- Update to 1.5.0

3 files changed, 41 insertions, 4 deletions

diff --git a/biology/pycogent/Makefile b/biology/pycogent/Makefile
index 12c45ec638fc..286e9d129b90 100644
--- a/biology/pycogent/Makefile
+++ b/biology/pycogent/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	pycogent
-PORTVERSION=	1.4.1
+PORTVERSION=	1.5
 CATEGORIES=	biology python
 MASTER_SITES=	SF/${PORTNAME}/PyCogent/${PORTVERSION}
 DISTNAME=	PyCogent-${PORTVERSION}
@@ -24,5 +24,6 @@ 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 b2b07ecb99f3..755af4b8330e 100644
--- a/biology/pycogent/distinfo
+++ b/biology/pycogent/distinfo
@@ -1,3 +1,2 @@
-MD5 (PyCogent-1.4.1.tgz) = c5f50b108d87001d0840a7f721f78977
-SHA256 (PyCogent-1.4.1.tgz) = 4f0275c7b97e22b8a8286e8c5831599871f66bcf6bbb8f2dd70d3e300df3a217
-SIZE (PyCogent-1.4.1.tgz) = 2596901
+SHA256 (PyCogent-1.5.tgz) = b20276c6607ca2c53f26df8837e5d43c7e7af45bf0aa5592da4c73060891ab8d
+SIZE (PyCogent-1.5.tgz) = 2992994
diff --git a/biology/pycogent/pkg-plist b/biology/pycogent/pkg-plist
index d29214841cae..81d4bebc9bdc 100644
--- a/biology/pycogent/pkg-plist
+++ b/biology/pycogent/pkg-plist
@@ -187,6 +187,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/cluster/__init__.py
 %%PYTHON_SITELIBDIR%%/cogent/cluster/__init__.pyc
 %%PYTHON_SITELIBDIR%%/cogent/cluster/__init__.pyo
+%%PYTHON_SITELIBDIR%%/cogent/cluster/approximate_mds.py
+%%PYTHON_SITELIBDIR%%/cogent/cluster/approximate_mds.pyc
+%%PYTHON_SITELIBDIR%%/cogent/cluster/approximate_mds.pyo
 %%PYTHON_SITELIBDIR%%/cogent/cluster/goodness_of_fit.py
 %%PYTHON_SITELIBDIR%%/cogent/cluster/goodness_of_fit.pyc
 %%PYTHON_SITELIBDIR%%/cogent/cluster/goodness_of_fit.pyo
@@ -477,6 +480,10 @@
 %%PYTHON_SITELIBDIR%%/cogent/maths/optimisers.py
 %%PYTHON_SITELIBDIR%%/cogent/maths/optimisers.pyc
 %%PYTHON_SITELIBDIR%%/cogent/maths/optimisers.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/_period.so
+%%PYTHON_SITELIBDIR%%/cogent/maths/period.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/period.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/period.pyo
 %%PYTHON_SITELIBDIR%%/cogent/maths/scipy_optimisers.py
 %%PYTHON_SITELIBDIR%%/cogent/maths/scipy_optimisers.pyc
 %%PYTHON_SITELIBDIR%%/cogent/maths/scipy_optimisers.pyo
@@ -517,12 +524,18 @@
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/histogram.py
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/histogram.pyc
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/histogram.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/information_criteria.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/information_criteria.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/information_criteria.pyo
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/kendall.py
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/kendall.pyc
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/kendall.pyo
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/ks.py
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/ks.pyc
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/ks.pyo
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/period.py
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/period.pyc
+%%PYTHON_SITELIBDIR%%/cogent/maths/stats/period.pyo
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/special.py
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/special.pyc
 %%PYTHON_SITELIBDIR%%/cogent/maths/stats/special.pyo
@@ -565,6 +578,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/parse/agilent_microarray.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/agilent_microarray.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/agilent_microarray.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/binary_sff.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/binary_sff.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/binary_sff.pyo
 %%PYTHON_SITELIBDIR%%/cogent/parse/blast.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/blast.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/blast.pyo
@@ -625,6 +641,9 @@
 %%PYTHON_SITELIBDIR%%/cogent/parse/fasta.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/fasta.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/fasta.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/fastq.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/fastq.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/fastq.pyo
 %%PYTHON_SITELIBDIR%%/cogent/parse/foldalign.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/foldalign.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/foldalign.pyo
@@ -652,12 +671,24 @@
 %%PYTHON_SITELIBDIR%%/cogent/parse/flowgram_parser.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/flowgram_parser.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/flowgram_parser.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/illumina_sequence.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/illumina_sequence.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/illumina_sequence.pyo
 %%PYTHON_SITELIBDIR%%/cogent/parse/ilm.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/ilm.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/ilm.pyo
 %%PYTHON_SITELIBDIR%%/cogent/parse/infernal.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/infernal.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/infernal.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/kegg_ko.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/kegg_ko.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/kegg_ko.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/kegg_pos.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/kegg_pos.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/kegg_pos.pyo
+%%PYTHON_SITELIBDIR%%/cogent/parse/kegg_taxonomy.py
+%%PYTHON_SITELIBDIR%%/cogent/parse/kegg_taxonomy.pyc
+%%PYTHON_SITELIBDIR%%/cogent/parse/kegg_taxonomy.pyo
 %%PYTHON_SITELIBDIR%%/cogent/parse/knetfold.py
 %%PYTHON_SITELIBDIR%%/cogent/parse/knetfold.pyc
 %%PYTHON_SITELIBDIR%%/cogent/parse/knetfold.pyo
@@ -915,12 +946,18 @@
 %%PYTHON_SITELIBDIR%%/cogent/util/parallel.py
 %%PYTHON_SITELIBDIR%%/cogent/util/parallel.pyc
 %%PYTHON_SITELIBDIR%%/cogent/util/parallel.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/progress_display.py
+%%PYTHON_SITELIBDIR%%/cogent/util/progress_display.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/progress_display.pyo
 %%PYTHON_SITELIBDIR%%/cogent/util/recode_alignment.py
 %%PYTHON_SITELIBDIR%%/cogent/util/recode_alignment.pyc
 %%PYTHON_SITELIBDIR%%/cogent/util/recode_alignment.pyo
 %%PYTHON_SITELIBDIR%%/cogent/util/table.py
 %%PYTHON_SITELIBDIR%%/cogent/util/table.pyc
 %%PYTHON_SITELIBDIR%%/cogent/util/table.pyo
+%%PYTHON_SITELIBDIR%%/cogent/util/terminal.py
+%%PYTHON_SITELIBDIR%%/cogent/util/terminal.pyc
+%%PYTHON_SITELIBDIR%%/cogent/util/terminal.pyo
 %%PYTHON_SITELIBDIR%%/cogent/util/transform.py
 %%PYTHON_SITELIBDIR%%/cogent/util/transform.pyc
 %%PYTHON_SITELIBDIR%%/cogent/util/transform.pyo