Updated to py-Scientific-2.2.

2.1.5 --> 2.2
-------------

Bug fixes:

- The sign convention for rotation angles was not correctly applied
  in Scientific.Geometry.Transformation and Scientific.Geometry.Quaternions.
  Everything was consistent, but with the wrong sign.

Improvements:

- Scientific.IO.PDB can handle a larger range of variant formats for DNA

New features:

- New module Scientific.Visualization.VPython.

- Scientific.IO.TextFile also handles bzip2 compressed files
  (extension .bz2). This only works if bzip2 is installed.


2.1.4 --> 2.1.5
---------------

New features:

- Scientific.TkWidgets.TkPlotCanvas:
  - Popup menu on right button
  - Value display on middle button
  - HorizontalLine, VerticalLine objects

Modifications:

- MPI interface no longer assumes that MPI_Op and MPI_Datatype are
  integers (they aren't in LAM, for example).


2.1.3 --> 2.1.4
---------------

New features:

- New MPI functions implemented by Jakob Schiotz:
  - nonblocking send and receive
  - abort
  - reduce and allreduce

Modifications:

- The Python interpreter lock is released during calls to the netCDF
  library, permitting other threads to continue during I/O operations.
  An internal lock has been added to prevent reentrant calls to the
  netCDF library, which is not thread safe.
  (If you don't understand any of this, you shouldn't care, it has
  no consequences unless you use threads.)
- Methods receive and receiveString on MPI communicator objects
  can be called without source and tag arguments (defaults to None).


Bug fixes:

- The compilation script did not work correctly for MPI support


2.1.2 --> 2.1.3
---------------

New features:

- Some small utility widgets have been added to Scientific.TkWidgets.
  They are not particularly "scientific", but not worth the effort
  of a separate distribution.

Bug fixes:

- The abs() function didn't work on DerivVar objects (modules
  Scientific.Functions.Derivatives and Scientific.Functions.FirstDerivatives)
  with negative values.

- The method projectionOf in Scientific.Geometry.Objects3D.Plane was
  wrong.


2.1.1 --> 2.1.2
---------------

Installation:

- The mpipython executable is compiled using 'mpicc', which should simplify
  installation significantly because all library specifications are
  automatically taken into account. In other words, MPI support should
  work on all platforms without any modifications to the Setup file.
  (Thanks to Jakob Schiotz for this suggestion!)

- Some 'extern' declarations were changed to 'staticforward' to please
  some compilers.

Documentation:

- the documentation for the methods receive and receiveString were
  wrong.


2.1.0 --> 2.1.1
---------------

Bug fixes:

- The upper bound for MPI message tags was not treated correctly,
  leading to a bound of zero on some platforms.

Modifications:

- The methods sendArray and sendString were combined into a single
  method send.

- broadcastArray was renamed to broadcast, shareArray was renamed to share,
  receiveArray was renamed to receive. The only function that retains
  a data type indication is receiveString.


2.0.1 --> 2.1.0
---------------

Additions:

- MPI interface in Scientific.MPI

6 files changed, 127 insertions, 46 deletions

diff --git a/math/py-Scientific/Makefile b/math/py-Scientific/Makefile
index 494cdf44cc1..4c1b07232d7 100644
--- a/math/py-Scientific/Makefile
+++ b/math/py-Scientific/Makefile
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.4 2001/03/29 01:00:10 jtb Exp $
+# $NetBSD: Makefile,v 1.5 2001/03/30 22:23:07 jtb Exp $
 
-DISTNAME=	ScientificPython-2.0.1
-PKGNAME=	py-Scientific-2.0.1
+DISTNAME=	ScientificPython-2.2
+PKGNAME=	py-Scientific-2.2
 CATEGORIES=	math
 MASTER_SITES=	http://starship.python.net/crew/hinsen/ \
 		http://dirac.cnrs-orleans.fr/programs/
@@ -23,39 +23,37 @@ PLIST_SRC=	${WRKDIR}/.PLIST_SRC
 EVAL_PREFIX+=	PYPREFIX=python NETCDFPREFIX=netcdf MPICHPREFIX=mpich
 
