| c701116 | Jerome Kelleher | 30 November 2015, 17:45:29 UTC | Bumped to 0.1.6a1 | 30 November 2015, 17:45:29 UTC |
| 23cff17 | Jerome Kelleher | 27 November 2015, 12:00:03 UTC | Added precision option for Newick command. | 27 November 2015, 12:00:03 UTC |
| 7a1b4e0 | Jerome Kelleher | 27 November 2015, 10:57:42 UTC | Merge branch 'develop' | 27 November 2015, 10:57:42 UTC |
| 5d766cc | Jerome Kelleher | 25 November 2015, 10:35:23 UTC | Tidied up compress implementation. | 25 November 2015, 10:35:23 UTC |
| 327a447 | Jerome Kelleher | 24 November 2015, 20:25:57 UTC | Bumped version number. | 24 November 2015, 20:25:57 UTC |
| e679c7d | Jerome Kelleher | 24 November 2015, 20:06:39 UTC | Added bounds on compress. | 24 November 2015, 20:06:39 UTC |
| 4176058 | Jerome Kelleher | 24 November 2015, 17:57:51 UTC | Rough first effort squashing. | 24 November 2015, 17:57:51 UTC |
| 41bb125 | Jerome Kelleher | 24 November 2015, 16:59:40 UTC | Crude fix for new breakpoints format. | 24 November 2015, 17:25:33 UTC |
| 75d2b36 | Jerome Kelleher | 24 November 2015, 16:42:42 UTC | Initial pass at new alg without defrag. | 24 November 2015, 16:42:42 UTC |
| e583576 | Jerome Kelleher | 23 November 2015, 17:27:45 UTC | Fix for subtle links bug. | 23 November 2015, 17:27:45 UTC |
| 1851eef | Jerome Kelleher | 23 November 2015, 16:27:06 UTC | Added extra sanity checks for run. | 23 November 2015, 16:27:06 UTC |
| cc9eec5 | Jerome Kelleher | 15 November 2015, 16:27:11 UTC | Bumped version to 0.1.6.dev1 | 15 November 2015, 16:27:11 UTC |
| 10483bf | Jerome Kelleher | 15 November 2015, 15:43:11 UTC | Added sigpipe handler to clean up piping. | 15 November 2015, 15:43:11 UTC |
| 6494bf6 | Jerome Kelleher | 09 November 2015, 16:16:35 UTC | Version bump. | 09 November 2015, 16:16:35 UTC |
| 3be729c | Jerome Kelleher | 09 November 2015, 16:07:07 UTC | Updated Homebrew instructions; svgwrite optional. | 09 November 2015, 16:07:07 UTC |
| 9715e1e | Jerome Kelleher | 09 November 2015, 13:02:05 UTC | Fixed bug in argparse code and bumped version. | 09 November 2015, 13:02:05 UTC |
| 16b686c | Jerome Kelleher | 06 November 2015, 15:40:46 UTC | Fixed test bug. | 06 November 2015, 15:40:46 UTC |
| 081c3c3 | Jerome Kelleher | 06 November 2015, 15:34:31 UTC | Fixed newer flake8 issues. | 06 November 2015, 15:34:31 UTC |
| 1cfe962 | Jerome Kelleher | 06 November 2015, 15:31:57 UTC | Version bump to 0.1.5a1. | 06 November 2015, 15:31:57 UTC |
| c1f5089 | Jerome Kelleher | 06 November 2015, 09:27:52 UTC | Polished up docs for msp. | 06 November 2015, 09:27:52 UTC |
| e48f604 | Jerome Kelleher | 05 November 2015, 16:12:38 UTC | Added CLI tests for msp. | 05 November 2015, 16:12:38 UTC |
| b98b205 | Jerome Kelleher | 05 November 2015, 09:52:40 UTC | Added console script. | 05 November 2015, 13:06:14 UTC |
| e9dac39 | Jerome Kelleher | 04 November 2015, 17:35:26 UTC | Initial working version. | 05 November 2015, 13:06:14 UTC |
| a34c9a7 | Jerome Kelleher | 04 November 2015, 17:01:36 UTC | Initial framework. | 05 November 2015, 13:06:14 UTC |
| da70f4a | Jerome Kelleher | 05 November 2015, 13:05:36 UTC | Updated README. | 05 November 2015, 13:05:36 UTC |
| 16d931e | Jerome Kelleher | 05 November 2015, 12:37:36 UTC | Mac installation instructions + bug fixes. | 05 November 2015, 12:37:36 UTC |
