- Updated from 0.07 to 0.12

Approved by:	tobez (implicit)

0.08 20/Feb/2006 15:14
                       Improved referential integrity between nodes,
                                taxa, and data.
                       Implemented Fastnexus parser
                       Node object silently implements Bio::Tree::NodeI
                       		interface if BioPerl is installed
                       Tree object silently implements Bio::Tree::TreeI
                       		interface if BioPerl is installed
                       Added convertor methods for XML and CIPRES
                       Implemented more Matrix methods
                       Implemented symbol tables in Bio::Phylo::Util::CONSTANT
                       Implemented visit method for listable objects
                       Implemented caching infrastructure for calculations
                       Changed object-model to inside-out arrays
                       Added Biodiversity measures code by Aki Mimoto
                       Moved constants and exceptions to Bio::Phylo::Util::*
                       Fixed memory leak due to circular references

3 files changed, 25 insertions, 12 deletions

diff --git a/biology/p5-Bio-Phylo/Makefile b/biology/p5-Bio-Phylo/Makefile
index edd4ea96ac55..32e882e5d35e 100644
--- a/biology/p5-Bio-Phylo/Makefile
+++ b/biology/p5-Bio-Phylo/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	Bio-Phylo
-PORTVERSION=	0.07
+PORTVERSION=	0.12
 CATEGORIES=	biology perl5
 MASTER_SITES=	${MASTER_SITE_PERL_CPAN}
 MASTER_SITE_SUBDIR=	Bio
@@ -18,12 +18,12 @@ COMMENT=	Phylogenetic analysis using perl
 BUILD_DEPENDS=	${SITE_PERL}/${PERL_ARCH}/Math/Random.pm:${PORTSDIR}/math/p5-Math-Random \
 		${SITE_PERL}/SVG.pm:${PORTSDIR}/textproc/p5-SVG \
 		${SITE_PERL}/Exception/Class.pm:${PORTSDIR}/devel/p5-Exception-Class \
-		${SITE_PERL}/${PERL_ARCH}/Scalar/Util.pm:${PORTSDIR}/lang/p5-Scalar-List-Utils
+		${SITE_PERL}/${PERL_ARCH}/Scalar/Util.pm:${PORTSDIR}/lang/p5-Scalar-List-Utils \
+		${SITE_PERL}/IO/String.pm:${PORTSDIR}/devel/p5-IO-String \
+		${SITE_PERL}/XML/Simple.pm:${PORTSDIR}/textproc/p5-XML-Simple
 RUN_DEPENDS=	${BUILD_DEPENDS}
 
 MAN3=	Bio::Phylo.3 \
-	Bio::Phylo::CONSTANT.3 \
-	Bio::Phylo::Exceptions.3 \
 	Bio::Phylo::Forest.3 \
 	Bio::Phylo::Forest::Node.3 \
 	Bio::Phylo::Forest::Tree.3 \
@@ -36,6 +36,8 @@ MAN3=	Bio::Phylo.3 \
 	Bio::Phylo::Matrices::Datum.3 \
 	Bio::Phylo::Matrices::Matrix.3 \
 	Bio::Phylo::Matrices::Sequence.3 \
+	Bio::Phylo::Parsers::Fastnewick.3 \
+	Bio::Phylo::Parsers::Fastnexus.3 \
 	Bio::Phylo::Parsers::Newick.3 \
 	Bio::Phylo::Parsers::Nexus.3 \
 	Bio::Phylo::Parsers::Table.3 \
@@ -43,9 +45,14 @@ MAN3=	Bio::Phylo.3 \
 	Bio::Phylo::Taxa.3 \
 	Bio::Phylo::Taxa::Taxon.3 \
 	Bio::Phylo::Treedrawer.3 \
-	Bio::Phylo::Treedrawer::SVG.3 \
+	Bio::Phylo::Treedrawer::Svg.3 \
+	Bio::Phylo::Unparsers::Mrp.3 \
 	Bio::Phylo::Unparsers::Newick.3 \
-	Bio::Phylo::Unparsers::Pagel.3
+	Bio::Phylo::Unparsers::Nexus.3 \
+	Bio::Phylo::Unparsers::Pagel.3 \
+	Bio::Phylo::Util::CONSTANT.3 \
+	Bio::Phylo::Util::Exceptions.3 \
+	Bio::Phylo::Util::IDPool.3
 
