| a3da1b0 | Jerome Kelleher | 20 July 2016, 15:58:14 UTC | Changelog for 0.3.2. | 20 July 2016, 15:58:14 UTC |
| 829f25c | Jerome Kelleher | 20 July 2016, 15:44:35 UTC | Minor tidy up of tests and docs for load_txt. | 20 July 2016, 15:44:35 UTC |
| 602e5fa | Jerome Kelleher | 20 July 2016, 15:28:11 UTC | Clarified diploid Ne in docs. Closes https://github.com/jeromekelleher/msprime/issues/19 | 20 July 2016, 15:28:11 UTC |
| 33df68c | Jerome Kelleher | 20 July 2016, 15:17:12 UTC | Adds the load_txt method and documentation. | 20 July 2016, 15:17:12 UTC |
| 8cf7362 | Jerome Kelleher | 20 July 2016, 13:06:20 UTC | Made mutation output API consistent with records. Also changed output of mutations() method to be a namedtuple and clarified the documentation. Closes https://github.com/jeromekelleher/msprime/issues/24 | 20 July 2016, 13:06:20 UTC |
| 3922b12 | Jerome Kelleher | 20 July 2016, 12:14:12 UTC | Tightened up low-level error handling for mutations. | 20 July 2016, 12:14:12 UTC |
| 51b9917 | Jerome Kelleher | 20 July 2016, 10:14:12 UTC | Added basic high-level text record input. | 20 July 2016, 10:14:12 UTC |
| 700428a | Jerome Kelleher | 20 July 2016, 09:05:23 UTC | Adds tests for some missing cases. | 20 July 2016, 09:10:01 UTC |
| af0d68c | Jerome Kelleher | 20 July 2016, 08:21:01 UTC | Fixed Python 3 buffer issue. | 20 July 2016, 08:21:01 UTC |
| 25ce032 | Jerome Kelleher | 20 July 2016, 08:13:17 UTC | Fixed low-level record checking bug. | 20 July 2016, 08:13:17 UTC |
| 5c9a428 | Jerome Kelleher | 19 July 2016, 16:45:49 UTC | Added msp vcf CLI and tidied tests for write_records. | 19 July 2016, 16:45:49 UTC |
| a1335eb | Jerome Kelleher | 19 July 2016, 16:12:03 UTC | Added the write_records method and updated CLI. | 19 July 2016, 16:12:03 UTC |
| 0e3bf6c | Jerome Kelleher | 19 July 2016, 14:01:14 UTC | Finished C-API for reading records & detecting errors. | 19 July 2016, 14:01:14 UTC |
| 3b8a41b | Jerome Kelleher | 19 July 2016, 10:47:06 UTC | Merge branch 'coverage-again' into input-records | 19 July 2016, 10:47:06 UTC |
| 1b5bbf5 | Jerome Kelleher | 19 July 2016, 09:22:58 UTC | Updated dev makefile. | 19 July 2016, 09:37:27 UTC |
| ab5d188 | Jerome Kelleher | 19 July 2016, 08:55:09 UTC | Clarified migration rate directionality. | 19 July 2016, 08:55:09 UTC |
| 537bbb9 | Jerome Kelleher | 18 July 2016, 15:56:24 UTC | Initial low-level interface for records input. | 18 July 2016, 15:56:48 UTC |
| 5402afa | Jerome Kelleher | 18 July 2016, 12:33:32 UTC | Fixed potential issue from coverity. | 18 July 2016, 12:33:32 UTC |
| 7548789 | Jerome Kelleher | 24 March 2016, 16:48:30 UTC | Added initial CUnit tests and support in travis. Getting CodeCov to track the udpated stats is a work in progress. | 18 July 2016, 12:27:12 UTC |
| a3d0bb9 | Jerome Kelleher | 15 July 2016, 14:00:06 UTC | Merge pull request #25 from jeromekelleher/vcf Vcf | 15 July 2016, 14:00:06 UTC |
| de9afad | Jerome Kelleher | 15 July 2016, 13:21:46 UTC | Full VCF support. Also fixed low-level iterator bug in vargen. | 15 July 2016, 13:48:27 UTC |
| 8176519 | Jerome Kelleher | 14 July 2016, 13:08:35 UTC | Refactored VCF output to use usual pattern. | 14 July 2016, 13:08:35 UTC |
| 046e5dc | Jerome Kelleher | 13 July 2016, 16:49:04 UTC | Added C VCF writer. | 13 July 2016, 16:55:12 UTC |
| 0642169 | Jerome Kelleher | 13 July 2016, 14:29:38 UTC | Temporary workaround to improve perf. | 13 July 2016, 14:29:38 UTC |
