fixed conflict with cdf (bug #191593), removed old versions

(Portage version: 2.1.2.12)

6 files changed, 34 insertions, 662 deletions

diff --git a/sci-libs/scipy/ChangeLog b/sci-libs/scipy/ChangeLog
index 768031c6bd64..5908ea6da1eb 100644
--- a/sci-libs/scipy/ChangeLog
+++ b/sci-libs/scipy/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-libs/scipy
 # Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/ChangeLog,v 1.21 2007/09/09 14:27:39 josejx Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/ChangeLog,v 1.22 2007/09/11 17:32:38 bicatali Exp $
+
+  11 Sep 2007; Sébastien Fabbro <bicatali@gentoo.org>
+  +files/scipy-0.5.2-cdf.patch, -files/scipy-0.5.2-getpath.patch,
+  -files/scipy-0.5.2-mio.patch, -files/scipy-0.5.2-umfpack.patch,
+  scipy-0.5.2.1.ebuild:
+  fixed conflict with cdf (bug #191593), removed old versions
 
   09 Sep 2007; Joseph Jezak <josejx@gentoo.org> scipy-0.5.2.1.ebuild:
   Marked ~ppc for bug #191600.
diff --git a/sci-libs/scipy/files/scipy-0.5.2-cdf.patch b/sci-libs/scipy/files/scipy-0.5.2-cdf.patch
new file mode 100644
index 000000000000..99a334071c15
--- /dev/null
+++ b/sci-libs/scipy/files/scipy-0.5.2-cdf.patch
@@ -0,0 +1,24 @@
+--- Lib/special/setup.py.orig	2007-09-11 18:11:04.457232054 +0100
++++ Lib/special/setup.py	2007-09-11 18:09:23.103456231 +0100
+@@ -20,9 +20,9 @@
+     # Fortran libraries
+     config.add_library('mach',sources=[join('mach','*.f')],
+                        config_fc={'noopt':(__file__,1)})
+-    config.add_library('toms',sources=[join('amos','*.f')])
+-    config.add_library('amos',sources=[join('toms','*.f')])
+-    config.add_library('cdf',sources=[join('cdflib','*.f')])
++    config.add_library('toms',sources=[join('toms','*.f')])
++    config.add_library('amos',sources=[join('amos','*.f')])
++    config.add_library('cdflib',sources=[join('cdflib','*.f')])
+     config.add_library('specfun',sources=[join('specfun','*.f')])
+ 
+     # Extension _cephes
+@@ -30,7 +30,7 @@
+                'toms_wrappers.c','cdf_wrappers.c','ufunc_extras.c']
+     config.add_extension('_cephes', sources=sources,
+                          libraries=['amos','toms','c_misc','cephes','mach',
+-                                    'cdf', 'specfun'],
++                                    'cdflib', 'specfun'],
+                          define_macros = define_macros
+                          )
+     # Extension specfun
diff --git a/sci-libs/scipy/files/scipy-0.5.2-getpath.patch b/sci-libs/scipy/files/scipy-0.5.2-getpath.patch
deleted file mode 100644
index fe98a999411e..000000000000
--- a/sci-libs/scipy/files/scipy-0.5.2-getpath.patch
+++ /dev/null
@@ -1,108 +0,0 @@
-diff -Nur Lib.orig/linalg/setup_atlas_version.py Lib/linalg/setup_atlas_version.py
---- Lib.orig/linalg/setup_atlas_version.py	2006-03-15 02:29:45.000000000 +0000
-+++ Lib/linalg/setup_atlas_version.py	2007-06-06 16:43:08.000000000 +0100
-@@ -4,14 +4,14 @@
- 
- import os
- from distutils.core import Extension
--from numpy.distutils.misc_util import get_path, default_config_dict
-+from numpy.distutils.misc_util import get_path_from_frame, default_config_dict
- from numpy.distutils.system_info import get_info,AtlasNotFoundError
- 
- def configuration (parent_package=''):
-     package = 'linalg'
-     config = default_config_dict(package,parent_package)
-     del config['fortran_libraries']
--    local_path = get_path(__name__)
-+    local_path = get_path_from_frame(__name__)
-     atlas_info = get_info('atlas_threads')
-     if not atlas_info:
-         atlas_info = get_info('atlas')
-diff -Nur Lib.orig/odr/setup.py Lib/odr/setup.py
---- Lib.orig/odr/setup.py	2006-12-02 03:24:44.000000000 +0000
-+++ Lib/odr/setup.py	2007-06-06 16:43:08.000000000 +0100
