CVS commit: pkgsrc/math/py-Scientific

[OBATA Akio <obache%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   obache
Date:           Sat May 29 03:18:54 UTC 2010

Modified Files:
        pkgsrc/math/py-Scientific: Makefile PLIST distinfo
        pkgsrc/math/py-Scientific/patches: patch-aa patch-ab

Log Message:
Update py-Scientific to 2.8.
Based on PR#43282 by Wen Heping.

2.7.9 --> 2.7.10
----------------

Bug fixes:

- Removed all occurrences of "as" as a variable name for compatibility
  with Python 2.6.

- Installation without the netCDF module did not work.

Improvements:

- Vector.dyadicProduct() was replaced by a more efficient implementation.

- Scientific.IO.PDB: Atom objects now have a parent attribute whose
  value is the containing group.

2.7.8 --> 2.7.9
---------------

License change: ScientificPython is now distributed under the
CeCILL-C license, which is an adaptation of the LGPL to French
law. The previously used CeCILL license, similar to the GPL, was
considered too restrictive.

Bug fixes:

- MPI interfaces did not work correctly with NumPy and/or Python 2.5.

Improvements:

- Compilation script for mpipython works around a Python configuration
  bug under MacOS X.
- Docstrings have been cleaned up.

2.7.7 --> 2.7.8
---------------

Bug fixes:

- Due to a typo in Scientific.IO.PDBSpaceGroups, some space group
  names were not found in the space group table.

Improvements:

- Vector objects can now be multiplied with NumPy scalar objects
  (which is what you get when extracting numbers from NumPy
  arrays). Due to the way NumPy scalars handle multiplication, the
  result used to be an array rather than a Vector, which caused
  various applications to crash.

- The build procedure under Windows has been improved. It can
  generate a binary installer that includes the netCDF DLL,
  making ScientificPython independent of a netCDF installation.

2.7.6 --> 2.7.7
---------------

Bug fixes:

- Installation on Windows didn't work because the Unix maths libraries
  don't exist there.

Improvements:

- InterpolatingFunction and TensorField objects can represent
  periodic functions/fields.

- DistributedComputing: the watchdog period of slave processes is now
  a user-definable parameter.

- PDBSpaceGroups was simplified, making it shorter and faster to load.

- Scientific.N contains the array type object in the variable array_type.
  This makes it possible to write Pyrex modules using arrays in such a
  way that they always use the numeric module for which ScientificPython
  was compiled.

2.7.5 --> 2.7.6
---------------

Bug fixes:

- NumPy compatibility fixes.

- Pyro 3.6 compatibility fix in DistributedComputing.MasterSlave

2.7.4 --> 2.7.5
---------------

New features:

- Scaling, inversion, and shear transformations added to
  Geometry.Transformations

Improvements:

- PDB parser handles CRYST1, SCALEn and MTRIXn records
- Better identification of the Numerics package that is being used

Bug fixes:

- Scientific_affinitypropagation.c compiles with NumPy

2.7.3 --> 2.7.4
---------------

New features:

- New module Clustering.AffinityPropagation.
- New class BSP.ParRootSequence.

Bug fixes:

- Replaced float equality test in Functions.InterpolatingFunction
- Removed exception for order > 1 in Derivatives.DerivVar.__init__
- Fixed reading of non-string attributes from netCDF files.

Improvements:

- New methods getBinIndices and getBinCount in Statistics.Histogram.Histogram
- Physics.PhysicalQuantities: unit definitions added to doc string

2.7.2 --> 2.7.3
---------------

Improvements:

- Added multi-module setup for master-slave computations.
- More information available through task_manager.
- task_manager can start slave processes.

2.7.1 --> 2.7.2
---------------

Bug fixes:

- Scientific_netcdf would not compile with NumPy under Python 2.4
  because NumPy also defined Py_ssize_t.

2.7 --> 2.7.1
-------------

Improvements:

- NumPy compatibility. Scientific_netcdf was revised by hand.
  The Python code was run through numpy.oldnumeric.alter_code1 to
  identify the critical sections, which were then all handled in
  some way. It is possible that there are still incompatibilities
  of the kind that numpy.oldnumeric.alter_code1 cannot detect

2.5.12hg --> 2.7
----------------

New features:

- Subpackage Scientific.DistributedComputing for easy parallelization
  of independent tasks.