| 543705d | Jerome Kelleher | 13 July 2016, 09:41:44 UTC | Fixed docs inconsistency. Thanks to Sharon Browning for the bug report. | 13 July 2016, 09:41:44 UTC |
| bc25c08 | Jerome Kelleher | 12 July 2016, 12:40:42 UTC | Experimental VCF support. | 12 July 2016, 13:52:51 UTC |
| fda9408 | Jerome Kelleher | 30 June 2016, 14:17:03 UTC | Tightened up error checking on HDF5 input. | 30 June 2016, 14:44:48 UTC |
| 772052e | Jerome Kelleher | 24 June 2016, 14:07:28 UTC | Added analytical verification for pi. | 24 June 2016, 14:07:28 UTC |
| f7497c4 | Jerome Kelleher | 24 June 2016, 13:36:43 UTC | Fixed C-API bug. | 24 June 2016, 13:36:43 UTC |
| 50d725d | Jerome Kelleher | 24 June 2016, 13:11:41 UTC | Added release notes for 0.3.1. | 24 June 2016, 13:11:41 UTC |
| bb579fd | Jerome Kelleher | 24 June 2016, 12:31:42 UTC | Merge branch 'c-api-stats' into develop | 24 June 2016, 12:31:42 UTC |
| 14692e4 | Jerome Kelleher | 24 June 2016, 12:30:52 UTC | Added C version of get_pairwise diversity. | 24 June 2016, 12:30:52 UTC |
| d767bd2 | Jerome Kelleher | 23 June 2016, 19:35:51 UTC | Merge pull request #23 from jeromekelleher/population-stats Population stats | 23 June 2016, 19:35:51 UTC |
| b63f3ed | Jerome Kelleher | 23 June 2016, 11:55:43 UTC | Added TreeSequence.get_samples(population_id) | 23 June 2016, 12:01:58 UTC |
| 99d2ebc | Jerome Kelleher | 23 June 2016, 11:38:18 UTC | Added TreeSequence.get_population() for samples. | 23 June 2016, 11:38:18 UTC |
| a393742 | Jerome Kelleher | 23 June 2016, 08:37:39 UTC | Added samples argument to get_pairwise_diversity. | 23 June 2016, 08:37:39 UTC |
| 965eeca | Jerome Kelleher | 06 June 2016, 15:05:04 UTC | Fixed memory overrun in recomb map translation. | 06 June 2016, 15:05:04 UTC |
| 7ca9002 | Jerome Kelleher | 02 June 2016, 12:34:49 UTC | Added support for codecov & cleaned up .travis.yml. | 02 June 2016, 14:53:05 UTC |
| 274343a | Jerome Kelleher | 31 May 2016, 11:05:25 UTC | Updated CHANGELOG for 0.3.0 | 31 May 2016, 11:05:25 UTC |
| 59f125e | Jerome Kelleher | 31 May 2016, 10:39:38 UTC | Bumped file format major version 2.0. This is to avoid silent errors where time values are misinterpreted. | 31 May 2016, 10:41:22 UTC |
| c143dd9 | Jerome Kelleher | 31 May 2016, 10:23:13 UTC | Minor doc updates. | 31 May 2016, 10:23:13 UTC |
| 02d85ae | Jerome Kelleher | 31 May 2016, 10:01:58 UTC | Set sphinx version using setuptools_scm. | 31 May 2016, 10:09:19 UTC |
| 9e84f89 | Jerome Kelleher | 31 May 2016, 09:45:48 UTC | Tidied up documentation. | 31 May 2016, 09:45:48 UTC |
| 5320736 | Jerome Kelleher | 27 May 2016, 15:57:33 UTC | Made a pass through documentation for generations. | 27 May 2016, 15:57:33 UTC |
| 5bd47a1 | Jerome Kelleher | 27 May 2016, 14:00:13 UTC | Implemented get_total_branch_length. Closes #12. | 27 May 2016, 14:00:13 UTC |
| df6a7f2 | Jerome Kelleher | 27 May 2016, 13:32:14 UTC | Changed to coalescent units for Newick trees. | 27 May 2016, 13:32:14 UTC |
| 02f4f4c | Jerome Kelleher | 27 May 2016, 11:29:46 UTC | Changed to generation times in all public APIs. | 27 May 2016, 11:29:46 UTC |
| 1df207e | Jerome Kelleher | 27 May 2016, 09:36:59 UTC | Changed to DemographyDebugger and updated. | 27 May 2016, 09:36:59 UTC |
| fcbc950 | Jerome Kelleher | 26 May 2016, 16:36:08 UTC | Implemented reset in the high-level code. | 26 May 2016, 16:45:01 UTC |
| 1232b2c | Jerome Kelleher | 26 May 2016, 16:13:55 UTC | Low-level access to the reset method. | 26 May 2016, 16:13:55 UTC |
