Changes for revision 2.0.2
==========================

* switch project from cvs to subversion

Biskit
------

* bugfixes

* new: Intervor.py
  a wrapper for Cazal et al.'s interface triangulation program

PVM
---

* simplified handling of pvm host lists


Changes for revision 2.0.1
==========================

* switch all modules to a new test/BiskitTest testing

Biskit
------

* add test cases for AmberCrdParser and AmberRstParser

* AmberRstParser:
  - bugfixes (concerning box info)
  - disconnect from AmberCrdParser

* ColorSpectrum:
  - prefer ColorSpectrum class rather than the perl-code
    (Unfortunately the perl-generated spectrum looks better than the
    ColorSpectrum one -- so it's too early to completely abandon the
    perl script.)

* PVM-related classes:
  - switch to externally installed pypvm
  - bugfixes
  - handle empty host lists (raise error rather than hanging)

* Hmmer:
  - switch all print statements to log.write* or EHandler calls
  - pass log and verbose flags to Executor instances
  - smaller bugfixes

* LogFile:
  - new methods write and writeln should superseed "add" and
  "add_no_break"

* MSMS:
  - use by default biskit-internal gpdb_to_xyzrn

* PDBModel:
  - new: renameAmberRes() (from AmberCrdParser)

* test.py:
  - classes and script for the new testing system

* tools.py:
  - fix for bug #1659132
  - move colorRange() to ColorSpectrum
  - new: gzopen() opens normal and gzipped files

* Xplorer:
  - transformed to Executor child class


Biskit.Mod
----------

* modUtils.py:
  - migrate verify_fasta from modUtils to Hmmer.py where it is only
    used.  This way, a standard Biskit import does not any longer
    import Biskit.Mod which is better for installations that have a
    broken or missing Biopython.

* SequenceSearcher:
  - bugfix: repair broken localBlast() and remoteBlast();
  - use XML-based NCBIXML.BlastParser instead of broken text parser in
    localBlast() and localPSIBlast(); 
  - bugfix: __blast2dict(): writeFasta was only called if verbose=1
    but is actually obligatory.

* TemplateCleaner:
  - write_tcoffee_pdb(): new t-coffee needs Chain ID also in SEQRES
    record

* TemplateSearcher:
  - reorganize remote/local PDB fetching
  - skip multiple NMR models
  - better error reports and fast failure for connection problems

Biskit.Dock
-----------

* ContactSlave:
  - test case that works stand-alone without a master
  - minor bugfixes

Biskit.PVM
----------

* replace hand-compiled pypvm_core by normally installed pypvm module

* pvm.py:
  - remove pvmTools, migrate functions into pvm.py
  - the previous overloading of pypvm functions in pvm is given up
    (although it was actually quite a good idea...perhaps revert that
    later)

* dispatcher.py:
  - don't start master if there are no nodes registered (hangs
    otherwise)
