=== Polymake 3.2r3 ===

-- distribution -- * small bug fixes * threejs is the default viewer if jreality is not configured * support for java 10 * adapt to changes in boost 1.67 * fix for JuPyMake support on Mac OS X * removed fink as the default package manager for Mac OS X * included support for the brew package manager on Mac OS X
polymake · May 7, 2018 · 8ba686f · 8ba686f
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diff --git a/ChangeLog b/ChangeLog
@@ -1,5 +1,17 @@
 Changelog
 
+=== Polymake 3.2r3 ===
+
+-- distribution --
+* small bug fixes
+* threejs is the default viewer if jreality is not configured
+* support for java 10
+* adapt to changes in boost 1.67
+* fix for JuPyMake support on Mac OS X
+* removed fink as the default package manager for Mac OS X
+* included support for the brew package manager on Mac OS X
+
+
 === Polymake 3.2r2 ===
 
 -- distribution --

diff --git a/INSTALL b/INSTALL
@@ -1,7 +1,7 @@
 The step-by-step installation instructions can be found on the
 polymake Wiki site:
 
-http://www.polymake.org/polymake/doku.php/howto/install
+https://www.polymake.org/doku.php/howto/install
 
 The shortest possible summary for the truly impatient:
 

diff --git a/apps/common/rules/algebraic_types b/apps/common/rules/algebraic_types
@@ -870,7 +870,7 @@ user_function householder_trafo(Vector<Float>) : c++ (include => "polymake/linal
 # QR decomposition of a Matrix //M// with rows > cols
 # @param Matrix<Float> M
 # @return Pair<Matrix,Matrix>
-# @example
+# @example [nocompare]
 # > $M = new Matrix<Float>([23,4],[6,42]);
 # > $qr = qr_decomp($M);
 # > print $qr->first;

diff --git a/apps/common/rules/jupyter.rules b/apps/common/rules/jupyter.rules
@@ -19,7 +19,10 @@ use feature 'state';
 
 prefer threejs
 
-prefer svg.lattice
+if (application::self()->configured->{"svg.rules"} > 0) {
+
+   prefer svg.lattice
+}
 
 $ThreeJS::is_used_in_jupyter=1;
 

diff --git a/apps/common/rules/threejs.rules b/apps/common/rules/threejs.rules
@@ -97,6 +97,8 @@ sub append {
 # Create a three.js file.
 label threejs
 
+prefer threejs
+
 # The following are rarely used.
 # Much more common are the methods in apps/{graph,polytope,...}/rules/threejs.rules
 

diff --git a/bundled/java/java/build.xml b/bundled/java/java/build.xml
@@ -3,14 +3,23 @@
   <property name="package.prefix" value="de/tuberlin/polymake" />
   <property name="build.sysclasspath" value="ignore" />
 
+  <condition property="use-nativeheaderdir">
+    <and>
+      <antversion atleast="1.9.8"/>
+      <not>
+        <equals arg1="${ant.java.version}" arg2="1.7"/>
+      </not>
+    </and>
+  </condition>
+
   <target name="init">
     <!-- Create the time stamp -->
     <tstamp/>
     <!-- Create the build directory structure used by compile -->
     <mkdir dir="${build.dir}/bundled/java/java" />
   </target>
 
-  <target name="compile" depends="init">
+  <target name="compile-with-javah" depends="init" unless="use-nativeheaderdir">
     <sequential>
       <javac
              executable="${javac}"
@@ -21,26 +30,39 @@
              encoding="UTF8">
         <include name="${package.prefix}/**"/>
       </javac>
-      <copy todir="${build.dir}/bundled/java/java"
-            preservelastmodified="yes">
-        <fileset
-                dir="src"
-                includes="**/*.txt"
-                excludes="**/*.java" />
-      </copy>
+      <javah
+           force="yes"
+           class="de.tuberlin.polymake.common.SharedMemoryMatrix"
+           outputfile="native/de_tuberlin_polymake_common_SharedMemoryMatrix.h">
+        <classpath location="${build.dir}/bundled/java/java" />
+      </javah>
     </sequential>
   </target>
 
-  <target name="native-header" depends="compile">
-    <javah
-           force="yes"
-           class="de.tuberlin.polymake.common.SharedMemoryMatrix"
-           outputfile="native/SharedMemoryMatrix_jni.h">
-      <classpath location="${build.dir}/bundled/java/java" />
-    </javah>
+  <target name="compile-with-native" depends="init" if="use-nativeheaderdir">
+    <javac
+           executable="${javac}"
+           srcdir="src"
+           destdir="${build.dir}/bundled/java/java"
+           nativeheaderdir="native"
+           failonerror="true"
+           debug="${debug}"
+           encoding="UTF8">
+      <include name="${package.prefix}/**"/>
+    </javac>
+  </target>
+
+  <target name="copy-files">
+    <copy todir="${build.dir}/bundled/java/java"
+          preservelastmodified="yes">
+      <fileset
+               dir="src"
+               includes="**/*.txt"
+               excludes="**/*.java" />
+    </copy>
   </target>
 
