| 8deb2b7 | Jerome Kelleher | 01 April 2016, 12:41:54 UTC | Updated CHANGELOG for 0.1.9 release. | 01 April 2016, 12:41:54 UTC |
| a06401b | Jerome Kelleher | 01 April 2016, 12:31:59 UTC | Added sphinx_rtd_theme for CI builds. | 01 April 2016, 12:31:59 UTC |
| c8b3fd9 | Jerome Kelleher | 01 April 2016, 12:18:30 UTC | Issues #6. Fix seeding bug in mspms. https://github.com/jeromekelleher/msprime/issues/6 | 01 April 2016, 12:31:33 UTC |
| 005a79c | Jerome Kelleher | 17 February 2016, 11:35:28 UTC | Minor updates to CHANGELOG. | 17 February 2016, 11:35:28 UTC |
| bcff53e | Jerome Kelleher | 17 February 2016, 11:27:15 UTC | Minor tidyups. | 17 February 2016, 11:27:15 UTC |
| 83b4871 | Jerome Kelleher | 17 February 2016, 11:21:02 UTC | Added the initial changelog. | 17 February 2016, 11:21:02 UTC |
| 98702fd | Jerome Kelleher | 17 February 2016, 10:30:13 UTC | Minor type tweaks for clang. | 17 February 2016, 10:30:13 UTC |
| 25a822d | Jerome Kelleher | 17 February 2016, 10:24:45 UTC | Fixed verification bug. | 17 February 2016, 10:24:45 UTC |
| 3aba61e | Jerome Kelleher | 17 February 2016, 10:20:39 UTC | Updated mspms documentation. | 17 February 2016, 10:20:39 UTC |
| 6272bd8 | Jerome Kelleher | 17 February 2016, 10:02:04 UTC | Added some basic test cases for pop models. | 17 February 2016, 10:02:04 UTC |
| e8f7b8e | Jerome Kelleher | 17 February 2016, 09:47:32 UTC | Minimal changes to support PopulationModels. | 17 February 2016, 09:47:32 UTC |
| 4820fa1 | Jerome Kelleher | 16 February 2016, 15:29:56 UTC | Added some examples from Konrad for verification. | 16 February 2016, 15:29:56 UTC |
| e367df7 | Jerome Kelleher | 16 February 2016, 13:32:59 UTC | Partial implementation of ms's -es option. | 16 February 2016, 13:32:59 UTC |
| 87253b6 | Jerome Kelleher | 16 February 2016, 10:36:34 UTC | Added code to detect split events in ms. | 16 February 2016, 11:42:46 UTC |
| 5b9dbe6 | Jerome Kelleher | 12 February 2016, 16:25:23 UTC | Added high-level support for population split. | 12 February 2016, 16:25:23 UTC |
| 3efa498 | Jerome Kelleher | 12 February 2016, 14:17:20 UTC | Added low-level Python support for mass migration. | 12 February 2016, 14:17:20 UTC |
| 433d338 | Jerome Kelleher | 12 February 2016, 12:24:16 UTC | Added C-level support for mass_migration. | 12 February 2016, 12:24:16 UTC |
| 71316b7 | Jerome Kelleher | 10 February 2016, 14:45:36 UTC | Added back PopulationModel classes to fix docs. | 10 February 2016, 14:45:36 UTC |
| 683e3d6 | Jerome Kelleher | 10 February 2016, 14:26:02 UTC | Added support for ms's -ema option. | 10 February 2016, 14:26:02 UTC |
| 33b01eb | Jerome Kelleher | 10 February 2016, 12:04:17 UTC | Implemented the -em ms option. | 10 February 2016, 12:04:17 UTC |
| 65a295e | Jerome Kelleher | 10 February 2016, 11:28:27 UTC | Added support for the -eM ms option. | 10 February 2016, 11:28:27 UTC |
| 012c7e6 | Jerome Kelleher | 10 February 2016, 10:28:20 UTC | Fixed logic error in demographic events. | 10 February 2016, 10:28:20 UTC |
