| 71b83cb | Jerome Kelleher | 07 October 2016, 16:16:43 UTC | Release notes for version 0.4.0. | 07 October 2016, 16:25:42 UTC |
| 486f92f | Jerome Kelleher | 07 October 2016, 15:41:00 UTC | Merge pull request #52 from jeromekelleher/polish-docs Polish docs | 07 October 2016, 15:41:00 UTC |
| 45f082b | Jerome Kelleher | 07 October 2016, 15:24:58 UTC | Updated the load_txt() documentation. Closes #44. | 07 October 2016, 15:24:58 UTC |
| 6d94256 | Jerome Kelleher | 07 October 2016, 15:15:39 UTC | Documented the msp upgrade command. | 07 October 2016, 15:15:39 UTC |
| 7e15074 | Jerome Kelleher | 07 October 2016, 15:02:28 UTC | Documented historical samples. Closes #46. | 07 October 2016, 15:02:28 UTC |
| 4fd190c | Jerome Kelleher | 07 October 2016, 14:18:07 UTC | Merge pull request #50 from jeromekelleher/update-variants Update variants | 07 October 2016, 14:18:07 UTC |
| 47b807e | Jerome Kelleher | 07 October 2016, 14:09:25 UTC | Updated the tutorial to include variants examples. Closes #51, #47. | 07 October 2016, 14:09:25 UTC |
| 8528de4 | Jerome Kelleher | 07 October 2016, 13:08:07 UTC | Merge branch 'update-variants' of github.com:jeromekelleher/msprime into update-variants | 07 October 2016, 13:08:07 UTC |
| e9b7c40 | Jerome Kelleher | 07 October 2016, 13:07:06 UTC | Added free() method to low level tree. This allows set_mutations() to be run without running del tree. | 07 October 2016, 13:07:06 UTC |
| 11d9ce7 | Jerome Kelleher | 07 October 2016, 11:39:01 UTC | Document & test mutations() method. | 07 October 2016, 11:39:01 UTC |
| f07ee80 | Jerome Kelleher | 06 October 2016, 16:20:08 UTC | Updated API to allow both bytes and numbers. | 06 October 2016, 16:20:08 UTC |
| b46a3a1 | Jerome Kelleher | 06 October 2016, 14:59:12 UTC | Initial changes for new variants() API. | 06 October 2016, 15:16:52 UTC |
| a0d453e | Jerome Kelleher | 06 October 2016, 12:29:48 UTC | Merge pull request #49 from jeromekelleher/finalise-file-format Finalise file format | 06 October 2016, 12:29:48 UTC |
| 9a45c07 | Jerome Kelleher | 06 October 2016, 12:17:25 UTC | Documented v3 HDF5 file format. Closes #41. | 06 October 2016, 12:17:25 UTC |
| e760b6d | Jerome Kelleher | 06 October 2016, 11:12:23 UTC | Added back vestigial root attributes in HDF5 file. Closes #42. | 06 October 2016, 11:12:23 UTC |
| 7befdcf | Jerome Kelleher | 06 October 2016, 10:50:33 UTC | Merge pull request #38 from jeromekelleher/fix-demography-debugger Fixes error in Demography Debugger. | 06 October 2016, 10:50:33 UTC |
| 3da4d1b | Jerome Kelleher | 31 August 2016, 09:52:35 UTC | Fix for demography debugger error. Closes #37. Adds an almost_equal function to allow us to approximately compare floats. | 06 October 2016, 10:40:51 UTC |
| 7b1a040 | Jerome Kelleher | 06 October 2016, 09:27:20 UTC | Merge pull request #45 from jeromekelleher/ldcalc LD calculation API plus many low-level improvements. | 06 October 2016, 09:27:20 UTC |
