polymake-VERSION-minimal.tar.bz2
+sha1=0c96b4f2c9e56d72131166d2c9a7f25fffa99107
+md5=c1f5d71cdd86d0339c3e642494d6ac67
+cksum=3739642796

build/pkgs/polymake/dependencies

@@ -0,0 +1,5 @@
+$(INST)/$(SAGE_MP_LIBRARY) bliss cddlib lrslib perl_term_readline_gnu
+
+----------
+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/polymake/package-version.txt

@@ -0,0 +1 @@
+3.0r2

build/pkgs/polymake/spkg-install

@@ -0,0 +1,44 @@
+#!/usr/bin/env bash
+
+die () {
+    echo "$@" 1>&2
+    exit 1
+}
+
+cd src
+
+for patch in ../patches/*.patch; do
+    [ -r "$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
+
+more_configure_options=
+
+if [ `uname` = Darwin ]; then
+    more_configure_options="$more_configure_options --without-fink"
+    # Setting the following variable changes the output of "perl
+    # -MExtUtils::Embed -e ldopts" and "perl -MExtUtils::Embed -e ccflags"
+    # so that they do not contain -arch flags.
+    export ARCHFLAGS=
+fi
+
+./configure --without-java \
+            --without-javaview \
+            --prefix="$SAGE_LOCAL" \
+            --exec-prefix="$SAGE_LOCAL" \
+            --includedir="$SAGE_LOCAL"/include \
+            --bindir="$SAGE_LOCAL"/bin \
+            --libdir="$SAGE_LOCAL"/lib \
+	    $more_configure_options || die "Error configuring Polymake"
+make || die "Error building polymake"
+# Remove old stuff. Polymake loads whatever it finds in
+# its installation directory.
+rm -Rf $SAGE_LOCAL/lib/polymake
+make install || die "Error installing polymake"
+# Reconfigure Polymake's rules.
+# This modifies ~/.polymake/customize.pl
+echo "exit;" | polymake --reconfigure - || die "Error calling 'polymake --reconfigure'"

build/pkgs/polymake/type

@@ -0,0 +1 @@
+experimental

build/pkgs/pycrypto/package-version.txt

@@ -1 +1 @@
-2.6.1.p0
+2.6.1.p1

build/pkgs/pycrypto/patches/cygwin/disable-std-c99.patch

@@ -0,0 +1,23 @@
+Required to build on Cygwin due to a bug (?) in Cygwin (specifically newlib)
+whereas the removed lines themselves were added apparently to fix building on
+BSDs:
+
+https://github.com/dlitz/pycrypto/commit/574ffac9f5d290933e8c0678c430fa8eabc962d0
+diff -u a/setup.py b/setup.py
+--- a/setup.py	2013-10-14 23:38:10.000000000 +0200
++++ b/setup.py	2016-07-06 15:10:54.271597100 +0200
+@@ -114,13 +114,6 @@
+ 
+         # Tweak compiler options
+         if self.compiler.compiler_type in ('unix', 'cygwin', 'mingw32'):
+-            # Tell GCC to compile using the C99 standard.
+-            self.__add_compiler_option("-std=c99")
+-
+-            # ... but don't tell that to the aCC compiler on HP-UX
+-            if self.compiler.compiler_so[0] == 'cc' and sys.platform.startswith('hp-ux'):
+-                self.__remove_compiler_option("-std=c99")
+-
+             # Make assert() statements always work
+             self.__remove_compiler_option("-DNDEBUG")
+ 
+Common subdirectories: a/src and b/src

build/pkgs/pycrypto/spkg-install

@@ -19,6 +19,17 @@ for patch in ../patches/*.patch; do
     fi
 done
 
+if [ "$UNAME" = "CYGWIN" ]; then
+    for patch in ../patches/cygwin/*.patch; do
+        [ -r "$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
+fi
+
 if [ "$SAGE_DEBUG" = "yes" ]; then
     echo "Building a debug version of PyCrypto."
     export CFLAGS="-O0 -g $CFLAGS"