- Added STAGE support

- Update to 3.5.0

PR:		190314
Submitted by:	Muhammad Moinur Rahman <5u623l20@gmail.com>

6 files changed, 10 insertions, 167 deletions

diff --git a/science/py-mlpy/Makefile b/science/py-mlpy/Makefile
index 95cbce39caa7..60bf37b8b4a2 100644
--- a/science/py-mlpy/Makefile
+++ b/science/py-mlpy/Makefile
@@ -2,26 +2,26 @@
 # $FreeBSD$
 
 PORTNAME=	mlpy
-PORTVERSION=	2.2.2
-PORTREVISION=	4
+PORTVERSION=	3.5.0
 CATEGORIES=	science python
-MASTER_SITES=	https://mlpy.fbk.eu/download/src/
+MASTER_SITES=	SF/${PORTNAME}/${PORTNAME}%20${PORTVERSION}
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
-DISTNAME=	MLPY-${PORTVERSION}
 
 MAINTAINER=	wen@FreeBSD.org
 COMMENT=	High performance Python package for predictive modeling
 
+LICENSE=	GPLv3
+
 BUILD_DEPENDS=	${PYTHON_SITELIBDIR}/numpy:${PORTSDIR}/math/py-numpy \
 		cython>0:${PORTSDIR}/lang/cython
 RUN_DEPENDS:=	${BUILD_DEPENDS}
-LIB_DEPENDS=	gsl:${PORTSDIR}/math/gsl
+LIB_DEPENDS=	libgsl.so:${PORTSDIR}/math/gsl
 
+USE_LDCONFIG=	yes
 CFLAGS+=	-I${LOCALBASE}/include -I${PYTHON_SITELIBDIR}/numpy/core
 LDFLAGS+=	-L${LOCALBASE}/lib
 USE_PYTHON=	yes
 USE_PYDISTUTILS=	yes
-PYDISTUTILS_PKGNAME=	MLPY
+PYDISTUTILS_AUTOPLIST=	yes
 
-NO_STAGE=	yes
 .include <bsd.port.mk>
diff --git a/science/py-mlpy/distinfo b/science/py-mlpy/distinfo
index 4e6aef4a6707..1994927e2a90 100644
--- a/science/py-mlpy/distinfo
+++ b/science/py-mlpy/distinfo
@@ -1,2 +1,2 @@
-SHA256 (MLPY-2.2.2.tar.gz) = 2c2864834ced9caddea83bc05ffc7526325cf5bffcfd6c3c4cf13097312b0057
-SIZE (MLPY-2.2.2.tar.gz) = 235665
+SHA256 (mlpy-3.5.0.tar.gz) = 344fa75fbf9f76af72f6a346d5309613defc4d244bac13c218e509a51d68bf6a
+SIZE (mlpy-3.5.0.tar.gz) = 1961206
diff --git a/science/py-mlpy/files/patch-mlpy-cwt-cwb.c b/science/py-mlpy/files/patch-mlpy-cwt-cwb.c
deleted file mode 100644
index 2d57adf4c507..000000000000
--- a/science/py-mlpy/files/patch-mlpy-cwt-cwb.c
+++ /dev/null
@@ -1,17 +0,0 @@
---- mlpy/cwt/cwb.c.orig	2010-12-21 09:10:04.000000000 +0800
-+++ mlpy/cwt/cwb.c	2010-12-21 09:12:05.000000000 +0800
-@@ -142,9 +142,12 @@
-   complex double p = 0.0 + 0.0I; 
-   double sw, norm = 1.0;
-   
--  
-+#ifndef __STD_IEC_559_COMPLEX__  /* FreeBSD lacks C99 cpow() */
-+  p = - gsl_complex_pow(0.0 + 1.0I, order) / sqrt(gsl_sf_gamma(order + 0.5));
-+#else
-   p = - cpow(0.0 + 1.0I, order) / sqrt(gsl_sf_gamma(order + 0.5));
--  
-+#endif /* __STD_IEC_559_COMPLEX__ */
-+
-   for (i=0; i<n; i++)
-     {
-       if (nm == 1)
diff --git a/science/py-mlpy/files/patch-setup.py b/science/py-mlpy/files/patch-setup.py
deleted file mode 100644
index 0aa0368edf6f..000000000000
--- a/science/py-mlpy/files/patch-setup.py
+++ /dev/null
@@ -1,17 +0,0 @@
---- setup.py.orig	2010-10-18 20:08:13.000000000 +0800
-+++ setup.py	2010-12-23 15:19:09.000000000 +0800
-@@ -158,11 +158,13 @@
-                               "mlpy/liblinear/liblinear/blas/daxpy.c",
-                               "mlpy/liblinear/liblinear/blas/ddot.c",
-                               "mlpy/liblinear/liblinear/blas/dnrm2.c",
--                              "mlpy/liblinear/liblinear/blas/dscal.c"], 
-+                              "mlpy/liblinear/liblinear/blas/dscal.c"],
-+                             include_dirs=base_include, 
-                              extra_compile_args=extra_compile_args),
-                    Extension("mlpy.libsvm",
-                              ["mlpy/libsvm/libsvm/svm.cpp",
-                               "mlpy/libsvm/libsvm.pyx"],
-+                             include_dirs=base_include,
-                              extra_compile_args=extra_compile_args)
-                    ],
-       scripts=["mlpy/tools/mlpy-test"],
diff --git a/science/py-mlpy/pkg-descr b/science/py-mlpy/pkg-descr
index a3ac58b890cc..d427b1c691b3 100644
--- a/science/py-mlpy/pkg-descr
+++ b/science/py-mlpy/pkg-descr
@@ -8,4 +8,4 @@ selection. Methods are available for feature weighting and ranking, data
 resampling, error evaluation and experiment landscaping.The package
 includes tools to measure stability in sets of ranked feature lists.
 