-@@ -6,7 +6,7 @@
- import warnings
- 
- from numpy.distutils.core import Extension
--from numpy.distutils.misc_util import get_path, Configuration, dot_join
-+from numpy.distutils.misc_util import get_path_from_frame, Configuration, dot_join
- 
- from numpy.distutils.system_info import get_info,dict_append,\
-      AtlasNotFoundError,LapackNotFoundError,BlasNotFoundError,\
-diff -Nur Lib.orig/sandbox/ga/setup_ga.py Lib/sandbox/ga/setup_ga.py
---- Lib.orig/sandbox/ga/setup_ga.py	2006-01-05 03:35:26.000000000 +0000
-+++ Lib/sandbox/ga/setup_ga.py	2007-06-06 16:43:08.000000000 +0100
-@@ -1,7 +1,7 @@
- #!/usr/bin/env python
- 
- import os
--from numpy.distutils.misc_util import get_path, default_config_dict
-+from numpy.distutils.misc_util import get_path_from_frame, default_config_dict
- 
- def configuration(parent_package='',parent_path=None):
-     package = 'ga'
-diff -Nur Lib.orig/sandbox/gplt/setup_gplt.py Lib/sandbox/gplt/setup_gplt.py
---- Lib.orig/sandbox/gplt/setup_gplt.py	2006-01-05 03:35:31.000000000 +0000
-+++ Lib/sandbox/gplt/setup_gplt.py	2007-06-06 16:43:08.000000000 +0100
-@@ -1,11 +1,11 @@
- #!/usr/bin/env python
- 
- import os, sys
--from numpy.distutils.misc_util import get_path, default_config_dict
-+from numpy.distutils.misc_util import get_path_from_frame, default_config_dict
- 
- def configuration(parent_package='',parent_path=None):
-     package = 'gplt'
--    local_path = get_path(__name__,parent_path)
-+    local_path = get_path_from_frame(__name__,parent_path)
-     config = default_config_dict(package,parent_package)
- 
-     if sys.platform == 'win32':
-diff -Nur Lib.orig/sandbox/image/setup_image.py Lib/sandbox/image/setup_image.py
---- Lib.orig/sandbox/image/setup_image.py	2006-03-15 02:29:18.000000000 +0000
-+++ Lib/sandbox/image/setup_image.py	2007-06-06 16:43:08.000000000 +0100
-@@ -6,12 +6,12 @@
- def configuration(parent_package='', parent_path=None):
-     from numpy.distutils.system_info import get_info, dict_append
-     from numpy.distutils.misc_util import default_config_dict, \
--         dot_join, get_path
-+         dot_join, get_path_from_frame
- 
-     package = 'image'
-     config = default_config_dict(package,parent_package)
- 
--    local_path = get_path(__name__, parent_path)
-+    local_path = get_path_from_frame(__name__, parent_path)
-     image_path = os.path.join(parent_package,'image')
- 
-     color_files = glob(os.path.join(local_path, '*.txt'))
-diff -Nur Lib.orig/sandbox/plt/setup_plt.py Lib/sandbox/plt/setup_plt.py
---- Lib.orig/sandbox/plt/setup_plt.py	2006-01-13 00:08:11.000000000 +0000
-+++ Lib/sandbox/plt/setup_plt.py	2007-06-06 16:43:08.000000000 +0100
-@@ -1,11 +1,11 @@
- #!/usr/bin/env python
- 
- import os
--from numpy.distutils.misc_util import get_path, default_config_dict
-+from numpy.distutils.misc_util import get_path_from_frame, default_config_dict
- 
- def configuration(parent_package='',parent_path=None):
-     package = 'plt'
--    local_path = get_path(__name__,parent_path)
-+    local_path = get_path_from_frame(__name__,parent_path)
-     config = default_config_dict(package,parent_package)
-     return config
- 
-diff -Nur Lib.orig/sandbox/pysparse/setup.py Lib/sandbox/pysparse/setup.py
---- Lib.orig/sandbox/pysparse/setup.py	2006-03-15 02:29:36.000000000 +0000
-+++ Lib/sandbox/pysparse/setup.py	2007-06-06 16:43:08.000000000 +0100
-@@ -12,7 +12,7 @@
- 
- import os
- from numpy.distutils.core import Extension
--from numpy.distutils.misc_util import get_path,Configuration,dot_join
-+from numpy.distutils.misc_util import get_path_from_frame,Configuration,dot_join
- join = os.path.join
- import glob
- 
diff --git a/sci-libs/scipy/files/scipy-0.5.2-mio.patch b/sci-libs/scipy/files/scipy-0.5.2-mio.patch
