Pypi ships also the plumed.cpp file, so it is not necessary to
ask users to install cython

I added some material needed for pypi packaging.

I made a few more changes to setup.py in order to work with MacPorts.
This allowed me to add a temporary Portfile for py-plumed
that is now used in travis tests.

The plan is to submit this Portfile to MacPorts after we release v2.5

Notice that one test is duplicated (python/test) in order to be available
when using nosetests from python.

Only install required files (.so).

Should fix #413

Now that exceptions are translated, it is possible to dlclose an image
that is not used anymore.

- renamed script to setup.py
- Use "make pip" to copy required files in this dir for pip
- Use try/except when importing numpy and cython so as to notify the user
- renamed env vars to plumed_xxx so that there is no risk of clashes

Plumed can now also be installed using

cd python
make pip
pip install --user .

make pip is just needed to bring version information and Plumed.h
in this directory. Might be solved differently in MacPorts / Pypi.

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.

Now we have explicit only used with C++11 and where it should be used.

Now every exception thrown within PLUMED is remapped in the wrapper.

In particular:
- All standard C++ exceptions are remapped to equivalent ones.
- PLUMED exceptions and lepton exceptions are remapped to ad hoc classes.
- Any other exception derived from std::exception is mapped to std::exception.
- Any other exception is rethrown after printing a warning.

I changed Plumed::invalid() to Plumed::makeInvalid() and added a new function
Plumed::makeValid(). These names are more inline with stdlib names
(e.g. make_shared), though with our conventions for capitalization.

Hopefully there's no code yet using this (beta) interface.

In addition, I made it possible to use a macro to change the behavior
of the default constructor to makeInvalid(). This might be
useful in python wrappers to avoid opening the library twice
(python objects always use the "nullary" - default - constructor first).

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.

now covered by the regtest better