| cbe477a | Jerome Kelleher | 05 November 2015, 10:47:27 UTC | Fixes for installation bugs. | 05 November 2015, 10:47:27 UTC |
| 07ead8e | Jerome Kelleher | 04 November 2015, 16:53:23 UTC | Updated tests to improve coverage. | 04 November 2015, 16:53:23 UTC |
| 6a31d02 | Jerome Kelleher | 04 November 2015, 15:22:40 UTC | Improved the documentation and tutorial. | 04 November 2015, 15:22:40 UTC |
| e4ba82f | Jerome Kelleher | 04 November 2015, 14:38:35 UTC | Improved docs for models. | 04 November 2015, 14:38:35 UTC |
| ece5b39 | Jerome Kelleher | 04 November 2015, 10:40:56 UTC | Fixed Python 3 error. | 04 November 2015, 10:40:56 UTC |
| 40f646b | Jerome Kelleher | 04 November 2015, 10:23:02 UTC | Merge branch 'leafsets' into develop | 04 November 2015, 10:23:02 UTC |
| c9197ea | Jerome Kelleher | 04 November 2015, 10:09:06 UTC | Added some tests for the leaf-list iterator. | 04 November 2015, 10:09:06 UTC |
| 80f0b2f | Jerome Kelleher | 23 October 2015, 15:18:19 UTC | Updated version to show dev status. | 23 October 2015, 15:18:19 UTC |
| 503d420 | Jerome Kelleher | 08 October 2015, 08:28:23 UTC | Dropped support for Python 3.2 in travis. | 08 October 2015, 08:28:23 UTC |
| 53c6638 | Jerome Kelleher | 08 October 2015, 08:10:32 UTC | Fixed interval notation error. | 08 October 2015, 08:10:32 UTC |
| 0b21546 | Jerome Kelleher | 15 September 2015, 11:56:34 UTC | Added framework for leaf access in Python. | 15 September 2015, 11:56:34 UTC |
| c919dad | Jerome Kelleher | 15 September 2015, 11:05:34 UTC | Use leaf list for haplotype generation. | 15 September 2015, 11:05:34 UTC |
| deee849 | Jerome Kelleher | 14 September 2015, 15:54:20 UTC | Fixed error due to shortcut. | 14 September 2015, 15:54:20 UTC |
| 47fc80a | Jerome Kelleher | 14 September 2015, 15:16:46 UTC | Initial pass at leaf lists. | 14 September 2015, 15:16:46 UTC |
| d3a3937 | Jerome Kelleher | 08 September 2015, 11:55:29 UTC | Version bump. | 08 September 2015, 11:55:29 UTC |
| 5b839f2 | Jerome Kelleher | 08 September 2015, 11:51:55 UTC | Added tree index. | 08 September 2015, 11:51:55 UTC |
| 99aaf34 | Jerome Kelleher | 08 September 2015, 11:25:24 UTC | Fixed dump for set_mutations bug. | 08 September 2015, 11:25:24 UTC |
| 93d6cb2 | Jerome Kelleher | 02 September 2015, 08:39:16 UTC | Fixed errors in plink conversion. | 02 September 2015, 08:39:16 UTC |
| 359220b | Jerome Kelleher | 01 September 2015, 19:43:18 UTC | Added numpy output. | 01 September 2015, 19:43:18 UTC |
| e84dd62 | Jerome Kelleher | 01 September 2015, 12:42:42 UTC | Merge branch 'diploid-example' into develop | 01 September 2015, 12:42:42 UTC |
| 8255bdd | Jerome Kelleher | 01 September 2015, 12:42:14 UTC | Made plink output converter. | 01 September 2015, 12:42:14 UTC |
| b389f99 | Jerome Kelleher | 01 September 2015, 09:03:20 UTC | Working outline of leaf set code. | 01 September 2015, 09:03:20 UTC |
| 1b1285a | Jerome Kelleher | 29 August 2015, 11:09:23 UTC | Working-ish outline of leaf set algorithm. | 29 August 2015, 11:09:23 UTC |
| 8f7c282 | Jerome Kelleher | 29 August 2015, 09:34:34 UTC | INitial pass at leaf set alg. | 29 August 2015, 09:34:34 UTC |