deleted file mode 100644
index b48c8eb4e770..000000000000
--- a/sci-libs/scipy/files/scipy-0.5.2-mio.patch
+++ /dev/null
@@ -1,524 +0,0 @@
-diff -Nur Lib/io.orig/mio4.py Lib/io/mio4.py
---- Lib/io.orig/mio4.py	2007-06-06 14:56:05.610464000 +0100
-+++ Lib/io/mio4.py	2007-06-06 14:56:17.015176750 +0100
-@@ -1,9 +1,9 @@
- ''' Classes for read / write of matlab (TM) 4 files
- '''
- 
--from numpy import *
-+import numpy as N
- 
--from miobase import *
-+from scipy.io.miobase import *
- 
- miDOUBLE = 0
- miSINGLE = 1
-@@ -76,7 +76,7 @@
-         header['mclass'] = T
-         header['dims'] = (data['mrows'], data['ncols'])
-         header['is_complex'] = data['imagf'] == 1
--        remaining_bytes = header['dtype'].itemsize * product(header['dims'])
-+        remaining_bytes = header['dtype'].itemsize * N.product(header['dims'])
-         if header['is_complex'] and not header['mclass'] == mxSPARSE_CLASS:
-             remaining_bytes *= 2
-         next_pos = self.mat_stream.tell() + remaining_bytes
-@@ -109,7 +109,7 @@
-         num_bytes = dt.itemsize
-         for d in dims:
-             num_bytes *= d
--        arr = ndarray(shape=dims,
-+        arr = N.ndarray(shape=dims,
-                       dtype=dt,
-                       buffer=self.mat_stream.read(num_bytes),
-                       order='F')
-@@ -122,9 +122,9 @@
-     def __init__(self, array_reader, header):
-         super(Mat4FullGetter, self).__init__(array_reader, header)
-         if header['is_complex']:
--            self.mat_dtype = dtype(complex128)
-+            self.mat_dtype = N.dtype(N.complex128)
-         else:
--            self.mat_dtype = dtype(float64)
-+            self.mat_dtype = N.dtype(N.float64)
-         
-     def get_raw_array(self):
-         if self.header['is_complex']:
-@@ -137,12 +137,12 @@
- 
- class Mat4CharGetter(Mat4MatrixGetter):
-     def get_raw_array(self):
--        arr = self.read_array().astype(uint8)
-+        arr = self.read_array().astype(N.uint8)
-         # ascii to unicode
-         S = arr.tostring().decode('ascii')
--        return ndarray(shape=self.header['dims'],
--                       dtype=dtype('U1'),
--                       buffer = array(S)).copy()
-+        return N.ndarray(shape=self.header['dims'],
-+                       dtype=N.dtype('U1'),
-+                       buffer = N.array(S)).copy()
- 
- 
- class Mat4SparseGetter(Mat4MatrixGetter):
-@@ -166,7 +166,7 @@
-         res = self.read_array()
-         tmp = res[:-1,:]
-         dims = res[-1,0:2]
--        ij = transpose(tmp[:,0:2]) - 1 # for 1-based indexing
-+        ij = N.transpose(tmp[:,0:2]) - 1 # for 1-based indexing
-         vals = tmp[:,2]
-         if res.shape[1] == 4:
-             vals = vals + res[:-1,3] * 1j
-@@ -196,15 +196,15 @@
-     def format_looks_right(self):
-         # Mat4 files have a zero somewhere in first 4 bytes
-         self.mat_stream.seek(0)
--        mopt_bytes = ndarray(shape=(4,),
--                             dtype=uint8,
-+        mopt_bytes = N.ndarray(shape=(4,),
-+                             dtype=N.uint8,
-                              buffer = self.mat_stream.read(4))
-         self.mat_stream.seek(0)
-         return 0 in mopt_bytes
-     
-     def guess_byte_order(self):
-         self.mat_stream.seek(0)
--        mopt = self.read_dtype(dtype('i4'))
-+        mopt = self.read_dtype(N.dtype('i4'))
-         self.mat_stream.seek(0)
-         if mopt < 0 or mopt > 5000:
-             return ByteOrder.swapped_code
-@@ -222,7 +222,7 @@
-         '''
-         if dims is None:
-             dims = self.arr.shape
--        header = empty((), mdtypes_template['header'])
-+        header = N.empty((), mdtypes_template['header'])