| 98a8012 | Jerome Kelleher | 06 October 2016, 09:16:43 UTC | Improved the threads example in docs. | 06 October 2016, 09:16:43 UTC |
| 1cb73f9 | Jerome Kelleher | 06 October 2016, 08:40:42 UTC | Improved test coverage. | 06 October 2016, 08:40:42 UTC |
| 0c35b9f | Jerome Kelleher | 05 October 2016, 16:34:52 UTC | Finished the LD calculator exmaple. | 06 October 2016, 07:56:01 UTC |
| 62b3a74 | Jerome Kelleher | 05 October 2016, 14:39:39 UTC | Documented the LdCalculator class. | 05 October 2016, 14:39:39 UTC |
| ed992a8 | Jerome Kelleher | 05 October 2016, 13:15:57 UTC | Added threading tests to verify behaviour under stress. | 05 October 2016, 13:15:57 UTC |
| 34190e9 | Jerome Kelleher | 05 October 2016, 12:24:34 UTC | Finished up threads example and started docs update. | 05 October 2016, 12:24:34 UTC |
| bfde205 | Jerome Kelleher | 05 October 2016, 10:53:47 UTC | Partial update of LD example with pthread safety. | 05 October 2016, 10:53:47 UTC |
| 50aca6d | Jerome Kelleher | 04 October 2016, 16:46:21 UTC | Changed name to get_r2_array, and updated examples. | 04 October 2016, 16:46:21 UTC |
| 23d88b9 | Jerome Kelleher | 04 October 2016, 13:32:56 UTC | Initial pass at high-level LD API. | 04 October 2016, 13:32:56 UTC |
| 84f6197 | Jerome Kelleher | 04 October 2016, 12:03:49 UTC | Added direction argument to get_r2. Also added low-level Python tests. | 04 October 2016, 12:03:49 UTC |
| 6448eb1 | Jerome Kelleher | 23 September 2016, 14:56:29 UTC | Experimental Python interface for LD. | 23 September 2016, 14:56:29 UTC |
| 852ca15 | Jerome Kelleher | 23 September 2016, 09:24:13 UTC | Changed the API for LD and added tests. Also fixed a bug in the reverse iterator for leaf sets. | 23 September 2016, 09:24:13 UTC |
| 20caca0 | Jerome Kelleher | 22 September 2016, 13:51:50 UTC | Fixed up the main.c developer interface. | 22 September 2016, 13:51:50 UTC |
| dc8b8cc | Jerome Kelleher | 22 September 2016, 11:50:01 UTC | Implemented bidirectional iterator and improved tests. | 22 September 2016, 11:50:01 UTC |
| d5085f1 | Jerome Kelleher | 21 September 2016, 14:08:03 UTC | Fixed memory leak in get_mutations(). Also added better memory leak tracking in stress_lowlevel.py. | 21 September 2016, 14:08:03 UTC |
| b110b6c | Jerome Kelleher | 20 September 2016, 20:17:50 UTC | Removed the sparse_tree_iterator C object. | 20 September 2016, 20:18:46 UTC |
| 985f71c | Jerome Kelleher | 20 September 2016, 14:13:53 UTC | Tidied mutations API and added index attribute. | 20 September 2016, 14:13:53 UTC |
| 1499c96 | Jerome Kelleher | 20 September 2016, 11:37:14 UTC | Added reference counting for trees. This guards against the possibility of having trees in memory that refer to mutations that no longer exist in the tree sequence. | 20 September 2016, 11:37:14 UTC |
| 0a76fc3 | Jerome Kelleher | 20 September 2016, 09:56:46 UTC | Fixed up test cases for bad mutations. | 20 September 2016, 09:56:46 UTC |