 do-configure:
-	${SED} -e "s|@NETCDFPREFIX@|${NETCDFPREFIX}|g"	\
-	       -e "s|@MPICHPREFIX@|${MPICHPREFIX}|g"		\
-	< ${FILESDIR}/Setup.in > ${WRKSRC}/Src/Setup.in
+	${SED} -e "s|@NETCDFPREFIX@|${NETCDFPREFIX}|g"			\
+	       -e "s|@MPICHPREFIX@|${MPICHPREFIX}|g"			\
+	${WRKSRC}/setup.py > ${WRKSRC}/setup.py.tmp
+	${MV} -f ${WRKSRC}/setup.py.tmp ${WRKSRC}/setup.py
+	${SED} -e "s|@MPICHPREFIX@|${MPICHPREFIX}|g"			\
+	${FILESDIR}/Setup.in > ${WRKSRC}/Src/MPI/Setup.in
 
 do-build:
-	(cd ${WRKSRC}/Src && ${PYPREFIX}/bin/python compile.py)
+	cd ${WRKSRC} && ${PYPREFIX}/bin/python setup.py build
+	cd ${WRKSRC}/Src/MPI && ${PYPREFIX}/bin/python compile.py
 
 post-build:
-	(eval `${PYPREFIX}/bin/python ${FILESDIR}/printpypath.py` && \
-	${SED} "s|PYINC|$${PYINC}|g;s|PYSITELIB|$${PYSITELIB}|g" \
-	< ${PKGDIR}/PLIST > ${PLIST_SRC})
+	(eval `${PYPREFIX}/bin/python ${FILESDIR}/printpypath.py` && 	\
+	${SED} "s|PYINC|$${PYINC}|g;s|PYSITELIB|$${PYSITELIB}|g" 	\
+	${PKGDIR}/PLIST > ${PLIST_SRC})
 
 do-install:
-	(cd ${WRKSRC} && ${PYPREFIX}/bin/python install.py)
-	${INSTALL_DATA_DIR} ${PREFIX}/include/python2.0/Scientific
-	@for f in ${WRKSRC}/Scientific/Include/Scientific/*; do \
-		i="${INSTALL_DATA} $$f ${PREFIX}/include/python2.0/Scientific/"; \
-		${ECHO} $$i; $$i; \
-	done
+	cd ${WRKSRC} && ${PYPREFIX}/bin/python setup.py install
+	${INSTALL_PROGRAM} ${WRKSRC}/Src/MPI/mpipython ${PREFIX}/bin
+	${INSTALL_DATA_DIR} ${PREFIX}/${PYINC}/Scientific
+	${INSTALL_DATA}	${WRKSRC}/Include/Scientific/* 			\
+	${PREFIX}/${PYINC}/Scientific/
 	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/py-Scientific
-	@for f in README COPYRIGHT Doc/PDF/manual.pdf; do \
-		i="${INSTALL_DATA} ${WRKSRC}/$$f ${PREFIX}/share/doc/py-Scientific/"; \
-		${ECHO} $$i; $$i; \
+	for f in README COPYRIGHT Doc/PDF/manual.pdf; do 		\
+	${INSTALL_DATA} ${WRKSRC}/$$f ${PREFIX}/share/doc/py-Scientific/; \
 	done
 	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/py-Scientific
-	@for f in ${WRKSRC}/Doc/HTML/*; do \
-		i="${INSTALL_DATA} $$f ${PREFIX}/share/doc/html/py-Scientific/"; \
-		${ECHO} $$i; $$i; \
-	done
+	${INSTALL_DATA} ${WRKSRC}/Doc/HTML/* 				\
+	${PREFIX}/share/doc/html/py-Scientific/
 	${INSTALL_DATA_DIR} ${PREFIX}/share/examples/py-Scientific
-	@for f in ${WRKSRC}/Examples/*; do \
-		i="${INSTALL_DATA} $$f ${PREFIX}/share/examples/py-Scientific/"; \
-		${ECHO} $$i; $$i; \
-	done
+	${INSTALL_DATA} ${WRKSRC}/Examples/* 				\
+	${PREFIX}/share/examples/py-Scientific/
 
 .include "../../mk/bsd.pkg.mk"
diff --git a/math/py-Scientific/files/Setup.in b/math/py-Scientific/files/Setup.in
index a3a8f706eb7..fd34be958a4 100644
--- a/math/py-Scientific/files/Setup.in
+++ b/math/py-Scientific/files/Setup.in
@@ -1,5 +1,8 @@
-*shared*
+# Uncomment the following line and change it to reflect the
+# requirements of your MPI installation; the line below is for MPICH
+# installed in a standard location searched by the compiler and
+# linker.
 