-         M = not ByteOrder.little_endian
-         O = 0
-         header['mopt'] = (M * 1000 +
-@@ -237,11 +237,10 @@
-         self.write_string(self.name + '\0')
-         
-     def arr_to_2d(self):
--        self.arr = atleast_2d(self.arr)
-+        self.arr = N.atleast_2d(self.arr)
-         dims = self.arr.shape
-         if len(dims) > 2:
--            dims = [product(dims[:-1]), dims[-1]]
--            self.arr = reshape(self.arr, dims)
-+            self.arr = self.arr.reshape(-1,dims[-1])
-             
-     def write(self):
-         assert False, 'Not implemented'
-@@ -280,12 +279,12 @@
-                           T=mxCHAR_CLASS)
-         if self.arr.dtype.kind == 'U':
-             # Recode unicode to ascii
--            n_chars = product(dims)
--            st_arr = ndarray(shape=(),
-+            n_chars = N.product(dims)
-+            st_arr = N.ndarray(shape=(),
-                              dtype=self.arr_dtype_number(n_chars),
-                              buffer=self.arr)
-             st = st_arr.item().encode('ascii')
--            self.arr = ndarray(shape=dims, dtype='S1', buffer=st)
-+            self.arr = N.ndarray(shape=dims, dtype='S1', buffer=st)
-         self.write_bytes(self.arr)
- 
- 
-@@ -296,9 +295,9 @@
-         See docstring for Mat4SparseGetter
-         '''
-         imagf = self.arr.dtype.kind == 'c'
--        N = self.arr.nnz
--        ijd = zeros((N+1, 3+imagf), dtype='f8')
--        for i in range(N):
-+        nnz = self.arr.nnz
-+        ijd = N.zeros((nnz+1, 3+imagf), dtype='f8')
-+        for i in range(nnz):
-             ijd[i,0], ijd[i,1] = self.arr.rowcol(i)
-         ijd[:-1,0:2] += 1 # 1 based indexing
-         if imagf:
-@@ -322,13 +321,13 @@
-     if have_sparse:
-         if scipy.sparse.issparse(arr):
-             return Mat4SparseWriter(stream, arr, name)
--    arr = array(arr)
-+    arr = N.array(arr)
-     dtt = arr.dtype.type
--    if dtt is object_:
-+    if dtt is N.object_:
-         raise TypeError, 'Cannot save object arrays in Mat4'
--    elif dtt is void:
-+    elif dtt is N.void:
-         raise TypeError, 'Cannot save void type arrays'
--    elif dtt in (unicode_, string_):
-+    elif dtt in (N.unicode_, N.string_):
-         return Mat4CharWriter(stream, arr, name)
-     else:
-         return Mat4NumericWriter(stream, arr, name)
-diff -Nur Lib/io.orig/mio5.py Lib/io/mio5.py
---- Lib/io.orig/mio5.py	2007-06-06 14:56:05.610464000 +0100
-+++ Lib/io/mio5.py	2007-06-06 14:56:17.019177000 +0100
-@@ -29,9 +29,9 @@
- import zlib
- from copy import copy as pycopy
- from cStringIO import StringIO
--from numpy import *
-+import numpy as N
- 
--from miobase import *
-+from scipy.io.miobase import *
- 
- try:  # Python 2.3 support
-     from sets import Set as set
-@@ -154,10 +154,10 @@
- 
-     def read_element(self, copy=True):
-         raw_tag = self.mat_stream.read(8)
--        tag = ndarray(shape=(),
-+        tag = N.ndarray(shape=(),
-                       dtype=self.dtypes['tag_full'],
-                       buffer = raw_tag)
--        mdtype = tag['mdtype']
-+        mdtype = tag['mdtype'].item()
-         byte_count = mdtype >> 16
-         if byte_count: # small data element format
-             if byte_count > 4:
-@@ -165,10 +165,10 @@
-             mdtype = mdtype & 0xFFFF
-             dt = self.dtypes[mdtype]
-             el_count = byte_count / dt.itemsize
--            return ndarray(shape=(el_count,),
-+            return N.ndarray(shape=(el_count,),
-                            dtype=dt,
-                            buffer=raw_tag[4:])
--        byte_count = tag['byte_count']
-+        byte_count = tag['byte_count'].item()
-         if mdtype == miMATRIX:
