| 135d94f | Jerome Kelleher | 23 June 2015, 12:50:46 UTC | Updated docs + version bump. | 23 June 2015, 12:50:46 UTC |
| 7883015 | Jerome Kelleher | 23 June 2015, 12:34:47 UTC | Updated CLI documentation and improved tests. | 23 June 2015, 12:34:47 UTC |
| a2f228d | Jerome Kelleher | 22 June 2015, 16:29:51 UTC | Finalised binary mutation generation. | 22 June 2015, 17:02:36 UTC |
| 7725cf4 | Jerome Kelleher | 22 June 2015, 15:04:21 UTC | Removed all online haplottype gen code. | 22 June 2015, 15:04:21 UTC |
| 7609bf2 | Jerome Kelleher | 22 June 2015, 11:25:44 UTC | Removed the online option from high-level API. | 22 June 2015, 14:27:21 UTC |
| f672dc4 | Jerome Kelleher | 19 June 2015, 12:51:04 UTC | Added uname information to provenance. | 19 June 2015, 12:51:04 UTC |
| 2f3e4cd | Jerome Kelleher | 17 June 2015, 09:00:49 UTC | Fixed PEP8 issue. | 17 June 2015, 09:00:49 UTC |
| 7cebefa | Jerome Kelleher | 16 June 2015, 21:16:40 UTC | Added API to access provenance JSON. | 16 June 2015, 21:16:40 UTC |
| d4ab178 | Jerome Kelleher | 16 June 2015, 08:42:47 UTC | Fixed Py3 bugs + low-level string errors. | 16 June 2015, 08:42:47 UTC |
| e741b7d | Jerome Kelleher | 15 June 2015, 23:00:30 UTC | Fixed JSON bugs and added tests. | 15 June 2015, 23:00:30 UTC |
| 42e839f | Jerome Kelleher | 15 June 2015, 22:30:42 UTC | Added the JSON encoding of pop models. | 15 June 2015, 22:30:42 UTC |
| 8dec8cd | Jerome Kelleher | 15 June 2015, 21:19:45 UTC | Finished refactor, and added stress script. | 15 June 2015, 21:21:52 UTC |
| 3d802d5 | Jerome Kelleher | 11 June 2015, 18:30:06 UTC | updated refactoring for Python interface. | 11 June 2015, 18:30:06 UTC |
| 20ea521 | Jerome Kelleher | 11 June 2015, 17:34:43 UTC | refactored poor simulator API. | 11 June 2015, 17:34:43 UTC |
| ec992b8 | Jerome Kelleher | 10 June 2015, 19:42:01 UTC | Added random seeds to provenance. | 10 June 2015, 19:42:01 UTC |
| 82f44d6 | Jerome Kelleher | 10 June 2015, 19:16:10 UTC | Basic working version of provenance information. | 10 June 2015, 19:16:10 UTC |
| f329a84 | Jerome Kelleher | 03 June 2015, 12:34:18 UTC | Fixed some portability issues. | 03 June 2015, 12:34:18 UTC |
| 51778d6 | Jerome Kelleher | 03 June 2015, 11:18:22 UTC | Made index creation tolerant of unstable qsort. | 03 June 2015, 11:18:22 UTC |
| c0499dd | Jerome Kelleher | 03 June 2015, 10:57:55 UTC | Fixed clang issues and updated Makefile. | 03 June 2015, 10:57:55 UTC |
| 5b984da | Jerome Kelleher | 03 June 2015, 10:39:47 UTC | fixed version parsing bug. | 03 June 2015, 10:39:47 UTC |
| 51c1f01 | Jerome Kelleher | 03 June 2015, 10:36:34 UTC | Changed rst file back to soft link. | 03 June 2015, 10:36:34 UTC |
| c43e3c3 | Jerome Kelleher | 03 June 2015, 10:35:29 UTC | Added version checks for HDF5. | 03 June 2015, 10:35:29 UTC |
| 4a579ba | Jerome Kelleher | 03 June 2015, 09:26:37 UTC | Fixed missing pkg-config case. | 03 June 2015, 09:26:37 UTC |
| 9f2a2ff | Jerome Kelleher | 03 June 2015, 09:02:30 UTC | Replaced removed rst file. | 03 June 2015, 09:02:30 UTC |
| 2480884 | Jerome Kelleher | 02 June 2015, 16:49:51 UTC | Fixed minor issues raised by coverity. | 02 June 2015, 16:49:51 UTC |
| a4305af | Jerome Kelleher | 02 June 2015, 08:04:10 UTC | Updated travis to conditionally run doc check. | 02 June 2015, 08:04:10 UTC |
