Handle input files

[chrispbradley]

The test framework fails when examples have input files. The test framework creates a directories (under testrunner-build) for each example then executes the absolute path to the example (executable or python script) from this directory. This process fails if the example has input files as the paths to the input files are now wrong as the example will look for these files in the testrunner-build directory. The current hack of making the input file a test argument is not sufficient as a) the examples should be able to run in the test framework unaltered and b) this solution does not scale for examples that have many input files.

[beauof]

I would propose the following:

1. Have a common input file data base (separate from or as subfolder in functional_test_database) that contains all input files needed for functional tests. The advantage here is that input files can be shared between functional tests. Secondly, we encourage users/developers to use these input files when setting up new tests for their code.
2. Provide the absolute path to the input file data base as example argument, which can easily be done via CMake and thus, be provided via the test description file as an environment variable.

To me this seems like a very simple approach, it is easy to implement and does not depend on the number of input files.

For example, VTK does something similar: https://www.vtk.org/Wiki/VTK_Datasets

Any comments @chrispbradley @hsorby @rchristie ?

[hsorby]

I have fixed a problem with input files in a recent commit. The other part of the fix is to improve the examples so that they can take information passed through the command line. An example of how this might be done can be seen in OpenCMISS-Examples/active_contraction#4.

[hsorby]

As of now I think we have part of what @beauof has proposed above. Some documentation specifying exactly how data is used from the test input database (PMR) should be added. I think this is a good idea for any models that can be shared or are significantly large to warrant separation.