-             return self.current_getter(byte_count).get_array()
-         if mdtype in self.codecs: # encoded char data
-@@ -180,7 +180,7 @@
-         else: # numeric data
-             dt = self.dtypes[mdtype]
-             el_count = byte_count / dt.itemsize
--            el = ndarray(shape=(el_count,),
-+            el = N.ndarray(shape=(el_count,),
-                          dtype=dt,
-                          buffer=self.mat_stream.read(byte_count))
-             if copy:
-@@ -193,8 +193,8 @@
-     def matrix_getter_factory(self):
-         ''' Returns reader for next matrix at top level '''
-         tag = self.read_dtype(self.dtypes['tag_full'])
--        mdtype = tag['mdtype']
--        byte_count = tag['byte_count']
-+        mdtype = tag['mdtype'].item()
-+        byte_count = tag['byte_count'].item()
-         next_pos = self.mat_stream.tell() + byte_count
-         if mdtype == miCOMPRESSED:
-             getter = Mat5ZArrayReader(self, byte_count).matrix_getter_factory()
-@@ -285,7 +285,7 @@
-         self.mat_dtype = 'f8'
-     
-     def get_raw_array(self):
--        return array([[]])
-+        return N.array([[]])
- 
- 
- class Mat5NumericMatrixGetter(Mat5MatrixGetter):
-@@ -293,7 +293,7 @@
-     def __init__(self, array_reader, header):
-         super(Mat5NumericMatrixGetter, self).__init__(array_reader, header)
-         if header['is_logical']:
--            self.mat_dtype = dtype('bool')
-+            self.mat_dtype = N.dtype('bool')
-         else:
-             self.mat_dtype = self.class_dtypes[header['mclass']]
- 
-@@ -305,7 +305,7 @@
-             res = res + (res_j * 1j)
-         else:
-             res = self.read_element()
--        return ndarray(shape=self.header['dims'],
-+        return N.ndarray(shape=self.header['dims'],
-                        dtype=res.dtype,
-                        buffer=res,
-                        order='F')
-@@ -334,14 +334,14 @@
-         stored in column order, this gives the column corresponding to
-         each rowind
-         '''
--        cols = empty((len(res)), dtype=rowind.dtype)
--        col_counts = diff(colind)
-+        cols = N.empty((len(res)), dtype=rowind.dtype)
-+        col_counts = N.diff(colind)
-         start_row = 0
--        for i in where(col_counts)[0]:
-+        for i in N.where(col_counts)[0]:
-             end_row = start_row + col_counts[i]
-             cols[start_row:end_row] = i
-             start_row = end_row
--        ij = vstack((rowind[:len(res)], cols))
-+        ij = N.vstack((rowind[:len(res)], cols))
-         if have_sparse:
-             result = scipy.sparse.csc_matrix((res,ij),
-                                              self.header['dims'])
-@@ -354,19 +354,19 @@
-     def get_raw_array(self):
-         res = self.read_element()
-         # Convert non-string types to unicode
--        if isinstance(res, ndarray):
--            if res.dtype.type == uint16:
-+        if isinstance(res, N.ndarray):
-+            if res.dtype.type == N.uint16:
-                 codec = miUINT16_codec
-                 if self.codecs['uint16_len'] == 1:
--                    res = res.astype(uint8)
--            elif res.dtype.type in (uint8, int8):
-+                    res = res.astype(N.uint8)
-+            elif res.dtype.type in (N.uint8, N.int8):
-                 codec = 'ascii'
-             else:
-                 raise TypeError, 'Did not expect type %s' % res.dtype
-             res = res.tostring().decode(codec)
--        return ndarray(shape=self.header['dims'],
--                       dtype=dtype('U1'),
--                       buffer=array(res),
-+        return N.ndarray(shape=self.header['dims'],
-+                       dtype=N.dtype('U1'),
