[makedoc]

Added in the list of options to be tested:
$($CXX --print-prog-name=ld) -r -o
As suggested by @alalazo

Since this option appears to work also with old compilers, I try
it as a first option.

See #291

[makedoc]

Improvements in drr module

This required changing a reset() used in the transition

Notice that this required changing back some reset() call.
Indeed, as an intermediate stage, some unique_ptr<Grid> objects
were assigned using reset(). Now that Grid::create correctly returns
a unique_ptr<Grid> they should be assigned using =

Spot out by cppcheck on master branch. Since the problem is relevant
also for v2.3, I fix it here.

This command should be more portable. Notice that with old
gcc (e.g. 4.6) this does not work. I added a test such that
when this does not work "ld -r -o" is tried instead

removed extra comma

# Conflicts:
#	src/lib/Makefile

This change allows to load libraries locate in src/lib more easily
on a mac. Notice that traditionally this was solved by setting
DYLD_LIBRARY_PATH. However, as of osx Capitan, DYLD_LIBRARY_PATH
does not work correctly. Fixing the installed path with
install_name_tool should solve the issue.

(backported from master)

C-style IO is faster than fstream in C++.

Fixed also buildPythonInterface script (was using LDSO)

The new name looks more standard (it is used in the python community)

V2.4 - Dimer CV update'

[makedoc]

@valsson what about hardcoding the current variables in case
environment is not defined?

The point is that env var set on travis are not visible, so at some point
we could even forget what are the right settings.

* 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