| c0e9199 | Jerome Kelleher | 05 September 2016, 16:52:33 UTC | Added high-level support for fine grained access to tree features. | 05 September 2016, 16:52:33 UTC |
| e1032f9 | Jerome Kelleher | 05 September 2016, 15:25:26 UTC | Updated low-level Tree interface to use flags. | 05 September 2016, 15:25:26 UTC |
| a23dc07 | Jerome Kelleher | 31 August 2016, 12:46:24 UTC | Fixed bugs in ld calculation. | 31 August 2016, 12:46:24 UTC |
| c345db5 | Jerome Kelleher | 30 August 2016, 16:27:12 UTC | Prototype LD calculator. | 30 August 2016, 16:27:12 UTC |
| 576d0cc | Jerome Kelleher | 29 August 2016, 16:01:06 UTC | Initial stab at LD using rewind. | 29 August 2016, 16:01:06 UTC |
| f8cc5bb | Jerome Kelleher | 29 August 2016, 15:04:17 UTC | Moved mutation storage to tree sequence. | 29 August 2016, 15:04:17 UTC |
| c5dd1b8 | Jerome Kelleher | 29 August 2016, 14:03:33 UTC | Partial implementation of fwd-backward tree iter. | 29 August 2016, 14:03:33 UTC |
| 6a76ec2 | Jerome Kelleher | 26 August 2016, 15:05:37 UTC | Added algorithm with circular tree iteration. | 26 August 2016, 15:05:37 UTC |
| ba5633d | Jerome Kelleher | 25 August 2016, 15:50:55 UTC | Fixed up some errors & improved single tree case. | 25 August 2016, 15:50:55 UTC |
| 8d03fe1 | Jerome Kelleher | 25 August 2016, 12:14:07 UTC | Made hacky initial interface for writing LD table. | 25 August 2016, 12:14:07 UTC |
| 001e19b | Jerome Kelleher | 25 August 2016, 11:14:04 UTC | Added MSP_COUNT_LEAVES support to tree copy. Also changed trees to compare using integer breakpoint indexes to avoid equality comparisons using doubles. | 25 August 2016, 11:14:04 UTC |
| d6890b4 | Jerome Kelleher | 24 August 2016, 14:52:49 UTC | Added O(1) get_num_trees() implementation. | 24 August 2016, 17:55:56 UTC |
| ab87700 | Jerome Kelleher | 24 August 2016, 14:39:06 UTC | Added copy interface for trees and MSP_LEAF_LISTS. | 24 August 2016, 14:39:06 UTC |
| e553eb8 | Jerome Kelleher | 24 August 2016, 08:44:44 UTC | Initial interface changes for sparse_tree_iter copy. | 24 August 2016, 08:44:44 UTC |
| 8d3fbc1 | Jerome Kelleher | 24 August 2016, 08:30:36 UTC | Merge pull request #34 from jeromekelleher/32bit-fixes 32bit fixes | 24 August 2016, 08:30:36 UTC |
| 927731d | Jerome Kelleher | 22 August 2016, 19:32:59 UTC | Improved test coverage for recomb_map. | 23 August 2016, 19:54:44 UTC |
| 515244a | Jerome Kelleher | 22 August 2016, 18:04:36 UTC | Removed assertions problematic on x87 FPU. On old x86 hardware, assumptions about exact equality for floating point values are problematic. | 22 August 2016, 18:04:36 UTC |
| 67e1c23 | Jerome Kelleher | 17 August 2016, 19:54:57 UTC | Added tests for recomb_map. | 17 August 2016, 19:56:58 UTC |
| a9222c0 | Jerome Kelleher | 16 August 2016, 13:49:29 UTC | Merge pull request #31 from jeromekelleher/nonbinary-records Nonbinary records | 16 August 2016, 13:49:29 UTC |
| 7d79072 | Jerome Kelleher | 16 August 2016, 13:15:11 UTC | Changed sorting key to for unstable qsort on OSX. | 16 August 2016, 13:15:11 UTC |
