Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 24 Aug 2007 16:58:25 -0400] rev 58
Fixed handling of degeneracies in KineticSort, Simulator is aware of the sign of the RationalFunction
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 17 Aug 2007 15:08:27 -0400] rev 57
Merged CGAL 3.3 changes with the work on ARVineyard
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 17 Aug 2007 15:04:28 -0400] rev 56
Work in progress on ARVineyard and KineticSort. Commit to merge in CGAL 3.3 changes.
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 15 Aug 2007 11:52:17 -0400] rev 55
tests/geometry now match the include/ breakup and are switched to CMake
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 04 Apr 2008 16:17:28 -0400] rev 54
Fixed the mislabeled Case 1.2
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 26 Mar 2008 05:53:03 -0400] rev 53
Added Poincare sphere example
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 26 Mar 2008 05:52:39 -0400] rev 52
Fixed to compile with GCC 4.3
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 19 Mar 2008 12:43:33 -0400] rev 51
Fixed CGAL assertion failures in alphashapes (explicitly checking for infinite simplices)
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 14 Mar 2008 20:21:15 -0400] rev 50
Added ability to disable the use of DSR-PDB (disabled by default)
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 14 Mar 2008 18:35:41 -0400] rev 49
Normalized persistence (#cff) + unpaired simplices output pairs with 0
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 25 Feb 2008 16:24:29 -0500] rev 48
avida-landscape: added MST (fixing #919) + switched to boost::program_options
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 25 Feb 2008 04:39:27 -0500] rev 47
avida-landscape pairs maxima of fitness rather than minima
Dmitriy Morozov <morozov@cs.duke.edu> [Sun, 17 Feb 2008 16:32:33 -0500] rev 46
avida-landscape computes 0-dimensional persistence of the fitness landscape
Dmitriy Morozov <morozov@cs.duke.edu> [Sun, 17 Feb 2008 09:16:30 -0500] rev 45
Merged the branch resulting from the upstream pull
Dmitriy Morozov <morozov@cs.duke.edu> [Sun, 17 Feb 2008 09:16:00 -0500] rev 44
Started examples/fitness/avida-landscape
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 27 Dec 2007 00:00:00 -0500] rev 43
Added initial Avida code (computes 0-dimensional persistence of the hamming distance function)
Dmitriy Morozov <morozov@cs.duke.edu> [Sun, 17 Feb 2008 08:47:20 -0500] rev 42
LowerStarFiltration provides a base class for VertexType
Dmitriy Morozov <morozov@cs.duke.edu> [Sun, 17 Feb 2008 08:23:55 -0500] rev 41
Added issues
Dmitriy Morozov <morozov@cs.duke.edu> [Sun, 25 Nov 2007 09:12:36 -0500] rev 40
Don't print a line if counters unused; in example/alphashapes converted cout to rInfo
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 11 Oct 2007 11:46:00 -0400] rev 39
Added 2D alpha shape filtration example
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 20 Sep 2007 08:02:49 -0400] rev 38
Added ability to not store trails in pair_simplices() computation
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 20 Sep 2007 07:31:40 -0400] rev 37
Added counter of total trail and cycle lengths. Added CountBy.
Dmitriy Morozov <morozov@cs.duke.edu> [Tue, 18 Sep 2007 05:45:19 -0400] rev 36
Minor fixed to CMake (fixed include directory for rlog)
Dmitriy Morozov <morozov@cs.duke.edu> [Tue, 18 Sep 2007 05:45:04 -0400] rev 35
Removed sz from Cycle (size is kept track of in the parent)
Dmitriy Morozov <morozov@cs.duke.edu> [Sat, 15 Sep 2007 14:31:36 -0400] rev 34
Counter omits color codes only if connected to a TTY
Dmitriy Morozov <morozov@cs.duke.edu> [Sat, 15 Sep 2007 04:42:15 -0400] rev 33
Updated README to reflect changes to the logging
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 14 Sep 2007 17:32:11 -0400] rev 32
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
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 14 Sep 2007 06:34:43 -0400] rev 31
Added counters to Cycle, added timestamp to Counter output
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 14 Sep 2007 05:51:51 -0400] rev 30
Fixed logging and counters
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 13 Sep 2007 10:31:39 -0400] rev 29
Counters straightened out (at least the code compiles)
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 13 Sep 2007 04:43:33 -0400] rev 28
Merged in changes from master
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 13 Sep 2007 04:42:39 -0400] rev 27
Changed counters and added setup for new logging. Everything but tests is broken.