| f8a4d55 | Jerome Kelleher | 02 June 2015, 07:44:25 UTC | Fixed error made by 'fixing' coverity issue. | 02 June 2015, 07:44:25 UTC |
| e6a5ad9 | Jerome Kelleher | 02 June 2015, 07:23:29 UTC | Updated test config to just search tests dir. | 02 June 2015, 07:23:29 UTC |
| 258d5f7 | Jerome Kelleher | 01 June 2015, 17:01:10 UTC | Removed some imports from dev.py. | 01 June 2015, 17:01:10 UTC |
| 4a43d7d | Jerome Kelleher | 01 June 2015, 16:59:54 UTC | Fixed PEP8 issues with newer flake8. | 01 June 2015, 16:59:54 UTC |
| a9f3ff1 | Jerome Kelleher | 01 June 2015, 16:56:40 UTC | Addressed minor issue pointed out by coverity. | 01 June 2015, 16:56:40 UTC |
| f509e5d | Jerome Kelleher | 01 June 2015, 16:16:08 UTC | Updated copyright notices. | 01 June 2015, 16:16:08 UTC |
| dd31cfc | Jerome Kelleher | 01 June 2015, 16:02:36 UTC | Various tidy-ups. 1. Flake8/pep8 cleanup 2. Updated travis config to run coverage and flake8. 3. Changed copyright year. | 01 June 2015, 16:04:57 UTC |
| 9f93a60 | Jerome Kelleher | 01 June 2015, 15:29:43 UTC | initial working outline of docs. | 01 June 2015, 15:29:43 UTC |
| a72f3a2 | Jerome Kelleher | 01 June 2015, 15:14:35 UTC | Initial addition of Sphinx docs. | 01 June 2015, 15:14:35 UTC |
| a632f92 | Jerome Kelleher | 26 May 2015, 17:06:16 UTC | Refined the comments for the example a little. | 26 May 2015, 17:06:16 UTC |
| 5e014d9 | Jerome Kelleher | 26 May 2015, 16:46:54 UTC | Bumped version number for pypi upload. | 26 May 2015, 16:46:54 UTC |
| 64e96f0 | Jerome Kelleher | 26 May 2015, 16:45:44 UTC | Updated example with smaller memory req. | 26 May 2015, 16:45:44 UTC |
| af59f58 | Jerome Kelleher | 26 May 2015, 16:13:18 UTC | Fixed malloc bug. | 26 May 2015, 16:13:18 UTC |
| 1f15499 | Jerome Kelleher | 26 May 2015, 16:00:51 UTC | Added example, and changed segment alloc formula. | 26 May 2015, 16:00:51 UTC |
| f52adc6 | Jerome Kelleher | 26 May 2015, 15:11:12 UTC | Implemented simpler hapgen algorithm. | 26 May 2015, 15:11:12 UTC |
| f4307a3 | Jerome Kelleher | 26 May 2015, 14:22:00 UTC | Added tweak to improve hapgen time. | 26 May 2015, 14:22:00 UTC |
| e4a1c47 | Jerome Kelleher | 26 May 2015, 13:45:02 UTC | Version bump for pypi. | 26 May 2015, 13:45:02 UTC |
| 5634df9 | Jerome Kelleher | 26 May 2015, 13:44:11 UTC | Fixed Py3 encoding issue. | 26 May 2015, 13:44:11 UTC |
| c5b3ef5 | Jerome Kelleher | 26 May 2015, 13:38:06 UTC | Version bump to test on pypi. | 26 May 2015, 13:38:06 UTC |
| e68407a | Jerome Kelleher | 26 May 2015, 13:37:10 UTC | Added custom pkg-config processing to setup.py. | 26 May 2015, 13:37:10 UTC |
| d4e32e1 | Jerome Kelleher | 26 May 2015, 10:25:56 UTC | Fixed mutation rate CLI corner case. | 26 May 2015, 10:25:56 UTC |
| 1ead257 | Jerome Kelleher | 26 May 2015, 09:10:33 UTC | Added framework for provenence information in file. | 26 May 2015, 09:10:33 UTC |
| 69799e7 | Jerome Kelleher | 26 May 2015, 06:47:29 UTC | Rethought high-level API. | 26 May 2015, 06:47:29 UTC |
| e63b9ce | Jerome Kelleher | 24 May 2015, 08:23:09 UTC | Better all-haplotypes algorithm. | 24 May 2015, 08:23:09 UTC |
| 19cc6b0 | Jerome Kelleher | 23 May 2015, 16:45:03 UTC | Added low-memory interface to high level code. | 23 May 2015, 16:45:03 UTC |
