Re: pkg/43282: [math/py-Scientific] Update to 2.8

To: pkg-manager%netbsd.org@localhost,gnats-admin%netbsd.org@localhost,pkgsrc-bugs%netbsd.org@localhost,wenheping%gmail.com@localhost
Subject: Re: pkg/43282: [math/py-Scientific] Update to 2.8
From: wen heping <wenheping%gmail.com@localhost>
Date: Wed, 26 May 2010 16:10:06 +0000 (UTC)
The following reply was made to PR pkg/43282; it has been noted by GNATS.

From: wen heping <wenheping%gmail.com@localhost>
To: gnats-bugs%netbsd.org@localhost
Cc: 
Subject: Re: pkg/43282: [math/py-Scientific] Update to 2.8
Date: Thu, 27 May 2010 00:07:35 +0800

 Please use this diff instead to fix:
 
 wen
 
 
 
 diff -urN py-Scientific.orig/Makefile py-Scientific/Makefile
 --- py-Scientific.orig/Makefile 2010-05-09 20:41:31.000000000 +0800
 +++ py-Scientific/Makefile      2010-05-10 05:58:43.000000000 +0800
 @@ -1,11 +1,9 @@
  # $NetBSD: Makefile,v 1.31 2009/03/05 18:51:30 joerg Exp $
 
 -DISTNAME=      ScientificPython-2.4.5
 +DISTNAME=      ScientificPython-2.8
  PKGNAME=       ${PYPKGPREFIX}-${DISTNAME:S/Python//}
 -PKGREVISION=   2
  CATEGORIES=    math python
 -MASTER_SITES=  http://starship.python.net/crew/hinsen/ScientificPython/ \
 -               http://dirac.cnrs-orleans.fr/programs/ScientificPython/
 +MASTER_SITES=  http://sourcesup.cru.fr/frs/download.php/2309/
 
  MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
  HOMEPAGE=      http://starship.python.net/crew/hinsen/scientific.html
 @@ -25,17 +23,16 @@
 
  INSTALLATION_DIRS=     bin
 
 -post-build:
 +post-install:
         @(cd ${WRKSRC}/Src/MPI && ${SETENV} CFLAGS="${CFLAGS}" \
           LDFLAGS="${LDFLAGS} ${PTHREAD_LDFLAGS} ${PTHREAD_LIBS}"
 ${PYTHONBIN} compile.py)
 
 -post-install:
         ${INSTALL_PROGRAM} ${WRKSRC}/Src/MPI/mpipython \
                 ${DESTDIR}${PREFIX}/bin/mpipython${PYVERSSUFFIX}
 
