Merged in Chris' changes

Modified cohomology code (unweighted and weighted) so that it doesn't use std::map for boundary computations, which should optimize memory usage.

Changed implementation of WeightedRips to store simplex values (max distance between simplices' vertices) as an invisible layer on top of each simplex object, so that the data() field of WeightedRips has been freed for use by the users again.

Added rips-weighted-cohomology, and channeled WeightedRips logging to the same channel as Rips

Merged upstream

Modified WeightedRips::generate() to incorporate the simplex-appearance-value computation (before it would have to be done explicitly by the user by a for-loop after the call to generate())

added logging to WeightedRips (still needs debugging)

Updated weighted rips libraries to make use of OOP--now WeightedRips inherits from Rips. It is possible that logging for WeightedRips does not work.

Added weighted rips code and libraries

Simplices are deleted from the complex after removal in triangle-zigzag.py + touched up documentation (to mention CohomologyPersistence better)

Consistency zigzag outputs intervals for dimensions less than the skeleton dimension only

Switched PairwiseDistances in Python bindings to C++

Added Python bindings for CohomologyPersistence (+ example + documentation)

Minor changes in distances.py + rips-pairwise.py wrapped into a main() function

Disable alphashapes in Python bindings if no CGAL

Made ListRandomAccessIterator generic with respect to value, and moved it to utils.h

Cleaner output in rips-pairwise.cpp + added make-zigzag-subsamples.py + added lsfiltration.py

Fixed plot.py in tools/plot-values

In documentation put contents into sidebar

Documentation for parametrization using persistent cohomology

Rips pairwise cohomology produces output necessary for 1-cocycle parametrization

Added field arithmetic to CohomologyPersistence (Zp + Q)

Moved PairwiseDistances and ExplicitDistances into include/geometry/distances.h

read_points() does not need ambient dimension and ignores lines starting with '#'

Added documentation; for now mostly for the Python bindings

Touch up to compile with GCC 4.4

Cleaned up simplex comparison functions, rip-pairwise.py outputs a diagram, auxilliary add_simplices() + remove_simplices() for zigzags

Alphashapes and Python bindings * converted alphashapes2d to the new format * added Python bindings for alphashapes * added sample alphashapes.py that dynamically distinguishes between 2D and 3D

Placed all Python bindings code into dionysus::python namespace

Cleaned up Python bindings to restore functionality: * StaticPersistence is iterable, its nodes are usable (sign, pair, cycle) * StaticPersistence knows how to map its nodes into Filtration indices * moved PythonCmp into utils.h * minor cosmetic changes

Renamed header files in bindings/python to get rid of the "python-" prefix

Changes in Python Bindings: * the exposed C++ simplex has Empty data * Python Simplex constructor with data as well as data-based comparison functions are implemented in pure Python

Added Python bindings for the Rips complex + an example

Cleaned up traits (chain and container) for static- and dynamic-persistence

Added tools/extract-diagram + minor fixes

Added intrusive containers issue and issue filters

Moved l2distance.h into include/geometry

Added categories to some of the issues

Fixed distance to diagonal calculation + added stand-alone bottleneck distance tool

Added ZigzagPersistence::is_alive() + consistency zigzag outputs betti 1 at each stage

Added consistency zigzag

Merged in cohomology branch

Added CohomologyPersistence and Rips pairwise distances computation

Added DynamicPersistenceChains (no dynamic part yet)

Updated Rips zigzags * Updated to use Bron-Kerbosch * Compute in the order of increasing epsilon, and decreasing point sizes * Split into plain zigzag (rips-zigzag) and image zigzag (rips-image-zigzag) * Added minor enhancements (show_progress and timers)

Switched Rips complex computation to Bron-Kerbosch algorithm

Added python bindings for ZigzagPersistence (as well as ImageZigzagPersistence)

Switched to CGAL 3.4 (native CMake configuration): for now only alphashapes

Implemented ImageZigzagPersistence * Changed ZigzagPersistence to support a visitor, and implemented ImageZigzagPersistence * examples/rips/rips-zigzag now computes using ImageZigzagPersistence * PersistenceDiagram no longer records zero persistence pairs * Added utilities/memory.h with report_memory() function

Debugged ZigzagPersistence (having added heavier consistency checking) * Added DEBUG_CONTAINERS option (uses std::__debug::* containers for chains and in ZigzagPersistence) * Added SizeStorage specialization for std::deque<T> * ZigzagPersistence got a lot more consistency checking (in debug mode only, which now crawls); as a result it's been debugged (running on non-trivial examples) * examples/rips/rips-zigzag takes command-line options * added ChainWrapper::clear() * added Simplex::VertexDimensionComparison * added PairwiseDistances class (for computing distances between points in a container according to a distance functor)

Added rips-zigzag; in the process caught a number of bugs in ZigzagPersistence (added check_consistency() to it)

Added DequeChains (for ZigzagPersistence)

Added ZigzagPersistence

Merged in Python branch

Initial commit of Python bindings

Empty is now a template, replaced RecursiveIterator with boost::counting_iterator

Removed boundary() from AlphaSimplex3D

Changed Simplex::boundary() to be iterator-based (replaced it with boundary_begin() and boundary_end())

Commit before merging in Python branch: * converted more examples: poincare, rips, some fitness * two generators for Rips complexes * ChainWrapper uses stl algorithms for everything, added CountingBackInserter and switched SizeStorage to use operators * retabbing files along the way * added #957a (namespace dionysus)

Initial addition of tools/diagram-viewer

Closed #8a1 and #96b, added #de6 and #f64

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

Switching README to PanDoc

Added Rips complex-based distance computation to fitness

Added ExplicitDistance + Evaluator to Rips complexes

Merged in Rips complexes

Added initial code for Rips complexes

Added join() operation for a Simplex

Removed inclusion of seemingly unnecessary boost/serialization/is_abstract.hpp header

Converted issues to Maildir format, added Boost 1.36 issue

Added cmake_minimum_required for compatibility with CMake 2.6

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