| 2a523c6 | Jerome Kelleher | 16 August 2016, 12:22:45 UTC | Improved tests to directly provoke OSX issue. | 16 August 2016, 12:24:24 UTC |
| 8bc5931 | Jerome Kelleher | 16 August 2016, 11:09:32 UTC | Fixed performance regression for replication. | 16 August 2016, 11:09:32 UTC |
| 5829d0b | Jerome Kelleher | 16 August 2016, 08:39:53 UTC | Updated errors for file versions & improved tests. Also removed trailing whitespace from .h files. | 16 August 2016, 09:18:11 UTC |
| 7cb6fcc | Jerome Kelleher | 16 August 2016, 08:13:15 UTC | Fixed issue with later version of CUnit. | 16 August 2016, 08:13:15 UTC |
| ced967c | Jerome Kelleher | 15 August 2016, 16:22:24 UTC | Tests to ensure internal node ordering is arbitrary. | 15 August 2016, 16:42:25 UTC |
| 180e77e | Jerome Kelleher | 15 August 2016, 14:42:58 UTC | Fixed memory leak in stress_lowlevel. | 15 August 2016, 14:42:58 UTC |
| 0b34e2e | Jerome Kelleher | 15 August 2016, 14:28:36 UTC | Fixed issues with travis & doxygen. | 15 August 2016, 14:28:36 UTC |
| ae6c227 | Jerome Kelleher | 15 August 2016, 13:35:09 UTC | Fixed file handle leak in HDF5 code. | 15 August 2016, 13:35:09 UTC |
| 896f264 | Jerome Kelleher | 15 August 2016, 13:00:19 UTC | Fixed minor docs issue and Py3 error. | 15 August 2016, 13:34:01 UTC |
| bedc9e5 | Jerome Kelleher | 15 August 2016, 12:28:18 UTC | Merge remote-tracking branch 'origin/nonbinary-records' into nonbinary-records | 15 August 2016, 12:28:18 UTC |
| 868e28e | Jerome Kelleher | 15 August 2016, 12:27:07 UTC | Removed h5close and reorganised HDF5 testing code. | 15 August 2016, 12:27:07 UTC |
| d165a04 | Jerome Kelleher | 15 August 2016, 08:41:22 UTC | Changed converter to use numpy. | 15 August 2016, 08:41:22 UTC |
| 428a35f | Jerome Kelleher | 12 August 2016, 16:44:48 UTC | Initial slow version of upgrade tool. | 12 August 2016, 16:44:48 UTC |
| 0109f2b | Jerome Kelleher | 12 August 2016, 11:29:42 UTC | Merge pull request #33 from shajoezhu/nonbinary-records include doxygen configuration file | 12 August 2016, 11:29:42 UTC |
| ea9e6bf | Jerome Kelleher | 03 August 2016, 20:08:08 UTC | Initial work on v2 format converter. Conflicts: dev.py msprime/__init__.py | 12 August 2016, 11:26:56 UTC |
| e53bf80 | Joe Zhu | 12 August 2016, 11:03:11 UTC | change project name update travis configure file | 12 August 2016, 11:19:08 UTC |
| 6845728 | Joe Zhu | 11 August 2016, 18:52:24 UTC | include doxygen configuration file | 12 August 2016, 11:00:54 UTC |
| 92ad940 | Jerome Kelleher | 12 August 2016, 09:33:55 UTC | Removed the root attributes sample_size and sequence_length. | 12 August 2016, 09:33:55 UTC |
| f01d369 | Jerome Kelleher | 11 August 2016, 17:13:42 UTC | Saved indexes in HDF5 file. | 11 August 2016, 17:13:42 UTC |
| 1469735 | Jerome Kelleher | 11 August 2016, 09:44:47 UTC | Removed old provenance attributes. | 11 August 2016, 09:44:47 UTC |
| 2bfff78 | Jerome Kelleher | 11 August 2016, 09:06:50 UTC | Initial pass at Python provenance strings. | 11 August 2016, 09:06:50 UTC |