  .include "../../devel/netcdf/buildlink3.mk"
  .include "../../lang/python/extension.mk"
 -.include "../../math/py-Numeric/buildlink3.mk"
 +.include "../../math/py-numpy/buildlink3.mk"
  .include "../../parallel/mpi-ch/buildlink3.mk"
  .include "../../mk/pthread.buildlink3.mk"
  .include "../../mk/bsd.pkg.mk"
 diff -urN py-Scientific.orig/PLIST py-Scientific/PLIST
 --- py-Scientific.orig/PLIST    2010-05-09 20:41:31.000000000 +0800
 +++ py-Scientific/PLIST 2010-05-27 08:02:40.000000000 +0800
 @@ -1,4 +1,6 @@
 -@comment $NetBSD: PLIST,v 1.7 2009/06/14 18:05:47 joerg Exp $
 +@comment $NetBSD$
 +bin/bsp_virtual
 +bin/task_manager
  bin/mpipython${PYVERSSUFFIX}
  ${PYINC}/Scientific/PyBSP_API.h
  ${PYINC}/Scientific/PyMPI_API.h
 @@ -11,15 +13,36 @@
  ${PYSITELIB}/Scientific/BSP/IO.py
  ${PYSITELIB}/Scientific/BSP/IO.pyc
  ${PYSITELIB}/Scientific/BSP/IO.pyo
 +${PYSITELIB}/Scientific/BSP/RemoteObjects.py
 +${PYSITELIB}/Scientific/BSP/RemoteObjects.pyc
 +${PYSITELIB}/Scientific/BSP/RemoteObjects.pyo
  ${PYSITELIB}/Scientific/BSP/__init__.py
  ${PYSITELIB}/Scientific/BSP/__init__.pyc
  ${PYSITELIB}/Scientific/BSP/__init__.pyo
  ${PYSITELIB}/Scientific/BSP/core.py
  ${PYSITELIB}/Scientific/BSP/core.pyc
  ${PYSITELIB}/Scientific/BSP/core.pyo
 +${PYSITELIB}/Scientific/Clustering/AffinityPropagation.py
 +${PYSITELIB}/Scientific/Clustering/AffinityPropagation.pyc
 +${PYSITELIB}/Scientific/Clustering/AffinityPropagation.pyo
 +${PYSITELIB}/Scientific/Clustering/__init__.py
 +${PYSITELIB}/Scientific/Clustering/__init__.pyc
 +${PYSITELIB}/Scientific/Clustering/__init__.pyo
  ${PYSITELIB}/Scientific/DictWithDefault.py
  ${PYSITELIB}/Scientific/DictWithDefault.pyc
  ${PYSITELIB}/Scientific/DictWithDefault.pyo
 +${PYSITELIB}/Scientific/DistributedComputing/MasterSlave.py
 +${PYSITELIB}/Scientific/DistributedComputing/MasterSlave.pyc
 +${PYSITELIB}/Scientific/DistributedComputing/MasterSlave.pyo
 +${PYSITELIB}/Scientific/DistributedComputing/TaskManager.py
 +${PYSITELIB}/Scientific/DistributedComputing/TaskManager.pyc
 +${PYSITELIB}/Scientific/DistributedComputing/TaskManager.pyo
 +${PYSITELIB}/Scientific/DistributedComputing/__init__.py
 +${PYSITELIB}/Scientific/DistributedComputing/__init__.pyc
 +${PYSITELIB}/Scientific/DistributedComputing/__init__.pyo
 +${PYSITELIB}/Scientific/FFT.py
 +${PYSITELIB}/Scientific/FFT.pyc
 +${PYSITELIB}/Scientific/FFT.pyo
  ${PYSITELIB}/Scientific/Functions/Derivatives.py
  ${PYSITELIB}/Scientific/Functions/Derivatives.pyc
  ${PYSITELIB}/Scientific/Functions/Derivatives.pyo
 @@ -83,15 +106,18 @@
  ${PYSITELIB}/Scientific/IO/PDBExportFilters.py
  ${PYSITELIB}/Scientific/IO/PDBExportFilters.pyc
  ${PYSITELIB}/Scientific/IO/PDBExportFilters.pyo
 +${PYSITELIB}/Scientific/IO/PDBSpaceGroups.py
 +${PYSITELIB}/Scientific/IO/PDBSpaceGroups.pyc
 +${PYSITELIB}/Scientific/IO/PDBSpaceGroups.pyo