-Scientific_netcdf -I@NETCDFPREFIX@/include -I../Scientific/Include \
-                  Scientific_netcdf.c -Wl,-R@NETCDFPREFIX@/lib -L@NETCDFPREFIX@/lib -lnetcdf
-Scientific_mpi -I@MPICHPREFIX@/include -I@MPICHPREFIX@/include -I../Scientific/Include Scientific_mpi.c -L@MPICHPREFIX@/lib  -lmpich
+# NOTE: The MPI compiler is specified at the top of compile.py .
+
+Scientific_mpi -I../../Include Scientific_mpi.c -L@MPICHPREFIX@/lib -lmpich
diff --git a/math/py-Scientific/files/md5 b/math/py-Scientific/files/md5
index 16a855f4fba..b9b9287c60e 100644
--- a/math/py-Scientific/files/md5
+++ b/math/py-Scientific/files/md5
@@ -1,3 +1,3 @@
-$NetBSD: md5,v 1.1.1.1 2001/01/30 02:01:44 jtb Exp $
+$NetBSD: md5,v 1.2 2001/03/30 22:23:07 jtb Exp $
 
-MD5 (ScientificPython-2.0.1.tar.gz) = 380248f3167afa1667db44cfe8b3fd3d
+SHA1 (ScientificPython-2.2.tar.gz) = f1fcf1ef1a54a1fd84b1e5df569dac13a1648225
diff --git a/math/py-Scientific/files/patch-sum b/math/py-Scientific/files/patch-sum
new file mode 100644
index 00000000000..f4c19389f21
--- /dev/null
+++ b/math/py-Scientific/files/patch-sum
@@ -0,0 +1,3 @@
+$NetBSD: patch-sum,v 1.1 2001/03/30 22:23:07 jtb Exp $
+
+SHA1 (patch-aa) = 31388d725e97bb28443618dca81d4760512b09e8
diff --git a/math/py-Scientific/patches/patch-aa b/math/py-Scientific/patches/patch-aa
new file mode 100644
index 00000000000..21221d63f24
--- /dev/null
+++ b/math/py-Scientific/patches/patch-aa
@@ -0,0 +1,13 @@
+$NetBSD: patch-aa,v 1.1 2001/03/30 22:23:07 jtb Exp $
+
+--- setup.py.orig	Fri Mar 30 20:58:10 2001
++++ setup.py
+@@ -7,7 +7,7 @@
+ 
+ # If your netCDF installation is in a non-standard place, set the following
+ # variable to the base directory.
+-netcdf_prefix = None
++netcdf_prefix = '@NETCDFPREFIX@'
+ 
+ 
+ if netcdf_prefix is None:
diff --git a/math/py-Scientific/pkg/PLIST b/math/py-Scientific/pkg/PLIST
index 0ef03254536..08fc3f6cbc3 100644
--- a/math/py-Scientific/pkg/PLIST
+++ b/math/py-Scientific/pkg/PLIST
@@ -1,10 +1,14 @@
-@comment $NetBSD: PLIST,v 1.1.1.1 2001/01/30 02:01:44 jtb Exp $
+@comment $NetBSD: PLIST,v 1.2 2001/03/30 22:23:07 jtb Exp $
+bin/mpipython
 PYINC/Scientific/PyMPI_API.h
 PYINC/Scientific/mpimodule.h
 PYINC/Scientific/netcdfmodule.h
-PYSITELIB/Scientific/${LOWER_OPSYS}1/Scientific_mpi.so
-PYSITELIB/Scientific/${LOWER_OPSYS}1/Scientific_netcdf.so
 PYSITELIB/Scientific/DictWithDefault.py
+PYSITELIB/Scientific/Installation.py
+PYSITELIB/Scientific/Mathematica.py
+PYSITELIB/Scientific/NumberDict.py
+PYSITELIB/Scientific/__init__.py
+PYSITELIB/Scientific/indexing.py
 PYSITELIB/Scientific/Functions/Derivatives.py
 PYSITELIB/Scientific/Functions/FindRoot.py
 PYSITELIB/Scientific/Functions/FirstDerivatives.py
@@ -13,6 +17,14 @@ PYSITELIB/Scientific/Functions/LeastSquares.py
 PYSITELIB/Scientific/Functions/Polynomial.py
 PYSITELIB/Scientific/Functions/Romberg.py
