Merge branch 'master', remote-tracking branch 'richard/master'
Merge branch 'master', remote-tracking branch 'josh/master'
Merge branch 'master', remote-tracking branch 'richard/master'
Merge branch 'master', remote-tracking branch 'richard/master'
Merge branch 'master' of git://github.com/jwallen/RMG-Py
Merge branch 'master' of git://github.com/jwallen/RMG-Py
Merge branch 'master' of git://github.com/jwallen/RMG-Py
Merge branch 'master' of git://github.com/jwallen/RMG-Py
Merge branch 'master', remote-tracking branch 'josh/master'
Added fromAdjacencyList() method to Species class.

This is a convenience function for creating a Species object with one
Molecule object as created from the adjacency list. It also attempts to
recover the first-line label (if present) and store it on the label
attribute.
Added uncertainty estimation to Arrhenius.fitToData().

Note that, if you were to propagate the uncertainty in each of the
individual Arrhenius parameters, you would get a larger overall uncertainty
in k(T) than simply by evaluating the sum-of-square error at the optimum
point. This is inherent to the linear least-squares method I believe. (It's
certainly better for this to be an overestimate than an underestimate!)
Can now pass optional weighting array to Arrhenius.fitToData().

In some circumstances you may wish to weight certain points more heavily
than others. How exactly you do that is up to you; at least now you have
the option to do so if you wish. If weights are not given, all points are
weighted equally.
Merge branch 'master' of git://github.com/jwallen/RMG-Py
Missing dependency within calculateRateCoefficients
Added toPrettyRepr() methods to Reference classes.

The toPrettyRepr() method is designed to give the same output that the
original __repr__() method would, but formatted to look a bit nicer (e.g.
spanning multiple lines). The __repr__() method now first calls
toPrettyRepr() and then adjusts that result into a one-line string
representation. (This is certainly much easier than going the other
direction!)
Added toPrettyRepr() methods to Kinetics classes.

The toPrettyRepr() method is designed to give the same output that the
original __repr__() method would, but formatted to look a bit nicer (e.g.
spanning multiple lines). The __repr__() method now first calls
toPrettyRepr() and then adjusts that result into a one-line string
representation. (This is certainly much easier than going the other
direction!)
Now using toPrettyRepr() method to save kinetics and references to database.

These methods are now much shorter as a result of this change. The
resulting database output should look a bit prettier as well.
Merge branch 'master', remote-tracking branch 'josh/master'
Now allowing separate energyLog in CanTherm input.

This is in case you complete your energy calculation in a separate job
from the geometry calculation. If the energyLog is not given, the the
ground-state energy is extracted from the geometry log as before.
Fixed a few minor bugs in thermo estimation for monatomics in CanTherm.

If there are no internal degrees of freedom (i.e. the species is
monatomic), then the Wilhoit.fitToData() won't work as expected. We must
set the Wilhoit parameters manually in this case.