| d321fd3 | Jerome Kelleher | 28 November 2020, 18:03:45 UTC | Merge pull request #1319 from mcveanlab/tskit-lib-update Tskit lib update | 28 November 2020, 18:03:45 UTC |
| 796d1ca | Jerome Kelleher | 27 November 2020, 21:41:02 UTC | Bump required tskit version to 0.3.3. | 27 November 2020, 22:12:27 UTC |
| 4f774f6 | Jerome Kelleher | 27 November 2020, 17:15:57 UTC | Raise warning for --compress in msp simulate cli. | 27 November 2020, 17:17:18 UTC |
| 6bdf0d4 | Jerome Kelleher | 27 November 2020, 16:15:09 UTC | Update tskit to C_0.99.8 Also fix breakage in C API and newer tskit APIs. | 27 November 2020, 17:17:03 UTC |
| e573049 | mergify[bot] | 26 November 2020, 09:40:30 UTC | Merge pull request #1315 from mufernando/fix_kept_mut clarifying mutation time error message | 26 November 2020, 09:40:30 UTC |
| 887309d | mufernando | 25 November 2020, 18:22:06 UTC | clarifying mutation time error message | 25 November 2020, 18:35:19 UTC |
| 3dd8fa7 | mergify[bot] | 18 November 2020, 18:03:30 UTC | Merge pull request #1252 from fbaumdicker/gc_tract_length_bugfix bugfix too long continuous tract length | 18 November 2020, 18:03:30 UTC |
| 1d776c2 | Jerome Kelleher | 18 November 2020, 17:57:30 UTC | Add gc_tract_length verification for continuous case. | 18 November 2020, 17:57:30 UTC |
| 0af5a06 | Franz Baumdicker | 22 October 2020, 14:05:31 UTC | bugfix and simplify gene conversion tract length generation | 18 November 2020, 17:51:01 UTC |
| f487d44 | mergify[bot] | 18 November 2020, 17:45:23 UTC | Merge pull request #1287 from mcveanlab/seeds-for-replicates Seeds for replicates | 18 November 2020, 17:45:23 UTC |
| 6b090e1 | Jerome Kelleher | 17 November 2020, 15:39:20 UTC | Reinstate replicate_index. | 18 November 2020, 17:40:48 UTC |
| 85485bc | Jerome Kelleher | 14 November 2020, 15:11:29 UTC | Tidy up ms frontend. | 18 November 2020, 17:40:48 UTC |
| a203626 | Jerome Kelleher | 11 November 2020, 19:51:02 UTC | Update verification tests to use new APIs. | 18 November 2020, 17:40:48 UTC |
| c2f435c | Jerome Kelleher | 11 November 2020, 15:15:37 UTC | Remove new arguments from simulate() - Remove discrete_genome and gene_conversion from simulate(). - Update the ms code to use sim_ancestry. Closes #1297 | 18 November 2020, 17:40:48 UTC |
| 4c294c0 | Jerome Kelleher | 08 November 2020, 19:27:00 UTC | Update to remove replicate_index. | 18 November 2020, 17:40:48 UTC |
| b5669aa | Jerome Kelleher | 05 November 2020, 14:45:33 UTC | Change RandomGenerator methods to return numpy arrays. | 18 November 2020, 17:40:48 UTC |
| a11c858 | Jerome Kelleher | 05 November 2020, 13:15:18 UTC | Add a 'seed' attribute to RNG Also set correct AttributeError condition on Simulator.model. | 18 November 2020, 17:40:48 UTC |
| 1d1dc8c | mergify[bot] | 18 November 2020, 11:18:03 UTC | Merge pull request #1306 from cdquinto/census_event_docs census events jupyter docs | 18 November 2020, 11:18:03 UTC |
| 8d9725e | Consuelo Quinto | 13 November 2020, 17:51:54 UTC | census events jupyter docs | 17 November 2020, 20:42:02 UTC |
