py-hcluster library provides Python functions for

agglomerative clustering. Its features include
* generating hierarchical clusters from distance matrices
* computing distance matrices from observation vectors
* computing statistics on clusters
* cutting linkages to generate flat clusters
* and visualizing clusters with dendrograms.

The interface is very similar to MATLAB's Statistics
Toolbox API to make code easier to port from MATLAB to
Python/Numpy. The core implementation of this library
is in C for efficiency.

WWW:	http://code.google.com/p/scipy-cluster/

PR:		ports/127515
Submitted by:	Wen Heping <wenheping at gmail.com>

6 files changed, 61 insertions, 0 deletions

diff --git a/science/Makefile b/science/Makefile
index cbba936942d3..ca306d307240 100644
--- a/science/Makefile
+++ b/science/Makefile
@@ -100,6 +100,7 @@
     SUBDIR += pcp
     SUBDIR += pnetcdf
     SUBDIR += psi3
+    SUBDIR += py-hcluster
     SUBDIR += py-openbabel
     SUBDIR += py-paida
     SUBDIR += py-scipy
diff --git a/science/py-hcluster/Makefile b/science/py-hcluster/Makefile
new file mode 100644
index 000000000000..fb5236dabc53
--- /dev/null
+++ b/science/py-hcluster/Makefile
@@ -0,0 +1,23 @@
+# New ports collection makefile for:	py-hcluster
+# Date created:		2008-09-04
+# Whom:			Wen Heping <wenheping@gmail.com>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	hcluster
+PORTVERSION=	0.1.9
+CATEGORIES=	science python
+MASTER_SITES=	CHEESESHOP
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER=	wenheping@gmail.com
+COMMENT=	A Hierarchical Clustering Package For Scipy
+
+BUILD_DEPENDS=	${PYTHON_SITELIBDIR}/numpy:${PORTSDIR}/math/py-numpy
+RUN_DEPENDS=	${BUILD_DEPENDS}
+
+USE_PYTHON=	yes
+USE_PYDISTUTILS=	yes
+
+.include <bsd.port.mk>
diff --git a/science/py-hcluster/distinfo b/science/py-hcluster/distinfo
new file mode 100644
index 000000000000..ddecba63ba31
--- /dev/null
+++ b/science/py-hcluster/distinfo
@@ -0,0 +1,3 @@
+MD5 (hcluster-0.1.9.tar.gz) = 1d24fd81648c8b154bca37b2fa91a274
+SHA256 (hcluster-0.1.9.tar.gz) = eb24c9ae0f2c65a2c2845d84350a4660af32fa36714a4ecca11c9085ae9d9bfa
+SIZE (hcluster-0.1.9.tar.gz) = 42642
diff --git a/science/py-hcluster/files/patch-setup.py b/science/py-hcluster/files/patch-setup.py
new file mode 100644
index 000000000000..620dff7de3df
--- /dev/null
+++ b/science/py-hcluster/files/patch-setup.py
@@ -0,0 +1,12 @@
+--- setup.py.orig	2008-09-21 22:20:16.000000000 +0800
++++ setup.py	2008-09-21 22:20:34.000000000 +0800
+@@ -33,7 +33,8 @@
+     print string.join(l, '\n')
+     # Prompt the user with a list of selections.
+     while not (s >= 1 and s <= len(valid_paths)):
+-        s = input('Selection [default=1]:' % s)
++#        s = input('Selection [default=1]:' % s)
++	s=1
+         if s == '':
+             s = 1
+         else:
diff --git a/science/py-hcluster/pkg-descr b/science/py-hcluster/pkg-descr
new file mode 100644
index 000000000000..650a24f72117
--- /dev/null
+++ b/science/py-hcluster/pkg-descr
@@ -0,0 +1,14 @@
+py-hcluster library provides Python functions for
+agglomerative clustering. Its features include
+* generating hierarchical clusters from distance matrices
+* computing distance matrices from observation vectors
+* computing statistics on clusters
+* cutting linkages to generate flat clusters
+* and visualizing clusters with dendrograms.
+
+The interface is very similar to MATLAB's Statistics
+Toolbox API to make code easier to port from MATLAB to
+Python/Numpy. The core implementation of this library
+is in C for efficiency. 
+
+WWW:	http://code.google.com/p/scipy-cluster/
diff --git a/science/py-hcluster/pkg-plist b/science/py-hcluster/pkg-plist
new file mode 100644
index 000000000000..71b2025b9d28
--- /dev/null
+++ b/science/py-hcluster/pkg-plist
@@ -0,0 +1,8 @@
+%%PYTHON_SITELIBDIR%%/_cluster_wrap.so
+%%PYTHON_SITELIBDIR%%/hcluster/__init__.py
+%%PYTHON_SITELIBDIR%%/hcluster/__init__.pyc
+%%PYTHON_SITELIBDIR%%/hcluster/__init__.pyo
+%%PYTHON_SITELIBDIR%%/hcluster/cluster.py
+%%PYTHON_SITELIBDIR%%/hcluster/cluster.pyc
+%%PYTHON_SITELIBDIR%%/hcluster/cluster.pyo
+@dirrm %%PYTHON_SITELIBDIR%%/hcluster