Merge in AR branch

Fixed #c42 for ar-vineyard

Merged in upstream changes and reopened #c42

KineticEvaluator takes the maximum time between the two simulators

Small logging additions + maintain_lazy = false + eventqueue - Filtration::transpose( ..., maintain_lazy = false ) - EventQueue inserts a new event after all the ones equal to it, not before

Marked #c66 and #d2a as fixed (fixes in f236c7d659d0 and abba2950aced, respectively)

Fixed Vineyard to preserve the vine addresses after we add a new dimension vine (was a major bug)

Using two simulators in ARVineyard (one for simplices and one for trajectories) - Fixes #c66 - Simulator::reached_infinity() examines the queue instead of keeping state in a variable

ConeSimplex and ARConeSimplex3D adjusted to work correctly with operator<(), operator==(), and boundary()

ConeSimplex correctly reports dimension()

program_options + trajectory knees - added boost::program_options - recording knees when trajectories change

Merged upstream changes (to get boost::program_options setup in CMake)

Merged in fitness branch

ar-vinyeard compiles and runs: - ar-function-kernel uses int for sign rather than bool in sign_at - switched to dealing with a single functions themselves in value_at - order of thresholds is handled correctly in ar-vineyard (max is the last one)

Added intostring() issue (#89a)

KineticSort can deal with equal trajectories: UPolynomial::sign_at_negative_infinity() can handle 0 and so can Simulator::add()

Fixed UPolynomial<T>::sign_at_negative_infinity() + Simulator::add() Bug in the former and resulting logic problems in the latter.

Added and fixed CGAL debugging problem (issue #c42)

Added EventQueue efficiency issue (#ebd)

Initial commit of KineticSort-based ARVineyard Compiles, but needs to be runtime debugged.

Issue #cd7: incorrect UPolynomial<double>::sign_at()

Fixed Simulator not processing events correctly Event that is being processed needed to be removed from the queue while its own process() method ran.

Fixed segfault in test-kinetic-sort (#b5d)

Added segfault in test-kinetic-sort issue

Changed PolynomialKernel to FunctionKernel

Changed geometry to RLog-based logging and counters

Added class groups to Doxygen documentation

Merged in changes from master

Commit to merge in changes from master.

Fixed handling of degeneracies in KineticSort, Simulator is aware of the sign of the RationalFunction

Merged CGAL 3.3 changes with the work on ARVineyard

Work in progress on ARVineyard and KineticSort. Commit to merge in CGAL 3.3 changes.

tests/geometry now match the include/ breakup and are switched to CMake

Fixed the mislabeled Case 1.2

Added Poincare sphere example

Fixed to compile with GCC 4.3

Fixed CGAL assertion failures in alphashapes (explicitly checking for infinite simplices)

Added ability to disable the use of DSR-PDB (disabled by default)

Normalized persistence (#cff) + unpaired simplices output pairs with 0

avida-landscape: added MST (fixing #919) + switched to boost::program_options

avida-landscape pairs maxima of fitness rather than minima

avida-landscape computes 0-dimensional persistence of the fitness landscape

Merged the branch resulting from the upstream pull

Started examples/fitness/avida-landscape

Added initial Avida code (computes 0-dimensional persistence of the hamming distance function)

LowerStarFiltration provides a base class for VertexType

Added issues

Don't print a line if counters unused; in example/alphashapes converted cout to rInfo

Added 2D alpha shape filtration example

Added ability to not store trails in pair_simplices() computation

Added counter of total trail and cycle lengths. Added CountBy.

Minor fixed to CMake (fixed include directory for rlog)

Removed sz from Cycle (size is kept track of in the parent)

Counter omits color codes only if connected to a TTY

Updated README to reflect changes to the logging

Changes to CMakeLists: * Optimize and debug options derive flags from CMKAE_CXX_FLAGS* * Moved CGAL CXX flags from the top level to the specific locations where they are required

Added counters to Cycle, added timestamp to Counter output

Fixed logging and counters

Counters straightened out (at least the code compiles)

Merged in changes from master

Changed counters and added setup for new logging. Everything but tests is broken.

Merged in README changes from master

Changed SimplexWithVertices<V>::VertexContainer to std::vector<V> from std::set<V>

Fixed typos in README

Fixed to compile with CGAL 3.3

Merged geometry and include breakup with AR vineyard

Initial AR vineyard commit (CGAL based, and not working)

Broke include/ into separate topology/ and utilities/ subdirectories

Initial geometry commit

Added Cech complex example

Switched counters to macros

Alpha shapes examples compile with debugging enabled (Added AlphaSimplex3D::boundary())

Switched to CMake

Added computation of PDBDistanceGrid for all atoms of the backbone (not just alpha-carbons)

Removed config/ directory

Options read from home or config directories; documentation built by default

Added option to maintain lazy RU-decomposition during transpositions. Plus minor fixes.

Added operator() to OrderList<T>::OrderComparison

Added pair_simplices() to Filtration (without arguments)

Added examples/alphashapes

Added combustion-vineyard, Grid2DVineyard records diagram after adding a grid

Removed missing tests/test-realtype from tests/SConscript

Switched to a new architecture (Vineyard is a visitor for Filtration), added LowerStarFilation, examples/grid (pdbdistance-vineyard in particular)

Split OrderList into OrderList and ConsistencyList. Made efficient insertions possible.

Moved config to a separate directory

Cleaned up AssertMsg in debug.h, and adjusted assertions in filtration.hpp

Disabled missing qt4 tool, and added missing src/Sconcript

Initial conversion to Dionysus architecture