2.5.11 --> 2.5.12hg
-------------------

Bug fixes:

- VRML2 output would crash for scenes containing Line objects
- Pyrex implmentation of vector objects could crash instead of raising
  an exception in divide operations.
- Pyrex implmentation of vector objects would raise exceptions incorrectly
  under Python 2.5

Improvements:

- builds Macintosh packages with documentation and examples

2.5.10 --> 2.5.11
-----------------

Bug fixes:

- Pyrex implementation of vector objects raised exceptions in comparisons
- Pyrex implementation of vector objects did not accept negative indices
- Some object deletions during conversion to epydoc had to be reversed

Improvements:

- Two test suites

2.5.9 --> 2.5.10
----------------

Bug fixes:

- Fixed netCDF error handling

Improvements:

- Support for NumPy (not very well tested yet)
- Scientific.NumberDict more efficient

2.5.8 --> 2.5.9
---------------

Improvements:

- Scientifc.IO.NetCDF supports the new 64-bit data structures in Python 2.5
  (not yet tested on a 64-bit machine)
- Docstrings modified for use with Epydoc.

2.5.7 --> 2.5.8
---------------

Bug fixes:

- Syntax error in Scientific.IO.PDB
- Attribute deletion in netCDF file and variable objects caused a crash.

2.5.6 --> 2.5.7
----------------

Bug fixes:

- Tensor-vector multiplication was incorrect with the Pyrex implementation
  of vector objects.

2.5.5 --> 2.5.6
----------------

Bug fixes:

- Scientific.BSP.ParClass did not pass on __call__ and __getitem__
  to local class
- Scientific.BSP.ParClass: Class wrappers did not always return the right
  global object.

2.5.4 --> 2.5.5
----------------

Bug fixes:

- Scientific.IO.NetCDF.NetCDFVariable.assignValue() had incomplete error
  reporting. Some errors would not raise exceptions as required.

2.5.3 --> 2.5.4
----------------

Improvements:

- A "test" method on MPI request objects permits to check if data
  is available (thanks to Jakob Schiotz for this addition).

Bug fixes:

- The new Pyrex vector objects could not be pickled.

2.5.1 --> 2.5.3
----------------

Improvements:

- The class Scientific.Geometry.Vector has been reimplemented in Pyrex,
  yielding much faster vector operations. There is, however, the restriction
  that the vector elements must be of type "float". For the rare applications
  where this condition is not fulfilled (such as
  Scientific.Functions.Derivatives.DerivVector), the Python implementation
  remains accessible as Scientific.Geometry.VectorModule.Vector.

2.4.9 --> 2.5.1
----------------

Improvements:

- Vector and Tensor objects permit comparison with other types
  of objects (which always return False)
- Numarray can be used instead of Numeric as far as possible
  (see README for details)

2.4.7 --> 2.4.9:
----------------

Bug fixes:

- Integer array attributes caused a TypeError with recent versions of
  Numeric (that don't do silent casts from Long to Int any more).

Additions:

- Method "threeAngles" in Geometry.Transformation.Rotation.

2.4.6 --> 2.4.7:
----------------

Bug fixes:

- Scientific.BSP: alltrue() and anytrue() sometimes returned wrong results.

Additions:

- Scientific.Visualization.VMD can now correctly launch VMD under Windows


To generate a diff of this commit:
cvs rdiff -u -r1.31 -r1.32 pkgsrc/math/py-Scientific/Makefile
cvs rdiff -u -r1.7 -r1.8 pkgsrc/math/py-Scientific/PLIST
cvs rdiff -u -r1.5 -r1.6 pkgsrc/math/py-Scientific/distinfo
cvs rdiff -u -r1.3 -r1.4 pkgsrc/math/py-Scientific/patches/patch-aa
cvs rdiff -u -r1.1 -r1.2 pkgsrc/math/py-Scientific/patches/patch-ab

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.