3 files changed, 41 insertions, 12 deletions

diff --git a/biology/pycogent/Makefile b/biology/pycogent/Makefile
index 8d8b03a815ef..ef1263c13d53 100644
--- a/biology/pycogent/Makefile
+++ b/biology/pycogent/Makefile
@@ -6,8 +6,7 @@
 #
 
 PORTNAME=	pycogent
-PORTVERSION=	1.5
-PORTREVISION=	1
+PORTVERSION=	1.5.1
 CATEGORIES=	biology python
 MASTER_SITES=	SF/${PORTNAME}/PyCogent/${PORTVERSION}
 DISTNAME=	PyCogent-${PORTVERSION}
@@ -25,6 +24,5 @@ RUN_DEPENDS=	${BUILD_DEPENDS}
 USE_PYTHON=		yes
 USE_PYDISTUTILS=	yes
 PYDISTUTILS_PKGNAME=	cogent
-PYDISTUTILS_PKGVERSION=	1.5.0
 
 .include <bsd.port.mk>
diff --git a/biology/pycogent/distinfo b/biology/pycogent/distinfo
index 755af4b8330e..ba89cd329511 100644
--- a/biology/pycogent/distinfo
+++ b/biology/pycogent/distinfo
@@ -1,2 +1,2 @@
-SHA256 (PyCogent-1.5.tgz) = b20276c6607ca2c53f26df8837e5d43c7e7af45bf0aa5592da4c73060891ab8d
-SIZE (PyCogent-1.5.tgz) = 2992994
+SHA256 (PyCogent-1.5.1.tgz) = 572345eb5f9ef0c4c5307145d27c2c69277dc7dffdbb772219532dce749513d7
+SIZE (PyCogent-1.5.1.tgz) = 3057837
diff --git a/biology/pycogent/pkg-plist b/biology/pycogent/pkg-plist
index 81d4bebc9bdc..addc2b2622df 100644
--- a/biology/pycogent/pkg-plist
+++ b/biology/pycogent/pkg-plist
@@ -145,6 +145,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/app/rdp_classifier.py
 %%PYTHON_SITELIBDIR%%/cogent/app/rdp_classifier.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/rdp_classifier.pyo
+%%PYTHON_SITELIBDIR%%/cogent/app/rdp_classifier20.py
+%%PYTHON_SITELIBDIR%%/cogent/app/rdp_classifier20.pyc
+%%PYTHON_SITELIBDIR%%/cogent/app/rdp_classifier20.pyo
 %%PYTHON_SITELIBDIR%%/cogent/app/rnaalifold.py
 %%PYTHON_SITELIBDIR%%/cogent/app/rnaalifold.pyc
 %%PYTHON_SITELIBDIR%%/cogent/app/rnaalifold.pyo
@@ -325,6 +328,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/draw/codon_usage.py
 %%PYTHON_SITELIBDIR%%/cogent/draw/codon_usage.pyc
 %%PYTHON_SITELIBDIR%%/cogent/draw/codon_usage.pyo
+%%PYTHON_SITELIBDIR%%/cogent/draw/compatibility.py
+%%PYTHON_SITELIBDIR%%/cogent/draw/compatibility.pyc
+%%PYTHON_SITELIBDIR%%/cogent/draw/compatibility.pyo
 %%PYTHON_SITELIBDIR%%/cogent/draw/dendrogram.py
 %%PYTHON_SITELIBDIR%%/cogent/draw/dendrogram.pyc
 %%PYTHON_SITELIBDIR%%/cogent/draw/dendrogram.pyo
@@ -356,6 +362,8 @@
 %%PYTHON_SITELIBDIR%%/cogent/evolve/__init__.pyc
 %%PYTHON_SITELIBDIR%%/cogent/evolve/__init__.pyo
 %%PYTHON_SITELIBDIR%%/cogent/evolve/_likelihood_tree.so
+%%PYTHON_SITELIBDIR%%/cogent/evolve/_pairwise_distance.so
+%%PYTHON_SITELIBDIR%%/cogent/evolve/_solved_models.so
 %%PYTHON_SITELIBDIR%%/cogent/evolve/best_likelihood.py
 %%PYTHON_SITELIBDIR%%/cogent/evolve/best_likelihood.pyc
 %%PYTHON_SITELIBDIR%%/cogent/evolve/best_likelihood.pyo
@@ -383,12 +391,18 @@
 %%PYTHON_SITELIBDIR%%/cogent/evolve/motif_prob_model.py
 %%PYTHON_SITELIBDIR%%/cogent/evolve/motif_prob_model.pyc
 %%PYTHON_SITELIBDIR%%/cogent/evolve/motif_prob_model.pyo
+%%PYTHON_SITELIBDIR%%/cogent/evolve/pairwise_distance.py
+%%PYTHON_SITELIBDIR%%/cogent/evolve/pairwise_distance.pyc
+%%PYTHON_SITELIBDIR%%/cogent/evolve/pairwise_distance.pyo
 %%PYTHON_SITELIBDIR%%/cogent/evolve/parameter_controller.py
 %%PYTHON_SITELIBDIR%%/cogent/evolve/parameter_controller.pyc
 %%PYTHON_SITELIBDIR%%/cogent/evolve/parameter_controller.pyo
 %%PYTHON_SITELIBDIR%%/cogent/evolve/predicate.py
 %%PYTHON_SITELIBDIR%%/cogent/evolve/predicate.pyc
 %%PYTHON_SITELIBDIR%%/cogent/evolve/predicate.pyo
+%%PYTHON_SITELIBDIR%%/cogent/evolve/solved_models.py
+%%PYTHON_SITELIBDIR%%/cogent/evolve/solved_models.pyc
+%%PYTHON_SITELIBDIR%%/cogent/evolve/solved_models.pyo
 %%PYTHON_SITELIBDIR%%/cogent/evolve/simulate.py
 %%PYTHON_SITELIBDIR%%/cogent/evolve/simulate.pyc
 %%PYTHON_SITELIBDIR%%/cogent/evolve/simulate.pyo
@@ -449,10 +463,12 @@
 %%PYTHON_SITELIBDIR%%/cogent/maths/__init__.py
 %%PYTHON_SITELIBDIR%%/cogent/maths/__init__.pyc
 %%PYTHON_SITELIBDIR%%/cogent/maths/__init__.pyo
-%%PYTHON_SITELIBDIR%%/cogent/maths/_matrix_exponentiation.so
 %%PYTHON_SITELIBDIR%%/cogent/maths/distance_transform.py
 %%PYTHON_SITELIBDIR%%/cogent/maths/distance_transform.pyc
 %%PYTHON_SITELIBDIR%%/cogent/maths/distance_transform.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/fit_function.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/fit_function.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/fit_function.pyo
 %%PYTHON_SITELIBDIR%%/cogent/maths/function_optimisation.py
 %%PYTHON_SITELIBDIR%%/cogent/maths/function_optimisation.pyc
 %%PYTHON_SITELIBDIR%%/cogent/maths/function_optimisation.pyo
@@ -474,9 +490,6 @@
 %%PYTHON_SITELIBDIR%%/cogent/maths/matrix_logarithm.py
 %%PYTHON_SITELIBDIR%%/cogent/maths/matrix_logarithm.pyc
 %%PYTHON_SITELIBDIR%%/cogent/maths/matrix_logarithm.pyo