-WWW:	http://mlpy.fbk.eu/
+WWW: http://mlpy.sourceforge.net/
diff --git a/science/py-mlpy/pkg-plist b/science/py-mlpy/pkg-plist
deleted file mode 100644
index 9b44ed417698..000000000000
--- a/science/py-mlpy/pkg-plist
+++ /dev/null
@@ -1,123 +0,0 @@
-bin/mlpy-test
-%%PYTHON_SITELIBDIR%%/mlpy/__init__.py
-%%PYTHON_SITELIBDIR%%/mlpy/__init__.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/__init__.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_borda.py
-%%PYTHON_SITELIBDIR%%/mlpy/_borda.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_borda.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_canberra.py
-%%PYTHON_SITELIBDIR%%/mlpy/_canberra.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_canberra.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_ci.py
-%%PYTHON_SITELIBDIR%%/mlpy/_ci.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_ci.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_cwt.py
-%%PYTHON_SITELIBDIR%%/mlpy/_cwt.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_cwt.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_data.py
-%%PYTHON_SITELIBDIR%%/mlpy/_data.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_data.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_dlda.py
-%%PYTHON_SITELIBDIR%%/mlpy/_dlda.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_dlda.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_dtw.py
-%%PYTHON_SITELIBDIR%%/mlpy/_dtw.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_dtw.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_dwt.py
-%%PYTHON_SITELIBDIR%%/mlpy/_dwt.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_dwt.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_dwtfs.py
-%%PYTHON_SITELIBDIR%%/mlpy/_dwtfs.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_dwtfs.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_elasticnet.py
-%%PYTHON_SITELIBDIR%%/mlpy/_elasticnet.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_elasticnet.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_extend.py
-%%PYTHON_SITELIBDIR%%/mlpy/_extend.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_extend.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_fda.py
-%%PYTHON_SITELIBDIR%%/mlpy/_fda.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_fda.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_fssun.py
-%%PYTHON_SITELIBDIR%%/mlpy/_fssun.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_fssun.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_hcluster.py
-%%PYTHON_SITELIBDIR%%/mlpy/_hcluster.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_hcluster.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_imputing.py
-%%PYTHON_SITELIBDIR%%/mlpy/_imputing.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_imputing.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_irelief.py
-%%PYTHON_SITELIBDIR%%/mlpy/_irelief.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_irelief.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_iuwt.py
-%%PYTHON_SITELIBDIR%%/mlpy/_iuwt.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_iuwt.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_kernel.py