| f7ff205 | Ben Jeffery | 17 November 2020, 01:25:01 UTC | Merge pull request #1309 from benjeffery/fix-actions Fix actions for removed set-env feature | 17 November 2020, 01:25:01 UTC |
| e2a01e8 | Ben Jeffery | 17 November 2020, 01:17:13 UTC | Fix actions for removed set-env feature | 17 November 2020, 01:17:13 UTC |
| 36127bd | Jerome Kelleher | 16 November 2020, 14:38:55 UTC | Merge pull request #1308 from mcveanlab/32bit-fixes Fixes for compile problems on 32bit i686 | 16 November 2020, 14:38:55 UTC |
| 98a949e | Jerome Kelleher | 16 November 2020, 11:41:33 UTC | Fixes for compile problems on 32bit i686 | 16 November 2020, 11:41:33 UTC |
| 3750039 | mergify[bot] | 15 November 2020, 15:53:18 UTC | Merge pull request #1299 from apragsdale/multiple_chrom_docs Docs for simulating with multiple chromosomes | 15 November 2020, 15:53:18 UTC |
| fcfb2da | Aaron Ragsdale | 12 November 2020, 05:02:07 UTC | docs for using sim_ancestry with multiple chromosomes | 15 November 2020, 15:21:36 UTC |
| 6aead5f | mergify[bot] | 12 November 2020, 10:02:27 UTC | Merge pull request #1298 from castedo/quickstart_install_tweak Minor simplification of quick start install text | 12 November 2020, 10:02:27 UTC |
| 8c2070d | Castedo Ellerman | 11 November 2020, 22:55:26 UTC | Minor simplification of quick start install text | 11 November 2020, 22:55:26 UTC |
| 2e686d2 | mergify[bot] | 11 November 2020, 11:45:20 UTC | Merge pull request #1296 from JereKoskela/multiple-merger Multiple merger docs update | 11 November 2020, 11:45:20 UTC |
| d52c503 | Jere Koskela | 11 November 2020, 11:34:45 UTC | Multiple merger docs update | 11 November 2020, 11:34:45 UTC |
| 1053c95 | mergify[bot] | 11 November 2020, 10:34:10 UTC | Merge pull request #1295 from JereKoskela/likelihood Likelihood + ARG documentation | 11 November 2020, 10:34:10 UTC |
| 230577d | Jere Koskela | 10 November 2020, 19:17:55 UTC | Likelihood + ARG documentation | 10 November 2020, 19:17:55 UTC |
| 585d18d | mergify[bot] | 10 November 2020, 10:02:06 UTC | Merge pull request #1294 from mcveanlab/docs-quickstart Docs structural updates | 10 November 2020, 10:02:06 UTC |
| bd7c8f6 | Jerome Kelleher | 09 November 2020, 19:37:02 UTC | High-level changes for docs. - Change the titles for ancestry etc - Move the API section to the bottom of the respective pages - Change the order of sections | 09 November 2020, 19:37:02 UTC |
| ab0c8a2 | Jerome Kelleher | 09 November 2020, 17:22:58 UTC | Add initial quickstart section. | 09 November 2020, 17:22:58 UTC |
| c10cdfb | mergify[bot] | 09 November 2020, 14:15:46 UTC | Merge pull request #1289 from benjeffery/fix-stress Fix stress script | 09 November 2020, 14:15:46 UTC |
| 4f7d52a | Ben Jeffery | 09 November 2020, 11:18:07 UTC | Fix stress script | 09 November 2020, 14:08:20 UTC |
| b12a64e | mergify[bot] | 09 November 2020, 14:08:09 UTC | Merge pull request #1290 from tskit-dev/dependabot/pip/requirements/CI-complete/daiquiri-3.0.0 Bump daiquiri from 2.1.1 to 3.0.0 in /requirements/CI-complete | 09 November 2020, 14:08:09 UTC |