| bc917e4 | Jerome Kelleher | 11 August 2016, 07:52:45 UTC | Initial interface for provenance strings. | 11 August 2016, 07:52:45 UTC |
| e69c3e2 | Jerome Kelleher | 10 August 2016, 16:19:43 UTC | Changed tree sequence to be more hierarchical. | 10 August 2016, 16:19:43 UTC |
| ab0325d | Jerome Kelleher | 10 August 2016, 14:32:19 UTC | Created nodes HDF5 group. | 10 August 2016, 14:32:19 UTC |
| 0d476b9 | Jerome Kelleher | 10 August 2016, 11:45:27 UTC | Fixed test coverage hole in CPython interface. | 10 August 2016, 11:45:27 UTC |
| e3f1af0 | Jerome Kelleher | 10 August 2016, 11:06:51 UTC | Added tests for Newick trees. | 10 August 2016, 11:06:51 UTC |
| b2ea0b0 | Jerome Kelleher | 10 August 2016, 08:18:47 UTC | Python implementation of non-binary trees. | 10 August 2016, 10:09:28 UTC |
| 6024777 | Jerome Kelleher | 09 August 2016, 12:34:52 UTC | Fixed subtle merge algorithm bug. | 09 August 2016, 12:34:52 UTC |
| 1262a32 | Jerome Kelleher | 08 August 2016, 16:24:23 UTC | Tests for demographic events. | 09 August 2016, 08:48:28 UTC |
| a2fbf19 | Jerome Kelleher | 08 August 2016, 15:17:58 UTC | Working version of Python leaf-list algorithm. | 08 August 2016, 15:17:58 UTC |
| 47a7cd0 | Jerome Kelleher | 08 August 2016, 09:23:23 UTC | Minor fixes for 32bit Solaris. | 08 August 2016, 09:23:23 UTC |
| 956b2e0 | Jerome Kelleher | 04 August 2016, 19:48:18 UTC | Bump up test coverage on simulator. | 04 August 2016, 19:48:18 UTC |
| 543a7a8 | Jerome Kelleher | 03 August 2016, 19:29:39 UTC | Exploratory work on leaf list algorithm. | 04 August 2016, 18:52:06 UTC |
| 6d6be53 | Jerome Kelleher | 03 August 2016, 13:36:01 UTC | Updated tests to exercise inner loops. | 04 August 2016, 08:22:24 UTC |
| 7ab6850 | Jerome Kelleher | 03 August 2016, 12:50:50 UTC | Updated HDF5 to support nonbinary records. | 03 August 2016, 12:50:50 UTC |
| 5d0d4c9 | Jerome Kelleher | 03 August 2016, 10:41:22 UTC | Verified bottleneck code and improved test examples. | 03 August 2016, 10:43:09 UTC |
| ac4b6e0 | Jerome Kelleher | 02 August 2016, 17:17:34 UTC | First pass at low-level bottlenecks. | 03 August 2016, 10:43:09 UTC |
| d5d0075 | Jerome Kelleher | 02 August 2016, 12:41:34 UTC | Initial draft of the bottleneck algorithm. | 03 August 2016, 10:43:09 UTC |
| 77a40d5 | Jerome Kelleher | 29 July 2016, 08:11:47 UTC | Added tests for leaf counts. | 03 August 2016, 10:43:09 UTC |
| 1fcfb2e | Jerome Kelleher | 28 July 2016, 16:07:06 UTC | Working iterators for non-binary trees. | 03 August 2016, 10:43:09 UTC |
| 7603906 | Jerome Kelleher | 28 July 2016, 16:06:36 UTC | Very rough initial pass on bottleneck algorithm. | 03 August 2016, 10:43:09 UTC |
| 1aa2952 | Jerome Kelleher | 27 July 2016, 19:43:20 UTC | Fixed reference counting bug in SparseTree. | 03 August 2016, 10:43:09 UTC |
| 255d502 | Jerome Kelleher | 27 July 2016, 14:35:42 UTC | First steps on supporting non-binary trees. | 03 August 2016, 10:43:08 UTC |