| 01b1c6c | Jerome Kelleher | 26 May 2016, 15:20:32 UTC | Removed from dead code. | 26 May 2016, 15:22:12 UTC |
| a1b52f7 | Jerome Kelleher | 26 May 2016, 15:08:44 UTC | Improved hapmap parsing. Closes #13. | 26 May 2016, 15:08:44 UTC |
| 83085d2 | Jerome Kelleher | 26 May 2016, 14:55:43 UTC | Fixed bug in mspms -ej; mixing up src and dest. | 26 May 2016, 14:55:43 UTC |
| a4675b1 | Jerome Kelleher | 26 May 2016, 14:15:51 UTC | Fixed minor test failures. | 26 May 2016, 14:15:51 UTC |
| 2dfe6f2 | Jerome Kelleher | 26 May 2016, 14:06:21 UTC | Bumped file format version & documented. | 26 May 2016, 14:06:21 UTC |
| 0c51901 | Jerome Kelleher | 26 May 2016, 13:51:48 UTC | Partial cleanup of docs for units. | 26 May 2016, 13:51:48 UTC |
| fb38591 | Jerome Kelleher | 26 May 2016, 12:43:31 UTC | Fixed source/dest swap in mspms. | 26 May 2016, 12:43:31 UTC |
| 8c868d5 | Jerome Kelleher | 26 May 2016, 09:32:21 UTC | Fixed bug in initial size for pop configs. | 26 May 2016, 09:32:21 UTC |
| 87b7d2b | Jerome Kelleher | 25 May 2016, 15:13:59 UTC | Added tests for population locations. | 25 May 2016, 15:13:59 UTC |
| 1c2e1a3 | Jerome Kelleher | 25 May 2016, 13:54:28 UTC | Added optional loading for samples/population. | 25 May 2016, 13:54:28 UTC |
| 8ad8830 | Jerome Kelleher | 25 May 2016, 12:45:41 UTC | Working population id code. | 25 May 2016, 12:45:41 UTC |
| f630113 | Jerome Kelleher | 25 May 2016, 11:06:49 UTC | Basic API for accessing population information. | 25 May 2016, 11:06:49 UTC |
| 0b7c071 | Jerome Kelleher | 25 May 2016, 10:35:21 UTC | Added high-level support for population in records. - Added an optional 'population' field to the HDF5 output. - Added the population ID to the end of the low-level tuple. - Changed the high-level output to return a named tuple. - Changed the format of msp records output to include this, and changed the form to prepare for non-binary trees. - Basic checks of the population field in various places. | 25 May 2016, 10:35:21 UTC |
| f8f1bdf | Jerome Kelleher | 24 May 2016, 17:04:52 UTC | C-level changes for adding population_id to CRs. | 24 May 2016, 17:04:52 UTC |
| b2ac8f2 | Jerome Kelleher | 24 May 2016, 15:52:54 UTC | Updated docs with full Gutenkunst OOA example. | 24 May 2016, 15:52:54 UTC |
| 3042d58 | Jerome Kelleher | 24 May 2016, 15:35:43 UTC | Fixed bug in migration rate change. | 24 May 2016, 15:35:43 UTC |
| 56a65c9 | Jerome Kelleher | 24 May 2016, 14:30:46 UTC | All tests passing for rescaled times/rates. | 24 May 2016, 14:30:46 UTC |
| 5e264d8 | Jerome Kelleher | 24 May 2016, 11:15:15 UTC | Low-level changes for population_parameter_change. Simplifies demographic events semantics by removing growth_rate_change and size_change and replacing with population_parameter_change. | 24 May 2016, 11:15:15 UTC |
| 67746d8 | Jerome Kelleher | 23 May 2016, 12:38:36 UTC | Added basic tests for demography debug. | 23 May 2016, 14:09:18 UTC |
| 9cc28c9 | Jerome Kelleher | 23 May 2016, 11:20:54 UTC | Changed confusing behaviour in MassMigrationEvent. | 23 May 2016, 11:20:54 UTC |
| 01c5b68 | Jerome Kelleher | 17 May 2016, 12:56:27 UTC | Basic plumbing to access high level demography debug | 17 May 2016, 12:56:27 UTC |
| 2800785 | Jerome Kelleher | 17 May 2016, 11:51:11 UTC | Low-level changes required for demography debug. | 17 May 2016, 11:51:11 UTC |
| 0695f32 | Jerome Kelleher | 12 May 2016, 09:00:21 UTC | Documentation fix for mass migration event. | 12 May 2016, 09:00:21 UTC |
| 996846c | Jerome Kelleher | 11 May 2016, 10:20:11 UTC | Pinned pyparsing < 2.1 to fix python 3 issue. | 11 May 2016, 10:20:11 UTC |
