Intermediate commit while converting to the new architecture
* Converted Filtration into StaticPersistence and DynamicPersistenceTrails
(both right now work with the underlying std::vector rather than std::list order)
* Filtration is now just an auxilliary glue (a map between Complex and Persistence)
* Whether chains are vectors or lists can be interchanged
* Added PersistenceDiagram with a simple bottleneck_distance() function
* Converted triangle, alphashapes3d, and cech-complex examples
* Lots of organizational changes
(factoring utilities out into containers.h, indirect.h, property-maps.h)
* Trying to document along the way with NaturalDocs-type comments
set (targets
avida-distance
avida-rips-distance
avida-landscape)
foreach (t ${targets})
add_executable (${t} ${t}.cpp)
target_link_libraries (${t} ${libraries} ${Boost_PROGRAM_OPTIONS_LIBRARY})
endforeach (t ${targets})