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 12 Sep 2007 09:40:23 -0400] rev 26
Merged in README changes from master
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 12 Sep 2007 09:39:34 -0400] rev 25
Changed SimplexWithVertices<V>::VertexContainer to std::vector<V> from std::set<V>
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 12 Sep 2007 08:28:33 -0400] rev 24
Fixed typos in README
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 16 Aug 2007 17:12:52 -0400] rev 23
Fixed to compile with CGAL 3.3
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 15 Aug 2007 11:39:34 -0400] rev 22
Merged geometry and include breakup with AR vineyard
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 15 Aug 2007 11:25:35 -0400] rev 21
Initial AR vineyard commit (CGAL based, and not working)
Dmitriy Morozov <morozov@cs.duke.edu> [Tue, 14 Aug 2007 17:15:08 -0400] rev 20
Broke include/ into separate topology/ and utilities/ subdirectories
Dmitriy Morozov <morozov@cs.duke.edu> [Sun, 01 Jul 2007 00:00:00 -0400] rev 19
Initial geometry commit
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 23 May 2007 10:48:04 -0400] rev 18
Added Cech complex example
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 07 Feb 2007 14:00:39 -0500] rev 17
Switched counters to macros
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 31 Jan 2007 16:53:35 -0500] rev 16
Alpha shapes examples compile with debugging enabled (Added AlphaSimplex3D::boundary())
Dmitriy Morozov <morozov@cs.duke.edu> [Tue, 30 Jan 2007 13:51:04 -0500] rev 15
Switched to CMake
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 24 Jan 2007 17:50:45 -0500] rev 14
Added computation of PDBDistanceGrid for all atoms of the backbone (not just alpha-carbons)
Dmitriy Morozov <morozov@cs.duke.edu> [Sat, 20 Jan 2007 13:39:51 -0500] rev 13
Removed config/ directory
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 12 Jan 2007 12:49:29 -0500] rev 12
Options read from home or config directories; documentation built by default
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 01 Jan 2007 11:45:28 -0500] rev 11
Added option to maintain lazy RU-decomposition during transpositions. Plus minor fixes.
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 29 Dec 2006 18:20:50 -0500] rev 10
Added operator() to OrderList<T>::OrderComparison
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 25 Dec 2006 12:28:13 -0500] rev 9
Added pair_simplices() to Filtration (without arguments)
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 22 Dec 2006 12:52:35 -0500] rev 8
Added examples/alphashapes
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 22 Dec 2006 10:25:26 -0500] rev 7
Added combustion-vineyard, Grid2DVineyard records diagram after adding a grid
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 21 Dec 2006 13:37:23 -0500] rev 6
Removed missing tests/test-realtype from tests/SConscript
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 21 Dec 2006 13:32:34 -0500] rev 5
Switched to a new architecture (Vineyard is a visitor for Filtration),
added LowerStarFilation, examples/grid (pdbdistance-vineyard in particular)
Dmitriy Morozov <morozov@cs.duke.edu> [Sat, 16 Dec 2006 15:34:46 -0500] rev 4
Split OrderList into OrderList and ConsistencyList. Made efficient insertions possible.
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 04 Dec 2006 22:39:35 -0500] rev 3
Moved config to a separate directory
Dmitriy Morozov <morozov@cs.duke.edu> [Sun, 03 Dec 2006 22:38:34 -0500] rev 2
Cleaned up AssertMsg in debug.h, and adjusted assertions in filtration.hpp
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 30 Oct 2006 14:40:34 -0500] rev 1
Disabled missing qt4 tool, and added missing src/Sconcript
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 30 Oct 2006 14:20:45 -0500] rev 0
Initial conversion to Dionysus architecture