| 61d52d4 | Jerome Kelleher | 11 May 2016, 09:10:43 UTC | Added position to variants iterator. | 11 May 2016, 09:10:43 UTC |
| b812b36 | Jerome Kelleher | 10 May 2016, 16:39:00 UTC | Added 'variants' command to msp cli. Also improved the 'macs' command to use new API. | 10 May 2016, 16:47:49 UTC |
| 15a9c4e | Jerome Kelleher | 10 May 2016, 15:59:40 UTC | Python APIs for variant strings. | 10 May 2016, 15:59:40 UTC |
| 6d66fd5 | Jerome Kelleher | 10 May 2016, 15:30:23 UTC | C library API for string variants. | 10 May 2016, 15:30:23 UTC |
| d5e1283 | Jerome Kelleher | 09 May 2016, 10:47:47 UTC | Added citation text to docs and CLI help. | 09 May 2016, 10:59:42 UTC |
| 04722d8 | Jerome Kelleher | 09 May 2016, 10:23:45 UTC | Merge branch 'master' into develop Conflicts: CHANGELOG.rst | 09 May 2016, 10:23:45 UTC |
| 6f7cde1 | Jerome Kelleher | 05 May 2016, 15:19:19 UTC | Updated changelog ready for 0.2.0. | 05 May 2016, 15:22:55 UTC |
| dfe4758 | Jerome Kelleher | 05 May 2016, 15:19:19 UTC | Updated changelog ready for 0.2.0. | 05 May 2016, 15:19:19 UTC |
| b5c3a20 | Jerome Kelleher | 05 May 2016, 14:32:00 UTC | Added variable recombination example. | 05 May 2016, 14:32:00 UTC |
| 94f08fb | Jerome Kelleher | 05 May 2016, 14:13:13 UTC | Added a 'breakpoints' method. | 05 May 2016, 14:13:13 UTC |
| 8ea9130 | Jerome Kelleher | 05 May 2016, 13:22:08 UTC | Tidied up docs and added migration example. | 05 May 2016, 13:22:08 UTC |
| 6ad24e8 | Jerome Kelleher | 05 May 2016, 12:25:17 UTC | Fixed remaining migration rate issues. | 05 May 2016, 12:25:17 UTC |
| 366e659 | Jerome Kelleher | 28 April 2016, 14:51:47 UTC | Fixed rate calculation bugs in mspms. | 28 April 2016, 14:51:47 UTC |
| fdd5609 | Jerome Kelleher | 27 April 2016, 15:55:12 UTC | Initial changes for per-generation migration rates.[p | 27 April 2016, 15:55:12 UTC |
| afdc198 | Jerome Kelleher | 27 April 2016, 15:06:09 UTC | Minor fix to verification script. | 27 April 2016, 15:06:09 UTC |
| 83dd78b | Jerome Kelleher | 27 April 2016, 14:51:26 UTC | Updated docs to make consistent with 0 indexing. | 27 April 2016, 14:51:26 UTC |
| 52f119c | Jerome Kelleher | 27 April 2016, 12:57:44 UTC | Changed to NULL_NODE everywhere. | 27 April 2016, 12:57:44 UTC |
| 87f9f22 | Jerome Kelleher | 27 April 2016, 12:10:00 UTC | High-level changes for zero indexed trees. | 27 April 2016, 12:10:00 UTC |
| 34509cb | Jerome Kelleher | 27 April 2016, 12:02:51 UTC | Found bug in mutation range checking. | 27 April 2016, 12:02:51 UTC |
| 7350bb3 | Jerome Kelleher | 26 April 2016, 17:12:56 UTC | Low-level modifications for zero-indexed trees. | 26 April 2016, 17:12:56 UTC |
| 5447d18 | Jerome Kelleher | 26 April 2016, 14:39:04 UTC | Updated documentation with demography and model. | 26 April 2016, 14:39:04 UTC |
| 306a4b5 | Jerome Kelleher | 26 April 2016, 14:03:11 UTC | Fixed num_loci printing issue. | 26 April 2016, 14:03:11 UTC |
| c06b6de | Jerome Kelleher | 26 April 2016, 11:14:08 UTC | Bumped file format version & updated docs. | 26 April 2016, 11:14:08 UTC |
| 7dd62ad | Jerome Kelleher | 25 April 2016, 12:55:18 UTC | Updated the tutorial for new API. | 26 April 2016, 08:16:19 UTC |
| 8a5333a | Jerome Kelleher | 25 April 2016, 09:15:40 UTC | Fixed gross problems with docs. | 25 April 2016, 09:15:40 UTC |
| ef22314 | Jerome Kelleher | 21 April 2016, 14:46:02 UTC | Added num_replicates interface to simulate. | 21 April 2016, 14:46:02 UTC |
