Fix typo in function name convertInitialKeysToSpeciesObjects
Save mole fractions instead of concentrations (easier comparison with chemkin)
Do not compute reverse rate coefficients in solver if the rxn is irreversible.

Apparently we were still considering reactions as reversible even when
they are irreversible.
Change "debug" logging level messages to level 1.

For some reason logging.log(0,"message") doesn't log anything
even if you have set the logger level to 0 with the --debug option.
Making these messages level 1 seems to fix it.
There are probably other places this should be fixed too.
More warning messages logged when failed to match template
More debug logging messages when generating reverse templates
Tweak database path in input documentation

This is still entirely wrong, in terms of how you enter the 
reaction libraries, but serves to show how easy it is
to update the documentation online :-)
Molepro imported to canther statmech

The Cantherm example uses a molepro output file, leading to
a failure in the cantherm example. This change fixes the failure,
however there are possibly further fixes needed for correct
implementation in StatMechJob.
Unit tests for pickle use the highest protocol.

If we change some stuff to use __slots__ then this will be necessary.
In the mean time it should just make it faster.
Improved debug logging for reaction family templates
More honest error message in when failing to draw species.

It used to assume the error was lack of molecular structure,
when in fact it could be anything.
Unit tests for molecule drawing.

We don't test a lot, but it should help check it doesn't crash.
Update molecule drawing unit tests.

I think older versions of the pycario libraries cannot create surfaces
without a temporary file. This makes most tests work with that scenario,
and adds another test for it.
Fix scipy.optimize.fmin call in statmech/conformer.pyx

This was giving trouble with a certain version of scipy.
Fix typo in arrheniusTest.py
TransportDatabase has no loadOld function.  Don't try to import old transport groups.
Use RDKit instead of Openbabel in toSMILES() for N2 species

fixes #175
Speed up the SMILES generation by looking up small molecules, and test it.

The previous algorithm checked the molecular formula anyway, so we may as well
use that to shortcut a bunch of things that can be uniquely identified that way,
to avoid calling OpenBabel or RDKit.

I also made a unit test that we get back the same SMILES we started with.

Inspired by and closes #175
Quick and dirty fix for #177 for Mopac parsing.

MOPAC has changed its output slightly.
This is a quick fix, but still not terribly robust.
Part of me feels we shouldn't be keeping a separate fork of cclib.
Fix PDep Pruning bug introduced in e712697

Commit e712697f18c01e0d6ab419c37bc5248e1e3d3e8b changed the way we store PDep networks
so they are in a dictionary (keyed by entrance source) instead of a long list. This
greatly sped things up. However, it meant you have to iterate over two loops instead of one.
In modifying the code, some parts were not indented so were not included in the inner loop.
Hopefully this is not the only reason things sped up!! (although it must have helped!)

I noticed this while looking at the code around issue #176, which was just an off-by-one 
problem indexing an array from 1 instead of 0. The off-by-one thing doesn't actually hurt things
much because we don't use the array for anything anyway! (I'll remove it in the next commit)