-%%PYTHON_SITELIBDIR%%/mlpy/_kernel.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_kernel.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_kmeans.py
-%%PYTHON_SITELIBDIR%%/mlpy/_kmeans.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_kmeans.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_kmedoids.py
-%%PYTHON_SITELIBDIR%%/mlpy/_kmedoids.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_kmedoids.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_knn.py
-%%PYTHON_SITELIBDIR%%/mlpy/_knn.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_lars.py
-%%PYTHON_SITELIBDIR%%/mlpy/_lars.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_lars.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_knn.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_metrics.py
-%%PYTHON_SITELIBDIR%%/mlpy/_metrics.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_metrics.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_minkowski.py
-%%PYTHON_SITELIBDIR%%/mlpy/_minkowski.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_minkowski.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_pda.py
-%%PYTHON_SITELIBDIR%%/mlpy/_pda.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_pda.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_ranking.py
-%%PYTHON_SITELIBDIR%%/mlpy/_ranking.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_ranking.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_resampling.py
-%%PYTHON_SITELIBDIR%%/mlpy/_resampling.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_resampling.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_ridgeregression.py
-%%PYTHON_SITELIBDIR%%/mlpy/_ridgeregression.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_ridgeregression.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_spectralreg.py
-%%PYTHON_SITELIBDIR%%/mlpy/_spectralreg.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_spectralreg.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_srda.py
-%%PYTHON_SITELIBDIR%%/mlpy/_srda.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_srda.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_svm.py
-%%PYTHON_SITELIBDIR%%/mlpy/_svm.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_svm.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/_uwt.py
-%%PYTHON_SITELIBDIR%%/mlpy/_uwt.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/_uwt.pyo
-%%PYTHON_SITELIBDIR%%/mlpy/canberra.so
-%%PYTHON_SITELIBDIR%%/mlpy/cwb.so
-%%PYTHON_SITELIBDIR%%/mlpy/dtw.so
-%%PYTHON_SITELIBDIR%%/mlpy/dwt.so
-%%PYTHON_SITELIBDIR%%/mlpy/elasticnet.so
-%%PYTHON_SITELIBDIR%%/mlpy/fssun.so
-%%PYTHON_SITELIBDIR%%/mlpy/hc.so
-%%PYTHON_SITELIBDIR%%/mlpy/irregularuwt.so
-%%PYTHON_SITELIBDIR%%/mlpy/gslpy.so
-%%PYTHON_SITELIBDIR%%/mlpy/kmeans.so
-%%PYTHON_SITELIBDIR%%/mlpy/kernel.so
-%%PYTHON_SITELIBDIR%%/mlpy/knn.so
-%%PYTHON_SITELIBDIR%%/mlpy/liblinear.so
-%%PYTHON_SITELIBDIR%%/mlpy/libsvm.so
-%%PYTHON_SITELIBDIR%%/mlpy/misc.so
-%%PYTHON_SITELIBDIR%%/mlpy/peaksd.so
-%%PYTHON_SITELIBDIR%%/mlpy/spectralreg.so
-%%PYTHON_SITELIBDIR%%/mlpy/svm.so
-%%PYTHON_SITELIBDIR%%/mlpy/uwt.so
-%%PYTHON_SITELIBDIR%%/mlpy/version.py
-%%PYTHON_SITELIBDIR%%/mlpy/version.pyc
-%%PYTHON_SITELIBDIR%%/mlpy/version.pyo
-@dirrm %%PYTHON_SITELIBDIR%%/mlpy