| b15765d | Jerome Kelleher | 10 February 2016, 09:40:22 UTC | Added the ms -en population size option. | 10 February 2016, 09:40:22 UTC |
| 5b65dcf | Jerome Kelleher | 09 February 2016, 15:05:53 UTC | Added population_growth_rate_change argument. | 09 February 2016, 15:05:53 UTC |
| c08aac4 | Jerome Kelleher | 09 February 2016, 15:03:40 UTC | Fixed logic bug in simulation termination. | 09 February 2016, 15:03:40 UTC |
| a181f46 | Jerome Kelleher | 09 February 2016, 13:46:37 UTC | Added the msprime -n option. | 09 February 2016, 13:46:37 UTC |
| 30bcd26 | Jerome Kelleher | 09 February 2016, 13:21:14 UTC | Added the ms -g option. | 09 February 2016, 13:21:14 UTC |
| 1452cdf | Jerome Kelleher | 09 February 2016, 12:03:50 UTC | Updated verification to add random command lines. | 09 February 2016, 12:03:50 UTC |
| 6d43408 | Jerome Kelleher | 09 February 2016, 11:14:38 UTC | Fixed npops=1 issue. | 09 February 2016, 11:14:38 UTC |
| 846be05 | Jerome Kelleher | 09 February 2016, 10:27:20 UTC | Added checks for recombination CLI. | 09 February 2016, 10:44:35 UTC |
| 2896888 | Jerome Kelleher | 08 February 2016, 13:39:18 UTC | Change mspms args from 'event' to 'change'. | 08 February 2016, 13:39:18 UTC |
| 58fbc29 | Jerome Kelleher | 05 February 2016, 16:42:51 UTC | Fixed simultaneous event support in mspms. | 05 February 2016, 16:42:51 UTC |
| 486973e | Jerome Kelleher | 05 February 2016, 15:10:06 UTC | Tracked down some bugs in verification. | 05 February 2016, 15:10:06 UTC |
| e7d36db | Jerome Kelleher | 05 February 2016, 14:09:45 UTC | Replaced functionality of verification script. | 05 February 2016, 14:09:45 UTC |
| 80a23fd | Jerome Kelleher | 05 February 2016, 12:32:57 UTC | Set random_seed for stress tester. | 05 February 2016, 12:32:57 UTC |
| 4a1f8cf | Jerome Kelleher | 04 February 2016, 17:00:15 UTC | Changed to Python string comparisons. | 04 February 2016, 17:01:17 UTC |
| bca7f6d | Jerome Kelleher | 04 February 2016, 16:16:06 UTC | Merge branch 'spatial-structure' into develop | 04 February 2016, 16:16:06 UTC |
| 3c21ee4 | Jerome Kelleher | 04 February 2016, 16:15:35 UTC | Minimal updates to high-level API. | 04 February 2016, 16:15:35 UTC |
| e2eed82 | Jerome Kelleher | 04 February 2016, 14:40:40 UTC | Changed the stress tester to run tests directly. | 04 February 2016, 14:40:40 UTC |
| eac12a6 | Jerome Kelleher | 04 February 2016, 14:19:26 UTC | Fixed all low-level tests. | 04 February 2016, 14:19:26 UTC |
| 77c2232 | Jerome Kelleher | 04 February 2016, 10:26:28 UTC | Added configuration json to hdf5 file. | 04 February 2016, 10:26:28 UTC |
| b2194c7 | Jerome Kelleher | 04 February 2016, 10:11:32 UTC | Made single json provenance string. | 04 February 2016, 10:11:32 UTC |
| 8b4fdb1 | Jerome Kelleher | 03 February 2016, 15:19:14 UTC | Added json formatting for low-level objects. | 03 February 2016, 15:19:14 UTC |
| a3f5ba0 | Jerome Kelleher | 03 February 2016, 13:07:08 UTC | Added interface for setting demographic events. | 03 February 2016, 13:07:08 UTC |
| 3ed00fd | Jerome Kelleher | 02 February 2016, 20:54:38 UTC | Partial cleanup of implemenation and tests. | 02 February 2016, 20:54:38 UTC |