-+                       buffer=N.array(res),
-                        order='F').copy()
- 
- 
-@@ -374,12 +374,11 @@
-     def get_raw_array(self):
-         # Account for fortran indexing of cells
-         tupdims = tuple(self.header['dims'][::-1])
--        length = product(tupdims)
--        result = empty(length, dtype=object)
-+        length = N.product(tupdims)
-+        result = N.empty(length, dtype=object)
-         for i in range(length):
-             result[i] = self.get_item()
--        result = transpose(reshape(result,tupdims))
--        return result
-+        return result.reshape(tupdims).T
- 
-     def get_item(self):
-         return self.read_element()
-@@ -507,7 +506,7 @@
-         ''' Read in mat 5 file header '''
-         hdict = {}
-         hdr = self.read_dtype(self.dtypes['file_header'])
--        hdict['__header__'] = hdr['description'].strip(' \t\n\000')
-+        hdict['__header__'] = hdr['description'].item().strip(' \t\n\000')
-         v_major = hdr['version'] >> 8
-         v_minor = hdr['version'] & 0xFF
-         hdict['__version__'] = '%d.%d' % (v_major, v_minor)
-@@ -516,8 +515,8 @@
-     def format_looks_right(self):
-         # Mat4 files have a zero somewhere in first 4 bytes
-         self.mat_stream.seek(0)
--        mopt_bytes = ndarray(shape=(4,),
--                             dtype=uint8,
-+        mopt_bytes = N.ndarray(shape=(4,),
-+                             dtype=N.uint8,
-                              buffer = self.mat_stream.read(4))
-         self.mat_stream.seek(0)
-         return 0 not in mopt_bytes
-@@ -525,7 +524,7 @@
- 
- class Mat5MatrixWriter(MatStreamWriter):
- 
--    mat_tag = zeros((), mdtypes_template['tag_full'])
-+    mat_tag = N.zeros((), mdtypes_template['tag_full'])
-     mat_tag['mdtype'] = miMATRIX
- 
-     def __init__(self, file_stream, arr, name, is_global=False):
-@@ -555,14 +554,14 @@
-         self._mat_tag_pos = self.file_stream.tell()
-         self.write_dtype(self.mat_tag)
-         # write array flags (complex, global, logical, class, nzmax)
--        af = zeros((), mdtypes_template['array_flags'])
-+        af = N.zeros((), mdtypes_template['array_flags'])
-         af['data_type'] = miUINT32
-         af['byte_count'] = 8
-         flags = is_complex << 3 | is_global << 2 | is_logical << 1
-         af['flags_class'] = mclass | flags << 8
-         af['nzmax'] = nzmax
-         self.write_dtype(af)
--        self.write_element(array(self.arr.shape, dtype='i4'))
-+        self.write_element(N.array(self.arr.shape, dtype='i4'))
-         self.write_element(self.name)
- 
-     def update_matrix_tag(self):
-@@ -598,12 +597,12 @@
-                           T=mxCHAR_CLASS)
-         if self.arr.dtype.kind == 'U':
-             # Recode unicode to ascii
--            n_chars = product(dims)
--            st_arr = ndarray(shape=(),
-+            n_chars = N.product(dims)
-+            st_arr = N.ndarray(shape=(),
-                              dtype=self.arr_dtype_number(n_chars),
-                              buffer=self.arr)
-             st = st_arr.item().encode('ascii')
--            self.arr = ndarray(shape=dims, dtype='S1', buffer=st)
-+            self.arr = N.ndarray(shape=dims, dtype='S1', buffer=st)
-         self.write_bytes(self.arr)
- 
- 
-@@ -615,7 +614,7 @@
-         '''
-         imagf = self.arr.dtype.kind == 'c'
-         N = self.arr.nnz
--        ijd = zeros((N+1, 3+imagf), dtype='f8')
-+        ijd = N.zeros((N+1, 3+imagf), dtype='f8')
-         for i in range(N):
-             ijd[i,0], ijd[i,1] = self.arr.rowcol(i)
-         ijd[:-1,0:2] += 1 # 1 based indexing
-@@ -649,7 +648,7 @@
-         if have_sparse:
-             if scipy.sparse.issparse(arr):
