Getting rid of legacy `history` field in database entries.

This field does nothing useful and only creates useless commit differences
on github.  Its removal lets the database be cleaner.
For kinetics databases, write reference and referenceType fields only if not None.
Merge pull request #197 from connie/universalDatabase

Universal database progress.
Looks good to me, and I merged the RMG-database commit too.
(And after all that effort that went into preserving the history entries and detecting changes....)
Remove unused `recommended` flags for databases.
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.

I also tweak the linux installation instructions.
Just formatting, really.
Change the default location of the database (I think this is more likely right)

It's very confusing to me where this is set, and in what priority.
(eg. the .rmgrc config file). I'm not sure why the prior one seems to work in other places
but not on Travis. Perhaps the $RMGpy environment variable?
Add work_in_progress decorator for currently failing Unit Tests

This is a proof (test) of concept. If it works, then we should add this
decorator to all the unit tests that we currently EXPECT to fail.
That way, the Travis-CI build test will pass - the failing tests will
just be skipped if they fail (still with an error message).

We shouldn't forget to go and fix the tests though!
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.
Remove redundant parts from Travis config file.

--use-mirrors has been deprecated, and pip install .  likely isn't needed
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
But modified to turn on InChI support
Once this is working we can worry about cacheing the finished
build to speed it up.
Travis gets and builds PyDAS and PyDQED

Unlike the instructions for users in our installation guide,
don't have Travis sudo the make install for PyDAS and PyDQED.
'sudo' on Ubuntu makes it discover the wrong python, which then doesn't
have Cython installed, and it all goes wrong. Hopefully this clears it up.
I also split into several lines, to make debugging the Travis log easier.
Try running eg1 as well as make test in travis testing.