| 3ea8714 | Jerome Kelleher | 02 February 2016, 19:31:09 UTC | Updated to use population models. Tests not passing. | 02 February 2016, 19:31:09 UTC |
| c940652 | Jerome Kelleher | 01 February 2016, 16:50:35 UTC | Starting low-level C interface | 01 February 2016, 16:50:35 UTC |
| 5639f66 | Jerome Kelleher | 01 February 2016, 14:06:53 UTC | Added initial C version of sim interface. | 01 February 2016, 14:06:53 UTC |
| ec6e34a | Jerome Kelleher | 29 January 2016, 15:09:53 UTC | Rough update on the interfact for demographic events. | 29 January 2016, 15:09:53 UTC |
| f9fd8f4 | Jerome Kelleher | 28 January 2016, 14:54:04 UTC | Progress on implementing general ms-model in Python. | 28 January 2016, 14:54:04 UTC |
| 163de3a | Jerome Kelleher | 27 January 2016, 16:05:27 UTC | Added migration to stress tests. | 27 January 2016, 16:05:27 UTC |
| 6b01912 | Jerome Kelleher | 27 January 2016, 15:48:38 UTC | Added the -ma option to mspms. | 27 January 2016, 15:48:38 UTC |
| eaf7239 | Jerome Kelleher | 27 January 2016, 15:07:04 UTC | Added plots for per-deme migration events. | 27 January 2016, 15:07:04 UTC |
| 873de0b | Jerome Kelleher | 27 January 2016, 14:28:49 UTC | Added detailed migration stats to ms. | 27 January 2016, 14:31:21 UTC |
| b547785 | Jerome Kelleher | 27 January 2016, 14:12:15 UTC | Fixed order of entries in migration matrix. | 27 January 2016, 14:12:15 UTC |
| 6c90663 | Jerome Kelleher | 27 January 2016, 12:14:29 UTC | Added tests for spatial counters. | 27 January 2016, 12:14:29 UTC |
| 9d8e6b7 | Jerome Kelleher | 26 January 2016, 17:00:05 UTC | Added interface to get all migration counts. | 26 January 2016, 17:00:05 UTC |
| 5c40956 | Jerome Kelleher | 25 January 2016, 13:41:39 UTC | Added counter for migration events. | 25 January 2016, 13:43:53 UTC |
| 0f28d0a | Jerome Kelleher | 25 January 2016, 13:26:26 UTC | Added counts for migration events. | 25 January 2016, 13:31:02 UTC |
| ec0ba44 | Jerome Kelleher | 22 January 2016, 14:48:47 UTC | Added CLI to update migration matrix. | 22 January 2016, 14:48:47 UTC |
| 4611cce | Jerome Kelleher | 22 January 2016, 12:06:03 UTC | Added checks for infinite waiting time. | 22 January 2016, 12:06:03 UTC |
| b3ea043 | Jerome Kelleher | 21 January 2016, 17:47:30 UTC | Initial verification code for migrations. | 21 January 2016, 17:47:30 UTC |
| e33ebed | Jerome Kelleher | 21 January 2016, 17:26:22 UTC | Working basic implementation of migration. | 21 January 2016, 17:26:22 UTC |
| 2702b76 | Jerome Kelleher | 21 January 2016, 16:50:53 UTC | Working C outline for migration. | 21 January 2016, 16:50:53 UTC |
| 589d161 | Jerome Kelleher | 21 January 2016, 14:52:00 UTC | Added C infrastructure for populations. | 21 January 2016, 15:55:32 UTC |
| 61f062a | Jerome Kelleher | 21 January 2016, 13:45:43 UTC | Changed segment->index to segment->id. | 21 January 2016, 13:45:43 UTC |
| 72f3ecc | Jerome Kelleher | 21 January 2016, 13:28:50 UTC | Basic C interface for pop structure. | 21 January 2016, 13:45:09 UTC |