| a5e6b65 | Jerome Kelleher | 23 May 2015, 16:31:39 UTC | Added simple all-haplotypes implementation. | 23 May 2015, 16:31:39 UTC |
| 2f4ff6e | Jerome Kelleher | 23 May 2015, 14:58:04 UTC | Added new SparseTree object, changed API. | 23 May 2015, 14:58:04 UTC |
| 79a7ca5 | Jerome Kelleher | 22 May 2015, 17:02:14 UTC | Changed to scalar for root attributes. | 22 May 2015, 17:02:14 UTC |
| 947ec34 | Jerome Kelleher | 22 May 2015, 15:17:47 UTC | Removed dendropy from requirements because of py3. | 22 May 2015, 15:17:47 UTC |
| 33d1242 | Jerome Kelleher | 22 May 2015, 15:16:39 UTC | Minor tweaks to high-level interface for trees. | 22 May 2015, 15:16:39 UTC |
| b3c8fd9 | Jerome Kelleher | 22 May 2015, 14:29:13 UTC | Removed breakpoints from Python interface. | 22 May 2015, 14:29:13 UTC |
| 49691bd | Jerome Kelleher | 22 May 2015, 14:15:30 UTC | Removed breakpoints, and moved metadata to root. | 22 May 2015, 14:15:30 UTC |
| 962059c | Jerome Kelleher | 22 May 2015, 13:47:38 UTC | Removed ALL_BREAKPOINTS option from diff iter. | 22 May 2015, 13:47:38 UTC |
| 507723b | Jerome Kelleher | 22 May 2015, 13:38:29 UTC | Updated unit tests for mspms interface. | 22 May 2015, 13:38:29 UTC |
| ea568dd | Jerome Kelleher | 21 May 2015, 20:08:10 UTC | Added framework for CLI tests. Also initial high-level all-breaks Newick tree iteration. | 21 May 2015, 20:08:10 UTC |
| 2fbabd9 | Jerome Kelleher | 21 May 2015, 17:02:23 UTC | Added extra tests for mutations. | 21 May 2015, 17:02:23 UTC |
| 0569faf | Jerome Kelleher | 21 May 2015, 13:25:05 UTC | Fixed travis config issue. | 21 May 2015, 13:25:05 UTC |
| 42cc84f | Jerome Kelleher | 21 May 2015, 13:20:55 UTC | Minor mods to dev script. | 21 May 2015, 13:20:55 UTC |
| c679f80 | Jerome Kelleher | 21 May 2015, 13:19:57 UTC | Fixed Python3 site packages issue. | 21 May 2015, 13:19:57 UTC |
| 3b6e233 | Jerome Kelleher | 21 May 2015, 13:12:05 UTC | Updated system site packages on Travis. | 21 May 2015, 13:13:23 UTC |
| 9aa7892 | Jerome Kelleher | 21 May 2015, 13:07:17 UTC | Trying system h5py packages again. | 21 May 2015, 13:07:17 UTC |
| 547a4fc | Jerome Kelleher | 21 May 2015, 13:03:07 UTC | Reenable tests. | 21 May 2015, 13:03:07 UTC |
| bc9d8ab | Jerome Kelleher | 21 May 2015, 12:50:47 UTC | Updated low-level tests for new file format. | 21 May 2015, 12:50:47 UTC |
| 9b8f34e | Jerome Kelleher | 21 May 2015, 12:44:29 UTC | Changed protocol for including mutations. | 21 May 2015, 12:44:29 UTC |
| fa99a74 | Jerome Kelleher | 21 May 2015, 11:45:45 UTC | Fixed travis config error. | 21 May 2015, 11:45:45 UTC |
| f9da82b | Jerome Kelleher | 21 May 2015, 11:43:05 UTC | Added workaround code for empty datasets. | 21 May 2015, 11:43:05 UTC |
| b9aa556 | Jerome Kelleher | 21 May 2015, 11:35:44 UTC | Added workaround for H5close issues. | 21 May 2015, 11:35:44 UTC |
| 8a7b169 | Jerome Kelleher | 21 May 2015, 10:49:38 UTC | Added interfaces for library versions. | 21 May 2015, 10:49:38 UTC |
| 65e05bf | Jerome Kelleher | 21 May 2015, 10:32:00 UTC | Added low-level tests for HDF5 formats. | 21 May 2015, 10:32:00 UTC |
| 1d6d638 | Jerome Kelleher | 21 May 2015, 09:55:21 UTC | Added basic tests for HDF5 format. Also removed the H5close() calls in the low level library as this interferes with h5py. | 21 May 2015, 09:55:21 UTC |