-  <target name="all" depends="compile,native-header">
+  <target name="all" depends="compile-with-native,compile-with-javah,copy-files">
     <jar destfile="${build.dir}/jars/${jar.name}">
         <fileset
                  dir="${build.dir}/bundled/java/java"

diff --git a/bundled/java/java/native/SharedMemoryMatrix.c b/bundled/java/java/native/SharedMemoryMatrix.c
@@ -14,7 +14,7 @@
 --------------------------------------------------------------------------------
 */
 
-#include "SharedMemoryMatrix_jni.h"
+#include "de_tuberlin_polymake_common_SharedMemoryMatrix.h"
 #include <sys/ipc.h>
 #include <sys/shm.h>
 #include <errno.h>

diff --git a/...java/java/native/SharedMemoryMatrix_jni.h → ...rlin_polymake_common_SharedMemoryMatrix.h b/...java/java/native/SharedMemoryMatrix_jni.h → ...rlin_polymake_common_SharedMemoryMatrix.h
diff --git a/bundled/java/support/configure.pl b/bundled/java/support/configure.pl
@@ -93,12 +93,12 @@ sub proceed {
    # check Java version
 
    my ($java_version)= `$JAVACMD -version 2>&1` =~ /version "([\d.]+)/s;
-   Polymake::Configure::v_cmp($java_version_num, "1.5") >= 0
+   Polymake::Configure::v_cmp($java_version, "1.7") >= 0
      or die "Java run-time interpreter $JAVACMD",
             $found_by eq "PATH"
             ? " found along your program PATH"
             : $found_by && " found by environment variable $found_by",
-            " reports its version as $java_version, while minimal required is 1.5\n",
+            " reports its version as $java_version, while minimal required is 1.7\n",
             "\nPlease upgrade your Java run-time system or JDK to a modern version,\n",
             $found_by && "or specify a correct location in the option --with-java,\n",
             "or disable using Java components completely: --without-java\n",
@@ -166,7 +166,10 @@ sub proceed {
       }
       my ($ant_version)= `$ANT -version` =~ /version ([\d.]+)/;
       Polymake::Configure::v_cmp($ant_version, "1.7.1") >= 0
-	or die "$ANT reports its version as $ant_version, while minimal required version is 1.7.1\n";
+         or die "$ANT reports its version as $ant_version, while minimal required version is 1.7.1\n";
+      # Java 10 needs javac with nativeheaderdir instead of javah task which requires ant 1.9.8
+      Polymake::Configure::v_cmp($java_version, "10") >= 0 and Polymake::Configure::v_cmp($ant_version, "1.9.8") < 0
+         and die "$ANT reports its version as $ant_version, while minimal required version for Java 10 is 1.9.8\n";
 
       $NativeSO="so";
 

diff --git a/external/permlib/include/permlib/bsgs.h b/external/permlib/include/permlib/bsgs.h
@@ -37,11 +37,18 @@
 #include <list>
 #include <vector>
 
+#include <boost/version.hpp>
+
 #include <boost/cstdint.hpp>
 #include <boost/foreach.hpp>
 #include <boost/scoped_ptr.hpp>
 #include <boost/shared_ptr.hpp>
+
+#if BOOST_VERSION / 100 >= 1067
+#include <boost/next_prior.hpp>
+#else
 #include <boost/utility.hpp>
+#endif
 
 #include <permlib/bsgs_core.h>
 

diff --git a/external/permlib/include/permlib/permutation.h b/external/permlib/include/permlib/permutation.h
@@ -48,7 +48,16 @@
 #include <boost/dynamic_bitset.hpp>
 #include <boost/foreach.hpp>
 #include <boost/cstdint.hpp>
+
+#include <boost/version.hpp>
+
+#if BOOST_VERSION / 100 >= 1067
+#include <boost/integer/common_factor_rt.hpp>
+#define permlib_boost_lcm boost::integer::lcm
+#else
 #include <boost/math/common_factor_rt.hpp>
+#define permlib_boost_lcm boost::math::lcm
+#endif
 
 namespace permlib {
 
@@ -343,7 +352,7 @@ inline boost::uint64_t Permutation::order() const {
 	std::list<CyclePair> cycleList = this->cycles();
 	boost::uint64_t ord = 1;
 	BOOST_FOREACH(const CyclePair& cyc, cycleList) {
-		ord = boost::math::lcm(ord, static_cast<boost::uint64_t>(cyc.second));
+		ord = permlib_boost_lcm(ord, static_cast<boost::uint64_t>(cyc.second));
 	}
 	return ord;
 }

diff --git a/external/permlib/include/permlib/test/primitivity_sgs_test.h b/external/permlib/include/permlib/test/primitivity_sgs_test.h
@@ -38,7 +38,15 @@
 