| 277a6e7 | Jerome Kelleher | 21 January 2016, 12:20:35 UTC | Low-level python interface for pop structure. | 21 January 2016, 12:20:35 UTC |
| 3137a13 | Jerome Kelleher | 21 January 2016, 09:57:12 UTC | Fixed signed-unsigned comparison. | 21 January 2016, 09:57:12 UTC |
| 3dcb3f6 | Jerome Kelleher | 20 January 2016, 16:05:40 UTC | Initial code for ms pop structure interface. | 20 January 2016, 16:05:40 UTC |
| 59674d4 | Jerome Kelleher | 19 January 2016, 17:03:02 UTC | Initial migration among demes. | 19 January 2016, 17:03:02 UTC |
| 6b022f9 | Jerome Kelleher | 19 January 2016, 14:46:34 UTC | Added algorithms python file for development. | 19 January 2016, 14:46:34 UTC |
| 5efb389 | Jerome Kelleher | 18 January 2016, 16:47:07 UTC | Implemented pairwise diversity calculation. | 18 January 2016, 16:47:07 UTC |
| 795b335 | Jerome Kelleher | 14 January 2016, 10:08:59 UTC | Changed default for max_memory to unlimited. | 14 January 2016, 10:08:59 UTC |
| 8ac0de7 | Jerome Kelleher | 13 January 2016, 15:32:06 UTC | Slightly better error message on out-of-memory. | 13 January 2016, 15:32:06 UTC |
| 55ead6b | Jerome Kelleher | 08 January 2016, 15:56:26 UTC | Switch to Travis container infrastructure + cache. | 08 January 2016, 16:20:33 UTC |
| 19ae13f | Jerome Kelleher | 08 January 2016, 15:47:24 UTC | Updated travis config to test dist tarball. | 08 January 2016, 15:47:24 UTC |
| 54d1480 | Jerome Kelleher | 08 January 2016, 15:41:57 UTC | Added support for setuptools_scm. | 08 January 2016, 15:41:57 UTC |
| f985483 | Jerome Kelleher | 11 December 2015, 18:08:41 UTC | Cleaned up ms arguments for pop models. | 11 December 2015, 18:08:41 UTC |
| 285d320 | Jerome Kelleher | 11 December 2015, 18:02:34 UTC | Added tweak to avoid defragments early in simulation. | 11 December 2015, 18:02:34 UTC |
| d067a56 | Jerome Kelleher | 11 December 2015, 15:02:52 UTC | Tweaked test case to deal with zeros. | 11 December 2015, 15:02:52 UTC |
| 7b4934d | Jerome Kelleher | 11 December 2015, 14:49:43 UTC | Added get_ms_command_line to simulator class. | 11 December 2015, 14:49:43 UTC |
| 86b2600 | Jerome Kelleher | 02 December 2015, 10:42:11 UTC | Fixed coverity issues. | 02 December 2015, 10:42:11 UTC |
| ed2b966 | Jerome Kelleher | 01 December 2015, 16:49:39 UTC | Updated version to 0.1.7.dev1. | 01 December 2015, 16:49:39 UTC |
| 5976e3c | Jerome Kelleher | 01 December 2015, 16:29:14 UTC | Bumped to version 0.1.6 | 01 December 2015, 16:29:14 UTC |
| 3b7628b | Jerome Kelleher | 01 December 2015, 16:13:12 UTC | Bumped version to 0.1.6a3 | 01 December 2015, 16:13:12 UTC |
| cb63ee9 | Jerome Kelleher | 01 December 2015, 15:56:57 UTC | Added low-level module version string. | 01 December 2015, 15:56:57 UTC |
| d8efcd4 | Jerome Kelleher | 01 December 2015, 15:49:15 UTC | Fixed bug in mspms positions output. | 01 December 2015, 15:49:15 UTC |
| a9da3dc | Jerome Kelleher | 01 December 2015, 14:13:23 UTC | Bumped version to 0.1.6a2. Previous version had incorrect version string. | 01 December 2015, 14:13:23 UTC |
| 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 |