-%%PYTHON_SITELIBDIR%%/cogent/maths/optimiser.py
-%%PYTHON_SITELIBDIR%%/cogent/maths/optimiser.pyc
-%%PYTHON_SITELIBDIR%%/cogent/maths/optimiser.pyo
 %%PYTHON_SITELIBDIR%%/cogent/maths/optimisers.py
 %%PYTHON_SITELIBDIR%%/cogent/maths/optimisers.pyc
 %%PYTHON_SITELIBDIR%%/cogent/maths/optimisers.pyo
@@ -515,6 +528,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/get_by_cai.py
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/get_by_cai.pyc
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/get_by_cai.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/jackknife.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/jackknife.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/jackknife.pyo
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/util.py
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/util.pyc
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/cai/util.pyo
@@ -587,6 +603,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/parse/blast_xml.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/blast_xml.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/blast_xml.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/bowtie.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/bowtie.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/bowtie.pyo
 %%PYTHON_SITELIBDIR%%/cogent/parse/bpseq.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/bpseq.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/bpseq.pyo
@@ -662,6 +681,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/parse/gibbs.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/gibbs.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/gibbs.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/greengenes.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/greengenes.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/greengenes.pyo
 %%PYTHON_SITELIBDIR%%/cogent/parse/flowgram.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/flowgram.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/flowgram.pyo
@@ -680,6 +702,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/parse/infernal.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/infernal.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/infernal.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/kegg_fasta.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/kegg_fasta.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/kegg_fasta.pyo
 %%PYTHON_SITELIBDIR%%/cogent/parse/kegg_ko.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/kegg_ko.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/kegg_ko.pyo
@@ -743,6 +768,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/parse/pknotsrg.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/pknotsrg.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/pknotsrg.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/psl.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/psl.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/psl.pyo
 %%PYTHON_SITELIBDIR%%/cogent/parse/rdb.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/rdb.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/rdb.pyo
@@ -779,6 +807,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/parse/sfold.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/sfold.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/sfold.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/stockholm.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/stockholm.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/stockholm.pyo
 %%PYTHON_SITELIBDIR%%/cogent/parse/sprinzl.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/sprinzl.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/sprinzl.pyo
@@ -809,9 +840,6 @@
 %%PYTHON_SITELIBDIR%%/cogent/phylo/__init__.py
 %%PYTHON_SITELIBDIR%%/cogent/phylo/__init__.pyc
 %%PYTHON_SITELIBDIR%%/cogent/phylo/__init__.pyo
-%%PYTHON_SITELIBDIR%%/cogent/phylo/compatibility.py
-%%PYTHON_SITELIBDIR%%/cogent/phylo/compatibility.pyc
-%%PYTHON_SITELIBDIR%%/cogent/phylo/compatibility.pyo
 %%PYTHON_SITELIBDIR%%/cogent/phylo/consensus.py
 %%PYTHON_SITELIBDIR%%/cogent/phylo/consensus.pyc
 %%PYTHON_SITELIBDIR%%/cogent/phylo/consensus.pyo
@@ -940,6 +968,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/util/modules.py
 %%PYTHON_SITELIBDIR%%/cogent/util/modules.pyc
 %%PYTHON_SITELIBDIR%%/cogent/util/modules.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/option_parsing.py
+%%PYTHON_SITELIBDIR%%/cogent/util/option_parsing.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/option_parsing.pyo
 %%PYTHON_SITELIBDIR%%/cogent/util/organizer.py
 %%PYTHON_SITELIBDIR%%/cogent/util/organizer.pyc
 %%PYTHON_SITELIBDIR%%/cogent/util/organizer.pyo