 #include <boost/foreach.hpp>
 #include <boost/scoped_ptr.hpp>
+
+#include <boost/version.hpp>
+
+#if BOOST_VERSION / 100 >= 1067
+#include <boost/next_prior.hpp>
+#else
 #include <boost/utility.hpp>
+#endif
+
 #include <vector>
 #include <list>
 

diff --git a/perllib/Polymake/Configure.pm b/perllib/Polymake/Configure.pm
@@ -22,6 +22,9 @@ use warnings qw(FATAL void syntax misc);
 # load the non-interactive basis routines first
 use Polymake::ConfigureStandalone;
 
+# the values of these variables are growing when extension configure script assigns something to them
+my %augmented_vars=( CFLAGS=>1, CXXFLAGS=>1, CflagsSuppressWarnings=>1, LDFLAGS=>1, LIBS=>1 );
+
 package Polymake::Configure;
 
 if ($ENV{POLYMAKE_HOST_AGENT}) {

diff --git a/perllib/Polymake/ConfigureStandalone.pm b/perllib/Polymake/ConfigureStandalone.pm
@@ -32,13 +32,12 @@ BEGIN {
                   GCCversion ICCversion CLANGversion CPPStd AppleClang
                   LDFLAGS LDsharedFLAGS LDcallableFLAGS LDsonameFLAGS LIBS
                   LIBXML2_CFLAGS LIBXML2_LIBS ExternalHeaders
-                  Arch FinkBase BundledExts BuildModes
+                  Arch FinkBase BrewBase BundledExts BuildModes
                   InstallTop InstallArch InstallBin InstallInc InstallLib InstallDoc DESTDIR );
 }
 
 use vars map { "\$$_" } @conf_vars;
 
-my %augmented_vars=( CFLAGS=>1, CXXFLAGS=>1, CflagsSuppressWarnings=>1, LDFLAGS=>1, LIBS=>1 );
 my %supported_build_modes=( Cov => 1, San => 1 );
 
 ###############################################################################################

diff --git a/perllib/Polymake/Test.pm b/perllib/Polymake/Test.pm
@@ -409,6 +409,7 @@ sub diff_with {
 # @param Int    expected completion offset from the end of input_string
 # @param String+ expected completions;
 #                the last one is interpreted as the expected append character if it consists of exactly one char
+#                if the last word is "..." all subsequent words in the output are ignored
 sub check_completion {
    unless (@_>3 && (is_string($_[0]) || is_integer($_[0])) && is_string($_[1]) && is_integer($_[2])) {
       croak( "usage: check_completion('ID', 'partial input', expected_offset, 'expected completion', ...)" );

diff --git a/perllib/Polymake/Test/Shell.pm b/perllib/Polymake/Test/Shell.pm
@@ -73,7 +73,9 @@ sub new {
 
 sub execute {
    my ($self)=@_;
-   my $eq=equal_string_lists($self->expected_words, $self->gotten_words);
+   my $eq= $self->expected_words->[-1] eq "..." ?
+         @{$self->expected_words}-1 == equal_string_list_prefixes($self->expected_words, $self->gotten_words) :
+         equal_string_lists($self->expected_words, $self->gotten_words);
    my $eq_append=!defined($self->expected_append) || $self->expected_append eq $self->gotten_append;
    unless ($eq && $eq_append && $self->expected_offset==$self->gotten_offset) {
       unless ($eq) {

diff --git a/resources/JuPyMake/setup.py b/resources/JuPyMake/setup.py
@@ -28,8 +28,8 @@ def conditional_decode( string ):
 os.environ["CC"] = polymake_cc
 os.environ["CXX"] = polymake_cc
 if platform.system() == "Darwin" :
-   version = platform.mac_ver()[0]
-   os.environ["MACOSX_DEPLOYMENT_TARGET"] = version.rsplit('.',1)[0]
+   version_arr = platform.mac_ver()[0].split('.')
+   os.environ["MACOSX_DEPLOYMENT_TARGET"] = version_arr[0]+'.'+version_arr[1]
 
 setup(
     name = 'JuPyMake',