 PYSITELIB/Scientific/Functions/__init__.py
+PYSITELIB/Scientific/Functions/Derivatives.pyc
+PYSITELIB/Scientific/Functions/FindRoot.pyc
+PYSITELIB/Scientific/Functions/FirstDerivatives.pyc
+PYSITELIB/Scientific/Functions/Interpolation.pyc
+PYSITELIB/Scientific/Functions/LeastSquares.pyc
+PYSITELIB/Scientific/Functions/Polynomial.pyc
+PYSITELIB/Scientific/Functions/Romberg.pyc
+PYSITELIB/Scientific/Functions/__init__.pyc
 PYSITELIB/Scientific/Geometry/Objects3D.py
 PYSITELIB/Scientific/Geometry/Quaternion.py
 PYSITELIB/Scientific/Geometry/TensorAnalysis.py
@@ -20,6 +32,13 @@ PYSITELIB/Scientific/Geometry/TensorModule.py
 PYSITELIB/Scientific/Geometry/Transformation.py
 PYSITELIB/Scientific/Geometry/VectorModule.py
 PYSITELIB/Scientific/Geometry/__init__.py
+PYSITELIB/Scientific/Geometry/Objects3D.pyc
+PYSITELIB/Scientific/Geometry/Quaternion.pyc
+PYSITELIB/Scientific/Geometry/TensorAnalysis.pyc
+PYSITELIB/Scientific/Geometry/TensorModule.pyc
+PYSITELIB/Scientific/Geometry/Transformation.pyc
+PYSITELIB/Scientific/Geometry/VectorModule.pyc
+PYSITELIB/Scientific/Geometry/__init__.pyc
 PYSITELIB/Scientific/IO/ArrayIO.py
 PYSITELIB/Scientific/IO/FortranFormat.py
 PYSITELIB/Scientific/IO/NetCDF.py
@@ -27,30 +46,58 @@ PYSITELIB/Scientific/IO/PDB.py
 PYSITELIB/Scientific/IO/PDBExportFilters.py
 PYSITELIB/Scientific/IO/TextFile.py
 PYSITELIB/Scientific/IO/__init__.py
-PYSITELIB/Scientific/Include/Scientific/PyMPI_API.h
-PYSITELIB/Scientific/Include/Scientific/mpimodule.h
-PYSITELIB/Scientific/Include/Scientific/netcdfmodule.h
-PYSITELIB/Scientific/Include/scientific_netcdfmodule.h
-PYSITELIB/Scientific/Installation.py
+PYSITELIB/Scientific/IO/ArrayIO.pyc
+PYSITELIB/Scientific/IO/FortranFormat.pyc
+PYSITELIB/Scientific/IO/NetCDF.pyc
+PYSITELIB/Scientific/IO/PDB.pyc
+PYSITELIB/Scientific/IO/PDBExportFilters.pyc
+PYSITELIB/Scientific/IO/TextFile.pyc
+PYSITELIB/Scientific/IO/__init__.pyc
 PYSITELIB/Scientific/MPI/IO.py
 PYSITELIB/Scientific/MPI/__init__.py
-PYSITELIB/Scientific/Mathematica.py
-PYSITELIB/Scientific/NumberDict.py
+PYSITELIB/Scientific/MPI/IO.pyc
+PYSITELIB/Scientific/MPI/__init__.pyc
 PYSITELIB/Scientific/Physics/PhysicalQuantities.py
 PYSITELIB/Scientific/Physics/Potential.py
 PYSITELIB/Scientific/Physics/__init__.py
+PYSITELIB/Scientific/Physics/PhysicalQuantities.pyc
+PYSITELIB/Scientific/Physics/Potential.pyc
+PYSITELIB/Scientific/Physics/__init__.pyc
 PYSITELIB/Scientific/Statistics/Histogram.py
 PYSITELIB/Scientific/Statistics/__init__.py
+PYSITELIB/Scientific/Statistics/Histogram.pyc
+PYSITELIB/Scientific/Statistics/__init__.pyc
+PYSITELIB/Scientific/Threading/TaskManager.py
+PYSITELIB/Scientific/Threading/__init__.py
+PYSITELIB/Scientific/Threading/TaskManager.pyc
+PYSITELIB/Scientific/Threading/__init__.pyc
 PYSITELIB/Scientific/TkWidgets/TkPlotCanvas.py
 PYSITELIB/Scientific/TkWidgets/TkVisualizationCanvas.py