  ${PYSITELIB}/Scientific/IO/TextFile.py
  ${PYSITELIB}/Scientific/IO/TextFile.pyc
  ${PYSITELIB}/Scientific/IO/TextFile.pyo
  ${PYSITELIB}/Scientific/IO/__init__.py
  ${PYSITELIB}/Scientific/IO/__init__.pyc
  ${PYSITELIB}/Scientific/IO/__init__.pyo
 -${PYSITELIB}/Scientific/Installation.py
 -${PYSITELIB}/Scientific/Installation.pyc
 -${PYSITELIB}/Scientific/Installation.pyo
 +${PYSITELIB}/Scientific/LA.py
 +${PYSITELIB}/Scientific/LA.pyc
 +${PYSITELIB}/Scientific/LA.pyo
  ${PYSITELIB}/Scientific/MPI/IO.py
  ${PYSITELIB}/Scientific/MPI/IO.pyc
  ${PYSITELIB}/Scientific/MPI/IO.pyo
 @@ -104,6 +130,12 @@
  ${PYSITELIB}/Scientific/Mathematica.py
  ${PYSITELIB}/Scientific/Mathematica.pyc
  ${PYSITELIB}/Scientific/Mathematica.pyo
 +${PYSITELIB}/Scientific/N.py
 +${PYSITELIB}/Scientific/N.pyc
 +${PYSITELIB}/Scientific/N.pyo
 +${PYSITELIB}/Scientific/NRNG.py
 +${PYSITELIB}/Scientific/NRNG.pyc
 +${PYSITELIB}/Scientific/NRNG.pyo
  ${PYSITELIB}/Scientific/NumberDict.py
  ${PYSITELIB}/Scientific/NumberDict.pyc
  ${PYSITELIB}/Scientific/NumberDict.pyo
 @@ -116,6 +148,18 @@
  ${PYSITELIB}/Scientific/Physics/__init__.py
  ${PYSITELIB}/Scientific/Physics/__init__.pyc
  ${PYSITELIB}/Scientific/Physics/__init__.pyo
 +${PYSITELIB}/Scientific/QtWidgets/QtPlotCanvas.py
 +${PYSITELIB}/Scientific/QtWidgets/QtPlotCanvas.pyc
 +${PYSITELIB}/Scientific/QtWidgets/QtPlotCanvas.pyo
 +${PYSITELIB}/Scientific/QtWidgets/QtVisualizationCanvas.py
 +${PYSITELIB}/Scientific/QtWidgets/QtVisualizationCanvas.pyc
 +${PYSITELIB}/Scientific/QtWidgets/QtVisualizationCanvas.pyo
 +${PYSITELIB}/Scientific/QtWidgets/__init__.py
 +${PYSITELIB}/Scientific/QtWidgets/__init__.pyc
 +${PYSITELIB}/Scientific/QtWidgets/__init__.pyo
 +${PYSITELIB}/Scientific/QtWidgets/qt_fake.py
 +${PYSITELIB}/Scientific/QtWidgets/qt_fake.pyc
 +${PYSITELIB}/Scientific/QtWidgets/qt_fake.pyo
  ${PYSITELIB}/Scientific/Signals/Models.py
  ${PYSITELIB}/Scientific/Signals/Models.pyc
  ${PYSITELIB}/Scientific/Signals/Models.pyo
 @@ -149,6 +193,9 @@
  ${PYSITELIB}/Scientific/Visualization/Color.py
  ${PYSITELIB}/Scientific/Visualization/Color.pyc
  ${PYSITELIB}/Scientific/Visualization/Color.pyo
 +${PYSITELIB}/Scientific/Visualization/PyMOL.py
 +${PYSITELIB}/Scientific/Visualization/PyMOL.pyc
 +${PYSITELIB}/Scientific/Visualization/PyMOL.pyo
  ${PYSITELIB}/Scientific/Visualization/VMD.py
  ${PYSITELIB}/Scientific/Visualization/VMD.pyc
  ${PYSITELIB}/Scientific/Visualization/VMD.pyo
 @@ -167,7 +214,14 @@
  ${PYSITELIB}/Scientific/__init__.py
  ${PYSITELIB}/Scientific/__init__.pyc
  ${PYSITELIB}/Scientific/__init__.pyo
 +${PYSITELIB}/Scientific/__pkginfo__.py
 +${PYSITELIB}/Scientific/__pkginfo__.pyc
 +${PYSITELIB}/Scientific/__pkginfo__.pyo
  ${PYSITELIB}/Scientific/indexing.py
  ${PYSITELIB}/Scientific/indexing.pyc
  ${PYSITELIB}/Scientific/indexing.pyo
 