| fdd3912 | dependabot-preview[bot] | 09 November 2020, 12:45:57 UTC | Bump daiquiri from 2.1.1 to 3.0.0 in /requirements/CI-complete Bumps [daiquiri](https://github.com/jd/daiquiri) from 2.1.1 to 3.0.0. - [Release notes](https://github.com/jd/daiquiri/releases) - [Commits](https://github.com/jd/daiquiri/compare/2.1.1...3.0.0) Signed-off-by: dependabot-preview[bot] <support@dependabot.com> | 09 November 2020, 14:02:18 UTC |
| ba5f0cb | mergify[bot] | 09 November 2020, 14:01:59 UTC | Merge pull request #1291 from tskit-dev/dependabot/pip/requirements/CI-tests-pip/daiquiri-3.0.0 Bump daiquiri from 2.1.1 to 3.0.0 in /requirements/CI-tests-pip | 09 November 2020, 14:01:59 UTC |
| 4b1cf2a | dependabot-preview[bot] | 09 November 2020, 12:45:57 UTC | Bump daiquiri from 2.1.1 to 3.0.0 in /requirements/CI-tests-pip Bumps [daiquiri](https://github.com/jd/daiquiri) from 2.1.1 to 3.0.0. - [Release notes](https://github.com/jd/daiquiri/releases) - [Commits](https://github.com/jd/daiquiri/compare/2.1.1...3.0.0) Signed-off-by: dependabot-preview[bot] <support@dependabot.com> | 09 November 2020, 13:56:01 UTC |
| e604282 | Ben Jeffery | 09 November 2020, 13:03:35 UTC | Merge pull request #1293 from benjeffery/fix-adminbot-comment Stop adminbot commenting on tag doc builds - second try | 09 November 2020, 13:03:35 UTC |
| 2f12212 | Ben Jeffery | 09 November 2020, 12:59:48 UTC | Stop adminbot commenting on tag doc builds - second try | 09 November 2020, 13:00:59 UTC |
| 74afcf6 | Ben Jeffery | 09 November 2020, 12:57:55 UTC | Merge pull request #1292 from benjeffery/fix-adminbot-comment Stop adminbot commenting on tag doc builds | 09 November 2020, 12:57:55 UTC |
| f7b3553 | Ben Jeffery | 09 November 2020, 12:54:27 UTC | Stop adminbot commenting on tag doc builds | 09 November 2020, 12:54:27 UTC |
| 987922e | Ben Jeffery | 09 November 2020, 12:44:50 UTC | Merge pull request #1284 from tskit-dev/actions-tests Move tests to actions | 09 November 2020, 12:44:50 UTC |
| 3314c50 | Ben Jeffery | 06 November 2020, 10:51:10 UTC | Move tests to actions | 09 November 2020, 10:31:34 UTC |
| fec5bc8 | Ben Jeffery | 07 November 2020, 00:45:44 UTC | Merge pull request #1281 from tskit-dev/docs-reuse Make docs action more reusable | 07 November 2020, 00:45:44 UTC |
| 6400872 | Ben Jeffery | 05 November 2020, 12:32:00 UTC | Make docs action more reusable | 07 November 2020, 00:42:46 UTC |
| 5510123 | mergify[bot] | 06 November 2020, 14:25:19 UTC | Merge pull request #1285 from mcveanlab/switch-theme Switch back to RTD theme. | 06 November 2020, 14:25:19 UTC |
| 9c9c656 | Jerome Kelleher | 06 November 2020, 13:53:07 UTC | Switch back to RTD theme. Furo was distracting from the process of creating content. | 06 November 2020, 13:53:07 UTC |
| 1cd73ef | Jerome Kelleher | 03 November 2020, 17:20:28 UTC | Merge pull request #1280 from mcveanlab/docs-model-structure Add definitions/examples structure to models section | 03 November 2020, 17:20:28 UTC |
| e835bc5 | Jerome Kelleher | 03 November 2020, 17:09:55 UTC | Add definitions/examples structure to models section | 03 November 2020, 17:09:55 UTC |
