2.9.3 --> 2.9.4 ---------------- Cleanup: - The module Scientific.BSP.RemoteObjects was removed. It was experimental and never fully functional. - Tabs were replaced by spaces in two files. Bug fixes: - MasterSlave computations without a name server didn't work. - Various typos in comments and docstrings 2.9.2 --> 2.9.3 ---------------- Cleanup: - Support for Numeric and numarray was removed, because it becomes difficult to test. The only supported array package is NumPy. - The Cython modules were updated following recent evolutions in Cython. In particular, Cython's numpy.pxd is used for accessing NumPy arrays. - Functions from the standard library module "string" were replaced by string methods as far as possible. Improvements: - No more platform-specific subpackages for the extension modules. They are placed at the same level as the Python modules. Bug fixes: - Scientific.BSP: Some operations created nested ParValue objects. (Thanks to Kelson Zawack!) 2.9.1 --> 2.9.2 ---------------- Improvements: - Allow unicode strings where reasonable, in particular for filenames. - Include C versions of Cython modules in the distribution, removing the build dependence on Cython. - New submodule of Visualization for the molecular viewer Chimera. Bug fixes: - NumPy compatibility fixes. - IO.TextFile: make sure that __del__ closes a file only if it was opened successfully - Geometry.Transformation: ensure that screwMotion returns a positive distance. - Physics.PhysicalQuantities: fix definition of barn. - IO.NetCDF: replace unsigned long by size_t in C interface to netCDF. - Functions.Interpolation: more checks on axis arrays. - DistributedComputing: fixed deadlock in task manager. 2.9.0 --> 2.9.1 ---------------- Improvements: - The task_manager script accepts an optional argument -w/--wait that makes it wait for the named task to start. - New classes DerivFn and NumDerivFn in Functions.FirstDerivatives. - New optional validator in Functions.LeastSquares. - PDB output can handle alternate location fields. - The NumPy header location is obtained from NumPy during installation. Bug fixes: - Better error handling in netCDF array write operations. - DistributedComputing: improved Windows compatibility 2.7.10 --> 2.9.0 ----------------- Improvements: - Scientific.IO.NetCDF.NetCDFFile accepts optional flags for the 64-bit file format (from netCDF 3.6) and the HDF5 file format (from netCDF 4). Bug fixes: - Methods derivative() and integral() crashed because index_expression was deleted at the end of the module. 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 2.4.3 --> 2.4.4: ---------------- Bug fixes: NetCDF error messages should now be correct. No more "unknown errors"! 2.4 --> 2.4.1: -------------- Bug fixes: - Scientific.MPI did not contain the _C_API object needed by C extension modules that call MPI. - The arguments to the receiveString method are now optional, as documented. 2.3.3 --> 2.4: -------------- Bug fixes: - Memory function calculation in Scientific.Signals.Models returned a wrong value for the first point. - Some indexing problems in Scientific.IO.NetCDF were fixed; none of them caused wrong results, just unjustified exceptions. 2.3.2 --> 2.3.3: ---------------- Bug fixes: - The method divide() assumed the wrong coefficient order. New features: - Module Scientific.Signals.Models - Class Scientific.Statistics.Histogram.WeightedHistogram 2.3.1 --> 2.3.2: ---------------- Incompatible changes: - Specification of routines in Scientific.BSP changed. 2.2 --> 2.3.1 ------------- New features: - New modules Scientific.BSP and Scientific.BSP.IO 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 2.0 --> 2.0.1 ------------- Bug fixes: - The method integral() in class Scientific.Functions.Interpolation.InterpolatingFunction didn't work. - Integer attributes were handled incorrectly on machines with 64 bit long types (DEC Alpha, 64-bit SGI machines) - Syntax errors in Scientific.Visualization.VRML2 fixed. - Memory leaks fixed. Additions: - Scientific.Functions.Interpolation.InterpolatingFunction instances support most array indexing operations (all except NewAxis, which makes no sense) - New class Scientific.Functions.Interpolation.NetCDFInterpolatingFunction represents a function defined by a variable stored in a netCDF file. - Append mode in Scientific.IO.TextFile.TextFile
