Add tests for checking the database
Merge branch 'master' of github.com:GreenGroup/RMG-Py
Add function LogicOr.matchToLogicOr

This function gives the boolean of whether two LogicOr objects are
equivilant or not. I needed this for database checking
Add new atom attributes to comparisons

The function equivilant and isSpecificCaseOf for GroupAtom now checks the
list of charges and atom label
Added function isIdentical to groups.py

The function isIsomorphic was meant to compare molecules to groups,
therefore it respects wildcards (seeing as a molecule will never have an
atom named Cs or Ct). However, this makes the function isIsomorphic not
useful when tryint to compare two groups.

I've created a new function isIdentical which will not respect wildcards
and can tell if two groups are the same.
Add function checkWellFormed to family.py

This function is used to check for malformed kinetic families. I have also
removed the function isWellFormed from base.py because it is deprecated by
this new function (and also didn't work due to the many changes we've been
making).

The new function checks for:
-rule labels that have group names which do not exist in groups.py
-rule adjLists that do not match with the corresponding adj list in
groups.py
-Each group must exist in the tree
-Each group adjList must actually be a more specific case of it's parent's adjList
Add check if groups are unique in the database

Coded another check in checkWellFormed to see if each node is unique inside
of a family.
Merge pull request #196 from nyee/rebaseDatabaseTest

Rebase database test
Makefile checks that you have PyDAS and PyDQED on your Python path
Change URLs of PyDAS and PyDQED to GreenGroup in installation instructions.

Hopefully Josh will alert us to any improvements he makes, now that he has left.
I also switched to https instead of git, so that you don't need a github account
and login etc.
Use the https not git@ protocol to get the RMG-database in .travis.yml

The builds got this far then stopped for 10 minutes and were killed:
$ git clone git@github.com:GreenGroup/RMG-database.git
Cloning into 'RMG-database'...
The authenticity of host 'github.com (192.30.252.128)' can't be established.
RSA key fingerprint is 16:27:ac:a5:76:28:2d:36:63:1b:56:4d:eb:df:a6:48.
Are you sure you want to continue connecting (yes/no)?

Hopefully the https version can continue without the RSA fingerprint check...
Use system site_packages (and numpy/scipy) in travis config.

Currently it spends thousands of lines of log file (and quite some time)
compiling scipy for each build. The Ubuntu apt-get install of python-scipy
should save this, but you need to enable the system site packages (instead
of the isolated virtual environment) to use it. [1,2]

Hopefully this (using the system site packages) also fixes the apparent
failure of rdkit: current build failed with:
echo "Checking you have rdkit..."
Checking you have rdkit...
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: No module named rdkit

[1] http://danielnouri.org/notes/2012/11/23/use-apt-get-to-install-python-dependencies-for-travis-ci/
[2] https://github.com/dnouri/nolearn/blob/master/.travis.yml
Simplify travis config: no QM and no Python 2.6

Trying to get the simplest possible configuration working first,
then will add complexity.
Try using the apt-get version of matplotlib too, in travis build.

This should speed up and simplify the build, if it works.
Try building RDKit from source during Travis-CI testing

These lines in the build script are based off the RDKit travis config
https://github.com/rdkit/rdkit/blob/master/.travis.yml
Once this is working we can worry about cacheing the finished
build to speed it up.
Turn on InChI support when building RDKit on Travis
Travis gets and builds PyDAS and PyDQED
Try running eg1 as well as make test in travis testing.