makes signatures available in notebooks

- Allow Plumed objects to be explicitly finalized
(can be used to make sure files are closed correctly)
- Allow Plumed objects to be used in context managers

`except:` might catch the wrong exception by mistake

In addition to numpy arrays, I make it possible to pass plain python arrays.

I think the inclusion of numpy headers was related to non used variables
forgotten from an intermediate implementation.
I just removed them. In this manner it is not necessary that numpy is
already installed when plumed extension is compiled.

Numpy would be anyway required to run our test.

This allows creating plumed objects with

p=plumed.Plumed(kernel="/path/to/libplumedKernel.so")

Not strictly necessary, but might be useful to allow more
flexibility.

It does not link to library anymore, but just includes Plumed.h file.
It thus could be compiled with different compilers and flags wrt plumed.

Notice that as of PLUMED 2.5 Plumed.h also contains the full implementation
of the dynamic loader, so it is sufficient to define the proper cpp
flags in order to recompile the loader and avoiding the need to link
plumedWrapper.a.

This basically allows the python wrapper to be selfcontained and installable
before having installed plumed.

I think python should use the C++ interface rather than the C one.
The reason is that the C++ interface included in PLUMED 2.5
rethrows exceptions and thus can be used to load
a shared library compiled with a different compiler or
linked against a different standard library.

In perspective, this will allow compiling PLUMED with
a different compiler/library than that used to compile
python itself.

This should ensure that plumed_finalize is called when the python/cython
class is destroyed

Addresses #295

* Added first working python interface

* Tidied up python interface

* Further simplification of python

* Added example which should be deleted later

* Added functions for getting values from plumed to python

* Added regression test for python interface

* Added mechanism to return exceptions from plumed to python

* First commit of experimental stuff to catch exceptions in python correctly

* Got rid of unecessarily duplicated method in PlumedMain

* Fixed crazy MAC input encoding

* Oops, had also broken the script..

* Removed debug messages. Works on Ubuntu Linux

Linus rules. Apple sucks.

* Fixed PlumedMain passing of data from plumed to outside code

* Hard coded real precision for python interface - this should have been with the last commit

* Added first go at working makefile for python interface

* Added options to configure to build python interface from makefile

* Small changes to where loading of python interface is done

* Removed unecessary wrapper c++ function from python interface

* Made python install work in a way that is consistent with the rest of plumed

* Added pythonpath to travis.yml

* Added installation of Cython to travis.yml

* Added ifdef block to stop cppcheck throwing an error

* Using uniqu_ptr for DataFetching object in PlumedMain

* Added install command for numpy to travis

* Added string to tell me whether plumed+python is being built

* Small change in travis.yml file to see if I can get python compile working

* Compilers for cython are now specified from Makefile.conf

* Now printing stuff on environment to try to work out why linking doesn't work

* A new attempt to fix the travis-ci issues

* Got rid of troubling TRAVIS_PYTHON_FLAG

* Small change to see if we can get this to work on travis

* Now setting LDSHARED from LDSO in makefile

* Added something to print everything in the python path when we run the python test

* Fixed python path in travis.yml

* Removed stuff for debugging configuration on travis

* Customized conda install (for python) in travis.yml so that osx version is installed for osx and linux version is installed for linux

* Set TMPDIR in .travis.yml to hopefully get osx to compile PLUMED + Python

* Made it so that python interface is rebuilt when user does make install so that correct paths are used

* Made it so that python interface is rebuilt in staging area during install procedure

* Corrected regtest script so that python tests are dealt with the same as everything else