 PERL_CONFIGURE=	yes
 
diff --git a/biology/p5-Bio-Phylo/distinfo b/biology/p5-Bio-Phylo/distinfo
index 3c4ba97880e8..3102dcf208cc 100644
--- a/biology/p5-Bio-Phylo/distinfo
+++ b/biology/p5-Bio-Phylo/distinfo
@@ -1,3 +1,3 @@
-MD5 (Bio-Phylo-0.07.tar.gz) = 12b6ca632bc25e5c3fd647990cb5c959
-SHA256 (Bio-Phylo-0.07.tar.gz) = c98ab09053b9b0e9b30c72f7b09448e908ddde71c5db2489b6924c710f654923
-SIZE (Bio-Phylo-0.07.tar.gz) = 69580
+MD5 (Bio-Phylo-0.12.tar.gz) = 82a8bbe68d7f2f2e67369c5c19ea1d72
+SHA256 (Bio-Phylo-0.12.tar.gz) = 7560554ba4e27296fa2411bf4c5beab26aef6dcaf729aa21a910509e894c455d
+SIZE (Bio-Phylo-0.12.tar.gz) = 105975
diff --git a/biology/p5-Bio-Phylo/pkg-plist b/biology/p5-Bio-Phylo/pkg-plist
index 19f9db94060e..d12ffba57be8 100644
--- a/biology/p5-Bio-Phylo/pkg-plist
+++ b/biology/p5-Bio-Phylo/pkg-plist
@@ -5,8 +5,6 @@ bin/dnd2svg.pl
 bin/droptip.pl
 bin/postmb.pl
 %%SITE_PERL%%/Bio/Phylo.pm
-%%SITE_PERL%%/Bio/Phylo/CONSTANT.pm
-%%SITE_PERL%%/Bio/Phylo/Exceptions.pm
 %%SITE_PERL%%/Bio/Phylo/Forest.pm
 %%SITE_PERL%%/Bio/Phylo/Forest/Node.pm
 %%SITE_PERL%%/Bio/Phylo/Forest/Tree.pm
@@ -19,6 +17,8 @@ bin/postmb.pl
 %%SITE_PERL%%/Bio/Phylo/Matrices/Datum.pm
 %%SITE_PERL%%/Bio/Phylo/Matrices/Matrix.pm
 %%SITE_PERL%%/Bio/Phylo/Matrices/Sequence.pm
+%%SITE_PERL%%/Bio/Phylo/Parsers/Fastnewick.pm
+%%SITE_PERL%%/Bio/Phylo/Parsers/Fastnexus.pm
 %%SITE_PERL%%/Bio/Phylo/Parsers/Newick.pm
 %%SITE_PERL%%/Bio/Phylo/Parsers/Nexus.pm
 %%SITE_PERL%%/Bio/Phylo/Parsers/Table.pm
@@ -26,12 +26,18 @@ bin/postmb.pl
 %%SITE_PERL%%/Bio/Phylo/Taxa.pm
 %%SITE_PERL%%/Bio/Phylo/Taxa/Taxon.pm
 %%SITE_PERL%%/Bio/Phylo/Treedrawer.pm
-%%SITE_PERL%%/Bio/Phylo/Treedrawer/SVG.pm
+%%SITE_PERL%%/Bio/Phylo/Treedrawer/Svg.pm
+%%SITE_PERL%%/Bio/Phylo/Unparsers/Mrp.pm
 %%SITE_PERL%%/Bio/Phylo/Unparsers/Newick.pm
+%%SITE_PERL%%/Bio/Phylo/Unparsers/Nexus.pm
 %%SITE_PERL%%/Bio/Phylo/Unparsers/Pagel.pm
+%%SITE_PERL%%/Bio/Phylo/Util/CONSTANT.pm
+%%SITE_PERL%%/Bio/Phylo/Util/Exceptions.pm
+%%SITE_PERL%%/Bio/Phylo/Util/IDPool.pm
 %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Phylo/.packlist
 @dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Phylo
 @dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
+@dirrm %%SITE_PERL%%/Bio/Phylo/Util
 @dirrm %%SITE_PERL%%/Bio/Phylo/Unparsers
 @dirrm %%SITE_PERL%%/Bio/Phylo/Treedrawer
 @dirrm %%SITE_PERL%%/Bio/Phylo/Taxa