bumped version to 0.3.2-devel
Fixed reST docs in gromacs and logger outputs release (version)
Simulation class: show ndx in status message
fixed Transformer.fit(): removed centering

The Transformer.fit() command (and also trj_xyfitted()) contained
trjconv options to center while fitting. This does not work well together
and really only rotations are properly removed. The fitting was removed
which improves the quality of the fitted trajectories substantially
(also for the StripWater plugin).
scripts/gw-fit_strip_trajectories.py: can use custom group for centering

A custom group for centering helps for e.g. dimers: choose a small
group at the dimer interface.
scripts/gw-fit_strip_trajectories.py: can use custom group for centering

A custom group for centering helps for e.g. dimers: choose a small
group at the dimer interface.
gw-fit_strip.py: fixed stupid typo
realpath: also expand ~ and environment variables
Merge branch 'develop' of github.com:orbeckst/GromacsWrapper into develop
gromacs.setup.MD_restrained: use Berendsen for pressure coupling
fit to Gaussian in numkit.fitting

- added numkit.fitting.FitGauss
- added much more documentation
regenerated html docs
catch more import problems in cbook
Merge branch 'develop' of github.com:orbeckst/GromacsWrapper into develop
cbook.Transformer and the StripWater plugin can generate files under outdir

- pretty ugly hack...
- new outdir keyword: if set then output files and trajectories will be
  placed under outdir (and not in the same directory where the original
  trajectories lived)
- The path mangling is pretty gruesome and it is not really always clear
  where output will end up. For instance, symbolic links won't work as expected
  because we use realpath() in many instances, which resolves to the original
  file (especially noteworthy for the StripWater plugin where one has fewer
  ways to customize).

  In principle the code *should* be written in such a way that the output
  really ends up in the current directory by default...
Merge branch 'develop' of github.com:orbeckst/GromacsWrapper into develop
XVG decimate: also raise MissingDataError if columns do not fit the array

This normally raises an IndexError but it is typically a sign that the transformation was inadequate or that too few data
was input.

THIS HACK MIGHT BE CHANGED/REVERTED IN THE FUTURE.
setup.topology(): cleaned up posres itp file generation
work around for bugs in make_ndx
summarized changes since 0.3.1