| 293bd25 | Jerome Kelleher | 21 May 2015, 08:59:01 UTC | Disabling mutation generation. | 21 May 2015, 08:59:01 UTC |
| 15cf938 | Jerome Kelleher | 21 May 2015, 08:43:34 UTC | Disabled mutations to track down segfault. | 21 May 2015, 08:43:34 UTC |
| c04963c | Jerome Kelleher | 21 May 2015, 08:29:58 UTC | Disabled failing iterator test. | 21 May 2015, 08:29:58 UTC |
| cdd9c37 | Jerome Kelleher | 21 May 2015, 08:25:12 UTC | Removed pip install section. We should be able to install all travis requirements from Debian packages. | 21 May 2015, 08:25:12 UTC |
| 69a9fe8 | Jerome Kelleher | 21 May 2015, 08:20:16 UTC | Added h5py Ubuntu package to CI build time. | 21 May 2015, 08:20:16 UTC |
| 1fcbc61 | Jerome Kelleher | 21 May 2015, 08:17:05 UTC | Trying to isolate Travis issue (2). | 21 May 2015, 08:17:05 UTC |
| 3a708bf | Jerome Kelleher | 20 May 2015, 16:37:44 UTC | Removed H5close() from error path for messages. | 20 May 2015, 16:37:44 UTC |
| ce274dd | Jerome Kelleher | 20 May 2015, 16:19:09 UTC | Added verbose output for travis. | 20 May 2015, 16:19:09 UTC |
| 2337816 | Jerome Kelleher | 20 May 2015, 16:17:56 UTC | Add cleanup for hdf5, reset tests. | 20 May 2015, 16:17:56 UTC |
| 6bb5fa6 | Jerome Kelleher | 20 May 2015, 14:47:23 UTC | Try to isolate Travis problem. | 20 May 2015, 14:47:23 UTC |
| 5c031af | Jerome Kelleher | 20 May 2015, 12:11:49 UTC | Changed default ordering of the records. | 20 May 2015, 12:11:49 UTC |
| 738b938 | Jerome Kelleher | 20 May 2015, 11:12:57 UTC | Updated mutations interface in high level. Changed mutation rate to be per site, and not scaled by length so that we are consistent with the recombination rate. | 20 May 2015, 11:12:57 UTC |
| 45b9f2d | Jerome Kelleher | 20 May 2015, 10:17:39 UTC | Added low-level code for storing mutations. This has a breaking change in the file format. | 20 May 2015, 10:17:39 UTC |
| 717916e | Jerome Kelleher | 20 May 2015, 08:19:21 UTC | Removed inaccurate README items. | 20 May 2015, 08:19:21 UTC |
| d3b88db | Jerome Kelleher | 20 May 2015, 08:12:58 UTC | Fixed compile error on 64bit. | 20 May 2015, 08:12:58 UTC |
| 6ef36f2 | Jerome Kelleher | 19 May 2015, 20:19:22 UTC | Moved mutations into tree_sequence. | 19 May 2015, 20:19:22 UTC |
| 9199716 | Jerome Kelleher | 19 May 2015, 16:58:19 UTC | Added note about parameters. | 19 May 2015, 16:58:19 UTC |
| 802a04b | Jerome Kelleher | 19 May 2015, 15:52:36 UTC | Fixed bug in haplotype generation. | 19 May 2015, 15:52:36 UTC |
| f5fd228 | Jerome Kelleher | 19 May 2015, 13:40:51 UTC | Added python interface and disable buggy code. | 19 May 2015, 13:40:51 UTC |
| 5c52e8c | Jerome Kelleher | 19 May 2015, 13:04:16 UTC | Initial working version of low-mem C haplotypes. | 19 May 2015, 13:04:16 UTC |
| 64d3993 | Jerome Kelleher | 19 May 2015, 11:44:22 UTC | Working version of sparse tree iterator. | 19 May 2015, 11:44:22 UTC |
| 0555654 | Jerome Kelleher | 18 May 2015, 15:38:29 UTC | Working mutation generation for low-memory method. | 18 May 2015, 15:38:29 UTC |
| ab334ff | Jerome Kelleher | 18 May 2015, 08:56:53 UTC | Working prototype for low-memory haplotypes. | 18 May 2015, 08:56:53 UTC |
| 65669ea | Jerome Kelleher | 15 May 2015, 14:55:53 UTC | Experimental code for new haplotype approach. | 15 May 2015, 14:55:53 UTC |