+PYSITELIB/Scientific/TkWidgets/Utility.py
 PYSITELIB/Scientific/TkWidgets/__init__.py
+PYSITELIB/Scientific/TkWidgets/TkPlotCanvas.pyc
+PYSITELIB/Scientific/TkWidgets/TkVisualizationCanvas.pyc
+PYSITELIB/Scientific/TkWidgets/Utility.pyc
+PYSITELIB/Scientific/TkWidgets/__init__.pyc
 PYSITELIB/Scientific/Visualization/Color.py
 PYSITELIB/Scientific/Visualization/VMD.py
+PYSITELIB/Scientific/Visualization/VPython.py
 PYSITELIB/Scientific/Visualization/VRML.py
 PYSITELIB/Scientific/Visualization/VRML2.py
 PYSITELIB/Scientific/Visualization/__init__.py
-PYSITELIB/Scientific/__init__.py
-PYSITELIB/Scientific/indexing.py
+PYSITELIB/Scientific/Visualization/Color.pyc
+PYSITELIB/Scientific/Visualization/VMD.pyc
+PYSITELIB/Scientific/Visualization/VPython.pyc
+PYSITELIB/Scientific/Visualization/VRML.pyc
+PYSITELIB/Scientific/Visualization/VRML2.pyc
+PYSITELIB/Scientific/Visualization/__init__.pyc
+PYSITELIB/Scientific/${LOWER_OPSYS}1/Scientific_netcdf.so
+PYSITELIB/Scientific/DictWithDefault.pyc
+PYSITELIB/Scientific/Installation.pyc
+PYSITELIB/Scientific/Mathematica.pyc
+PYSITELIB/Scientific/NumberDict.pyc
+PYSITELIB/Scientific/__init__.pyc
+PYSITELIB/Scientific/indexing.pyc
 share/doc/html/py-Scientific/Scientific.html
 share/doc/html/py-Scientific/Scientific_1.html
 share/doc/html/py-Scientific/Scientific_10.html
@@ -83,7 +130,12 @@ share/doc/html/py-Scientific/Scientific_34.html
 share/doc/html/py-Scientific/Scientific_35.html
 share/doc/html/py-Scientific/Scientific_36.html
 share/doc/html/py-Scientific/Scientific_37.html
+share/doc/html/py-Scientific/Scientific_38.html
+share/doc/html/py-Scientific/Scientific_39.html
 share/doc/html/py-Scientific/Scientific_4.html
+share/doc/html/py-Scientific/Scientific_40.html
+share/doc/html/py-Scientific/Scientific_41.html
+share/doc/html/py-Scientific/Scientific_42.html
 share/doc/html/py-Scientific/Scientific_5.html
 share/doc/html/py-Scientific/Scientific_6.html
 share/doc/html/py-Scientific/Scientific_7.html
@@ -96,8 +148,20 @@ share/examples/py-Scientific/README
 share/examples/py-Scientific/Setup.template
 share/examples/py-Scientific/compile.py
 share/examples/py-Scientific/demomodule.c
+share/examples/py-Scientific/mpi.py
 share/examples/py-Scientific/netcdf_demo.py
+@dirrm PYINC/Scientific
+@dirrm PYSITELIB/Scientific/Functions
+@dirrm PYSITELIB/Scientific/Geometry
+@dirrm PYSITELIB/Scientific/IO
+@dirrm PYSITELIB/Scientific/MPI
+@dirrm PYSITELIB/Scientific/Physics
+@dirrm PYSITELIB/Scientific/Statistics
+@dirrm PYSITELIB/Scientific/Threading
+@dirrm PYSITELIB/Scientific/TkWidgets
+@dirrm PYSITELIB/Scientific/Visualization
+@dirrm PYSITELIB/Scientific/${LOWER_OPSYS}1
+@dirrm PYSITELIB/Scientific
 @dirrm share/examples/py-Scientific
 @dirrm share/doc/py-Scientific
 @dirrm share/doc/html/py-Scientific
-@dirrm PYINC/Scientific