| d0fb9ed | Jerome Kelleher | 28 August 2015, 12:51:28 UTC | Version bump. | 28 August 2015, 12:51:28 UTC |
| 23ef05e | Jerome Kelleher | 28 August 2015, 12:50:41 UTC | Updated documentation. | 28 August 2015, 12:50:41 UTC |
| 8c9e1f2 | Jerome Kelleher | 28 August 2015, 12:16:39 UTC | Implemented the leaf counts for tracked leaves. | 28 August 2015, 12:16:39 UTC |
| ff02209 | Jerome Kelleher | 27 August 2015, 20:10:19 UTC | Initial implementation of the leaf-specific count. | 27 August 2015, 20:10:19 UTC |
| 5d94d3c | Jerome Kelleher | 27 August 2015, 12:47:47 UTC | Version bump. | 27 August 2015, 12:47:47 UTC |
| 03ba98e | Jerome Kelleher | 27 August 2015, 12:40:46 UTC | Updated documentation. | 27 August 2015, 12:40:46 UTC |
| cdcc760 | Jerome Kelleher | 27 August 2015, 10:46:48 UTC | Added set_mutations support. | 27 August 2015, 10:46:48 UTC |
| f092669 | Jerome Kelleher | 26 August 2015, 15:28:30 UTC | Implemented leaf counting. | 26 August 2015, 15:28:30 UTC |
| dd7526a | Jerome Kelleher | 26 August 2015, 12:45:19 UTC | Diffs return out_records in reverse time order. Also, rewrote the diff iterator to be much simpler. | 26 August 2015, 12:45:19 UTC |
| 568bcef | Jerome Kelleher | 25 August 2015, 08:57:38 UTC | Exploratory code. | 25 August 2015, 08:57:38 UTC |
| 5387422 | Jerome Kelleher | 23 July 2015, 11:16:00 UTC | Added dev code for visualising trees sequence. | 23 July 2015, 11:16:00 UTC |
| 2d281a7 | Jerome Kelleher | 23 July 2015, 11:02:14 UTC | Merge branch 'master' into develop | 23 July 2015, 11:02:14 UTC |
| 3919543 | Jerome Kelleher | 20 July 2015, 19:58:06 UTC | Added preorder support to the nodes method. Also changed the sparse_trees iterator to trees. | 20 July 2015, 19:58:06 UTC |
| 25b646b | Jerome Kelleher | 20 July 2015, 13:00:56 UTC | Added a simple R interface to the HDF5 file. | 20 July 2015, 13:03:43 UTC |
| 0dbb2f7 | Jerome Kelleher | 19 July 2015, 15:51:59 UTC | Added missing documentation files. | 19 July 2015, 15:51:59 UTC |
| 1a7e7fa | Jerome Kelleher | 19 July 2015, 15:48:25 UTC | Bumped to 0.1.2a2. | 19 July 2015, 15:48:25 UTC |
| 4f10d5f | Jerome Kelleher | 19 July 2015, 15:43:23 UTC | Fixed version number issue. | 19 July 2015, 15:43:23 UTC |
| 9bc444e | Jerome Kelleher | 19 July 2015, 15:35:15 UTC | Alpha version of 0.1.2 ready for release. | 19 July 2015, 15:35:15 UTC |
| 725fb87 | Jerome Kelleher | 19 July 2015, 15:33:43 UTC | Added examples for mutations. | 19 July 2015, 15:33:43 UTC |
| 55024da | Jerome Kelleher | 19 July 2015, 13:12:22 UTC | Added section on tree sequences. | 19 July 2015, 13:12:22 UTC |
| 179b91a | Jerome Kelleher | 19 July 2015, 12:11:06 UTC | Added time and mutations to tree drawing. | 19 July 2015, 12:11:06 UTC |
| 1e71a2c | Jerome Kelleher | 17 July 2015, 16:38:46 UTC | Minor doc updates. | 17 July 2015, 16:38:46 UTC |
| 86fa688 | Jerome Kelleher | 17 July 2015, 14:44:40 UTC | Added a leaves iterator to tree. | 17 July 2015, 14:44:40 UTC |
| 0ebc5c6 | Jerome Kelleher | 17 July 2015, 13:28:59 UTC | Reverted sequence-length to num_loci change. | 17 July 2015, 13:28:59 UTC |
| 3bba13e | Jerome Kelleher | 17 July 2015, 12:29:40 UTC | Added tests for mutations + fixed rare root bug. Also fixed memory access issue when the number of population models is 0. | 17 July 2015, 12:29:40 UTC |