-                 return Mat5SparseWriter(self.stream, arr, name, is_global)
--        arr = array(arr)
-+        arr = N.array(arr)
-         if arr.dtype.hasobject:
-             types, arr_type = classify_mobjects(arr)
-             if arr_type == 'c':
-@@ -680,13 +679,13 @@
-                         o  - object array
-         '''
-         N = objarr.size
--        types = empty((N,), dtype='S1')
-+        types = N.empty((N,), dtype='S1')
-         types[:] = 'i'
-         type_set = set()
-         flato = objarr.flat
-         for i in range(N):
-             obj = flato[i]
--            if isinstance(obj, ndarray):
-+            if isinstance(obj, N.ndarray):
-                 types[i] = 'a'
-                 continue
-             try:
-@@ -743,7 +742,7 @@
-                 ).write()
-             if self.do_compression:
-                 str = zlib.compress(stream.getvalue())
--                tag = empty((), mdtypes_template['tag_full'])
-+                tag = N.empty((), mdtypes_template['tag_full'])
-                 tag['mdtype'] = miCOMPRESSED
-                 tag['byte_count'] = len(str)
-                 self.file_stream.write(tag.tostring() + str)
-diff -Nur Lib/io.orig/miobase.py Lib/io/miobase.py
---- Lib/io.orig/miobase.py	2007-06-06 14:56:05.610464000 +0100
-+++ Lib/io/miobase.py	2007-06-06 14:56:17.019177000 +0100
-@@ -6,7 +6,7 @@
- 
- import sys
- 
--from numpy import *
-+import numpy as N
- 
- try:
-     import scipy.sparse
-@@ -71,10 +71,10 @@
-         a_dtype is assumed to be correct endianness
-         '''
-         num_bytes = a_dtype.itemsize
--        arr = ndarray(shape=(),
--                      dtype=a_dtype,
--                      buffer=self.mat_stream.read(num_bytes),
--                      order='F')
-+        arr = N.ndarray(shape=(),
-+                        dtype=a_dtype,
-+                        buffer=self.mat_stream.read(num_bytes),
-+                        order='F')
-         return arr
- 
-     def read_ztstring(self, num_bytes):
-@@ -184,7 +184,7 @@
-     def convert_dtypes(self, dtype_template):
-         dtypes = dtype_template.copy()
-         for k in dtypes:
--            dtypes[k] = dtype(dtypes[k]).newbyteorder(
-+            dtypes[k] = N.dtype(dtypes[k]).newbyteorder(
-                 self.order_code)
-         return dtypes
-     
-@@ -227,10 +227,10 @@
-                 if len(dims) >= 2: # return array of strings
-                     dtt = self.order_code + 'U'
-                     n_dims = dims[:-1]
--                    str_arr = reshape(arr,
--                                    (small_product(n_dims),
--                                     dims[-1]))
--                    arr = empty(n_dims, dtype=object)
-+                    str_arr = arr.reshape(
-+                        (small_product(n_dims),
-+                         dims[-1]))
-+                    arr = N.empty(n_dims, dtype=object)
-                     for i in range(0, n_dims[-1]):
-                         arr[...,i] = self.chars_to_str(str_arr[i])
-                 else: # return string
-@@ -241,9 +241,9 @@
-                 if getter.mat_dtype is not None:
-                     arr = arr.astype(getter.mat_dtype)
-             if self.squeeze_me:
--                arr = squeeze(arr)
-+                arr = N.squeeze(arr)
-                 if not arr.size:
--                    arr = array([])
-+                    arr = N.array([])
-                 elif not arr.shape: # 0d coverted to scalar
-                     arr = arr.item()
-             return arr
-@@ -251,8 +251,8 @@
- 
-     def chars_to_str(self, str_arr):
-         ''' Convert string array to string '''
--        dt = dtype('U' + str(small_product(str_arr.shape)))