+${PYSITELIB}/Scientific/${LOWER_OPSYS}${OSVER}/Scientific_affinitypropagation.so
 +${PYSITELIB}/Scientific/${LOWER_OPSYS}${OSVER}/Scientific_interpolation.so
  ${PYSITELIB}/Scientific/${LOWER_OPSYS}${OSVER}/Scientific_netcdf.so
 
+${PYSITELIB}/Scientific/${LOWER_OPSYS}${OSVER}/Scientific_numerics_package_id.so
 +${PYSITELIB}/Scientific/${LOWER_OPSYS}${OSVER}/Scientific_vector.so
 diff -urN py-Scientific.orig/distinfo py-Scientific/distinfo
 --- py-Scientific.orig/distinfo 2010-05-09 20:41:31.000000000 +0800
 +++ py-Scientific/distinfo      2010-05-27 08:01:19.000000000 +0800
 @@ -1,7 +1,6 @@
  $NetBSD: distinfo,v 1.5 2005/02/23 12:06:57 agc Exp $
 
 -SHA1 (ScientificPython-2.4.5.tar.gz) = 
452b04a20dd065fd9ea01092ae2e1e726406d2be
 -RMD160 (ScientificPython-2.4.5.tar.gz) =
 5a5620856fce81726110e12a03871b39d4b462b0
 -Size (ScientificPython-2.4.5.tar.gz) = 487379 bytes
 -SHA1 (patch-aa) = 651049ac032c3b0a232ec052e80e2cdb1134b4e0
 -SHA1 (patch-ab) = b682b71ecfbe0c815203f74bf19ae5870d113f8f
 +SHA1 (ScientificPython-2.8.tar.gz) = c0847eac6359d70b0e4687c5c65af49b3986e55b
 +RMD160 (ScientificPython-2.8.tar.gz) = 
0501829586253fe3986458529c436b6d93e6667f
 +Size (ScientificPython-2.8.tar.gz) = 559613 bytes
 +SHA1 (patch-ab) = b245ef461cb80e34f5fdcb1da36777da80b6279c
 diff -urN py-Scientific.orig/patches/CVS/Entries
 py-Scientific/patches/CVS/Entries
 --- py-Scientific.orig/patches/CVS/Entries      2010-05-09
 20:41:31.000000000 +0800
 +++ py-Scientific/patches/CVS/Entries   2010-05-18 04:43:16.000000000 +0800
 @@ -1 +1,3 @@
 +/patch-aa/1.3/Sun Jan 18 23:57:50 2004//
 +/patch-ab/1.1/Sun Jan 18 23:57:50 2004//
  D
 diff -urN py-Scientific.orig/patches/patch-aa py-Scientific/patches/patch-aa
 --- py-Scientific.orig/patches/patch-aa 2010-05-09 20:41:31.000000000 +0800
 +++ py-Scientific/patches/patch-aa      1970-01-01 07:00:00.000000000 +0700
 @@ -1,12 +0,0 @@
 -$NetBSD: patch-aa,v 1.3 2004/01/18 23:57:50 recht Exp $
 -
 ---- setup.py.orig      2004-01-15 11:53:49.000000000 +0100
 -+++ setup.py   2004-01-18 17:06:15.000000000 +0100
 -@@ -32,6 +32,7 @@
 -                              ['Src/Scientific_netcdf.c'],
 -                              include_dirs=['Include', netcdf_include],
 -                              library_dirs=[netcdf_lib],
 -+                             runtime_library_dirs=[netcdf_lib],
 -                              libraries = ['netcdf'])]
 -
 - packages = ['Scientific', 'Scientific.Functions',
 diff -urN py-Scientific.orig/patches/patch-ab py-Scientific/patches/patch-ab
 --- py-Scientific.orig/patches/patch-ab 2010-05-09 20:41:31.000000000 +0800
 +++ py-Scientific/patches/patch-ab      2010-05-10 05:56:06.000000000 +0800
 @@ -1,25 +1,24 @@
 -$NetBSD: patch-ab,v 1.1 2004/01/18 23:57:50 recht Exp $
 -
 ---- Src/MPI/compile.py.orig    2003-12-19 20:33:31.000000000 +0100
 -+++ Src/MPI/compile.py 2004-01-18 21:57:52.000000000 +0100
 -@@ -12,10 +12,19 @@
 - mpicompiler = 'mpicc'
 - sources='mpipython.c Scientific_mpi.c'
 +--- Src/MPI/compile.py.orig    2008-08-18 20:54:41.000000000 +0800
 ++++ Src/MPI/compile.py 2010-05-10 05:55:47.000000000 +0800
 +@@ -32,9 +32,20 @@
 +             items[i] = os.path.join(frameworkdir[0], items[i])
 +     linkforshared = ' '.join(items)
 
 +-cmd = '%s %s -o mpipython -I%s %s %s -L%s -lpython%s %s %s' % \
  +ldflags=""
  +if os.environ.has_key('LDFLAGS'):
 -+    ldflags = os.environ['LDFLAGS']
 -
 --cmd = '%s %s -o mpipython -I%s %s -L%s -lpython%s %s %s' % \
 ++      ldflags = os.environ['LDFLAGS']
 ++
 ++#cmd = '%s %s -o mpipython -I%s %s %s -L%s -lpython%s %s %s' % \
  +cflags=""
  +if os.environ.has_key('CFLAGS'):
  +    cflags = os.environ['CFLAGS']
  +
 -+cmd = '%s %s %s -o mpipython -I../../Include %s -I%s %s -L%s -lmpich
 -lpython%s %s %s' % \
 ++cmd = '%s %s %s -o mpipython -I../../Include %s -I%s %s %s -L%s
 -lmpich -lpython%s %s %s' % \
       (mpicompiler,
 -+    ldflags,
 -     cfgDict['LINKFORSHARED'],
 -+    cflags,
 -     cfgDict['INCLUDEPY'],
 -     sources,
 -     cfgDict['LIBPL'],
 ++     ldflags,
 +      linkforshared,
 ++     cflags,
 +      cfgDict['INCLUDEPY'],
 +      extra_compile_args,
 +      sources,
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