| 2159fed | Jerome Kelleher | 17 July 2015, 09:27:15 UTC | Added low-level support for mutations on trees. | 17 July 2015, 09:27:15 UTC |
| d95229b | Jerome Kelleher | 16 July 2015, 15:28:00 UTC | Added SVG output and started tutorial. | 16 July 2015, 15:28:00 UTC |
| 192185c | Jerome Kelleher | 16 July 2015, 12:05:07 UTC | Made a start on tutorial. | 16 July 2015, 12:05:07 UTC |
| 224fe28 | Jerome Kelleher | 16 July 2015, 11:06:31 UTC | Added library version to environment. | 16 July 2015, 11:06:31 UTC |
| eecd99b | Jerome Kelleher | 16 July 2015, 10:51:47 UTC | Updated file format docs. | 16 July 2015, 10:51:47 UTC |
| d90dfb1 | Jerome Kelleher | 15 July 2015, 15:59:56 UTC | Added an initial pass at the file format. | 15 July 2015, 15:59:56 UTC |
| afbe22a | Jerome Kelleher | 15 July 2015, 13:16:12 UTC | Updated docs, and tweaked API. | 15 July 2015, 13:16:12 UTC |
| 72facce | Jerome Kelleher | 14 July 2015, 19:54:14 UTC | Added initial outlines of API docs. | 14 July 2015, 19:54:14 UTC |
| 52be8e4 | Jerome Kelleher | 14 July 2015, 19:31:53 UTC | Added get_mrca support. | 14 July 2015, 19:31:53 UTC |
| 34a1089 | Jerome Kelleher | 13 July 2015, 16:10:12 UTC | Merge branch 'sparse_tree_conversion' into develop | 13 July 2015, 16:28:34 UTC |
| 803558d | Jerome Kelleher | 13 July 2015, 16:09:36 UTC | Working version of new sparse tree interface. | 13 July 2015, 16:09:36 UTC |
| fbbb95e | Jerome Kelleher | 10 July 2015, 12:01:58 UTC | Added counter for multiple recombination. | 10 July 2015, 12:07:40 UTC |
| f629de7 | Jerome Kelleher | 09 July 2015, 19:42:31 UTC | Partial conversion to new sparse tree interface. Lots of stuff broken. | 09 July 2015, 19:42:31 UTC |
| f99e9ae | Jerome Kelleher | 09 July 2015, 12:28:23 UTC | Added event-by-event simulation API. | 09 July 2015, 12:49:49 UTC |
| 92a0326 | Jerome Kelleher | 08 July 2015, 20:17:23 UTC | Initial low-level interface for sparse trees. | 08 July 2015, 20:17:23 UTC |
| 6b1bd41 | Jerome Kelleher | 01 July 2015, 20:03:01 UTC | Fixed dendropy deprecation warning. | 02 July 2015, 08:34:47 UTC |
| 81a4a9c | Jerome Kelleher | 01 July 2015, 20:01:01 UTC | intial version of sparse_tree_iterator. | 01 July 2015, 20:01:01 UTC |
| da510e8 | Jerome Kelleher | 01 July 2015, 15:34:11 UTC | Added good draft algorithm for sparse trees. | 01 July 2015, 15:34:11 UTC |
| 7557dd3 | Jerome Kelleher | 25 June 2015, 09:55:42 UTC | Added some portability information to the README. | 25 June 2015, 09:55:42 UTC |
| 3c096c7 | Jerome Kelleher | 25 June 2015, 09:11:39 UTC | Added tests to tarball, + added dev version. | 25 June 2015, 09:11:39 UTC |
| 4b8992f | Jerome Kelleher | 25 June 2015, 08:40:55 UTC | Fixed Python 3 issue. | 25 June 2015, 08:40:55 UTC |
| 20e22bb | Jerome Kelleher | 24 June 2015, 22:28:22 UTC | Changed harmonic number to approx. | 24 June 2015, 22:28:22 UTC |
| cc711b4 | Jerome Kelleher | 24 June 2015, 21:21:18 UTC | Fixed bug in 32bit haplotype generation. | 24 June 2015, 21:21:18 UTC |
| f735400 | Jerome Kelleher | 24 June 2015, 20:54:16 UTC | Added low-level file format tests. | 24 June 2015, 20:54:16 UTC |
| dd8522b | Jerome Kelleher | 24 June 2015, 19:05:27 UTC | Cleared out cruft in dev.py, added examples. | 24 June 2015, 19:05:27 UTC |