--        return ndarray(shape=(),
-+        dt = N.dtype('U' + str(small_product(str_arr.shape)))
-+        return N.ndarray(shape=(),
-                        dtype = dt,
-                        buffer = str_arr.copy()).item()
- 
-@@ -354,7 +354,7 @@
-         
-     def arr_dtype_number(self, num):
-         ''' Return dtype for given number of items per element'''
--        return dtype(self.arr.dtype.str[:2] + str(num))
-+        return N.dtype(self.arr.dtype.str[:2] + str(num))
- 
-     def arr_to_chars(self):
-         ''' Convert string array to char array '''
-@@ -362,7 +362,7 @@
-         if not dims:
-             dims = [1]
-         dims.append(int(self.arr.dtype.str[2:]))
--        self.arr = ndarray(shape=dims,
-+        self.arr = N.ndarray(shape=dims,
-                            dtype=self.arr_dtype_number(1),
-                            buffer=self.arr)
- 
-diff -Nur Lib/io.orig/mio.py Lib/io/mio.py
---- Lib/io.orig/mio.py	2007-06-06 14:56:05.610464000 +0100
-+++ Lib/io/mio.py	2007-06-06 14:56:17.015176750 +0100
-@@ -7,10 +7,10 @@
- import os
- import sys
- 
--from numpy import *
-+from scipy.io.mio4 import MatFile4Reader, MatFile4Writer
-+from scipy.io.mio5 import MatFile5Reader, MatFile5Writer
- 
--from mio4 import MatFile4Reader, MatFile4Writer
--from mio5 import MatFile5Reader, MatFile5Writer
-+__all__ = ['find_mat_file','mat_reader_factory','loadmat', 'savemat']
- 
- def find_mat_file(file_name, appendmat=True):
-     ''' Try to find .mat file on system path
diff --git a/sci-libs/scipy/files/scipy-0.5.2-umfpack.patch b/sci-libs/scipy/files/scipy-0.5.2-umfpack.patch
deleted file mode 100644
index 21916b097ed9..000000000000
--- a/sci-libs/scipy/files/scipy-0.5.2-umfpack.patch
+++ /dev/null
@@ -1,28 +0,0 @@
---- Lib/linsolve/umfpack/umfpack.i.orig	2007-06-06 14:53:42.261505250 +0100
-+++ Lib/linsolve/umfpack/umfpack.i	2007-06-06 14:54:12.167374250 +0100
-@@ -114,6 +114,7 @@
-     return NULL; \
-   } \
-   $1 = (double *) obj->data; \
-+  Py_DECREF( obj ); \
- };
- 
- /*!
-@@ -127,7 +128,7 @@
- }; \
- %typemap( python, argout ) ttype* opaque_argout { \
-   PyObject *obj; \
--  obj = SWIG_NewPointerObj( (ttype) (*$1), $*1_descriptor, 1 ); \
-+  obj = SWIG_NewPointerObj( (ttype) (*$1), $*1_descriptor, 0 ); \
-   $result = helper_appendToTuple( $result, obj ); \
- };
- 
-@@ -143,7 +144,7 @@
- }; \
- %typemap( python, argout ) ttype* opaque_arginout { \
-   PyObject *obj; \
--  obj = SWIG_NewPointerObj( (ttype) (*$1), $*1_descriptor, 1 ); \
-+  obj = SWIG_NewPointerObj( (ttype) (*$1), $*1_descriptor, 0 ); \
-   $result = helper_appendToTuple( $result, obj ); \
- };
- 
diff --git a/sci-libs/scipy/scipy-0.5.2.1.ebuild b/sci-libs/scipy/scipy-0.5.2.1.ebuild
index 8e0d861f2e27..c5dca7e416e4 100644
--- a/sci-libs/scipy/scipy-0.5.2.1.ebuild
+++ b/sci-libs/scipy/scipy-0.5.2.1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2007 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/scipy-0.5.2.1.ebuild,v 1.3 2007/09/09 14:27:39 josejx Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/scipy-0.5.2.1.ebuild,v 1.4 2007/09/11 17:32:38 bicatali Exp $
 
 NEED_PYTHON=2.3
 
@@ -61,6 +61,7 @@ scipy_fortran_setup() {
 # see numpy ebuild about unsetting LDFLAGS
 LDFLAGS_sav="${LDFLAGS}"
 unset LDFLAGS
+
 pkg_setup() {
 	[[ -n "${LDFLAGS_sav}" ]] && einfo "Ignoring LDFLAGS=${LDFLAGS_sav}"
 	if use umfpack && ! built_with_use dev-lang/swig python; then
@@ -90,6 +91,7 @@ src_unpack() {
 	epatch "${FILESDIR}"/${TP}-minpack.patch
 	epatch "${FILESDIR}"/${TP}-bspline.patch
 	epatch "${FILESDIR}"/${TP}-nonexisting.patch
+	epatch "${FILESDIR}"/${TP}-cdf.patch
 	use sandbox && cp "${FILESDIR}"/enabled_packages.txt Lib/sandbox/
 }