| 13d5f84 | mergify[bot] | 03 November 2020, 08:46:55 UTC | Merge pull request #1258 from mcveanlab/more-docs-refactoring More docs refactoring | 03 November 2020, 08:46:55 UTC |
| f9a7174 | Jerome Kelleher | 28 October 2020, 12:45:19 UTC | Initial porting of docs to new format. Also trying out the "furo" sphinx template. | 02 November 2020, 17:19:34 UTC |
| bb0cee9 | Ben Jeffery | 30 October 2020, 08:56:36 UTC | Merge pull request #1260 from tskit-dev/fix-doc-build Don't push docs for PRs with no doc changes, prevent doc push on forks. | 30 October 2020, 08:56:36 UTC |
| f57022d | Ben Jeffery | 29 October 2020, 22:44:21 UTC | Only push docs for PRs that change them | 30 October 2020, 00:52:01 UTC |
| aed15cb | Ben Jeffery | 29 October 2020, 23:19:01 UTC | Merge pull request #1261 from benjeffery/fix-doc-build2 Fix docs not updating on push to PRs | 29 October 2020, 23:19:01 UTC |
| b52ce3f | Ben Jeffery | 29 October 2020, 21:55:14 UTC | Fix docs not updating on push to PRs | 29 October 2020, 23:16:33 UTC |
| ce1f7dd | mergify[bot] | 27 October 2020, 15:45:20 UTC | Merge pull request #1215 from mcveanlab/test_lwt_interface Use LightweightTableCollection code from tskit | 27 October 2020, 15:45:20 UTC |
| 7a72ae1 | Jerome Kelleher | 25 September 2020, 16:56:46 UTC | Use lightweight table collection interface from tskit. Note: this commit uses a non-release version of tskit. This should be updated before msprime is released. | 27 October 2020, 14:51:07 UTC |
| 45bc021 | mergify[bot] | 23 October 2020, 13:25:44 UTC | Merge pull request #1254 from hyanwong/fix-floating-point-pop Don't specify a floating point population ID in tests | 23 October 2020, 13:25:44 UTC |
| 58945d4 | Yan Wong | 23 October 2020, 12:21:06 UTC | Don't specify a floating point population ID in tests | 23 October 2020, 12:21:06 UTC |
| 85def8b | mergify[bot] | 23 October 2020, 11:27:48 UTC | Merge pull request #1253 from hyanwong/gitignore-mac-files Ignore MacOS desktop files | 23 October 2020, 11:27:48 UTC |
| dd392e6 | Yan Wong | 23 October 2020, 10:42:46 UTC | Ignore MacOS desktop files | 23 October 2020, 10:42:46 UTC |
| 2d482af | mergify[bot] | 16 October 2020, 19:16:21 UTC | Merge pull request #1249 from fbaumdicker/change_name changed track_length to tract_length | 16 October 2020, 19:16:21 UTC |
| 5f0434d | Franz Baumdicker | 16 October 2020, 12:09:21 UTC | changed track_length to tract_length | 16 October 2020, 19:06:32 UTC |
| 8f40963 | Ben Jeffery | 16 October 2020, 15:12:45 UTC | Merge pull request #1250 from benjeffery/fix-doc-build Build docs with python3.8 as no hdf5 wheels for 3.9 | 16 October 2020, 15:12:45 UTC |
| d6bd7bd | Ben Jeffery | 16 October 2020, 15:06:36 UTC | Build docs with python3.8 as no hdf5 wheels for 3.9 | 16 October 2020, 15:06:36 UTC |
| 750012d | mergify[bot] | 12 October 2020, 21:38:58 UTC | Merge pull request #1246 from castedo/more_c_coverage enable coverage data for _msprimemodule.c | 12 October 2020, 21:38:58 UTC |
| 3dd72e2 | Castedo Ellerman | 12 October 2020, 10:56:27 UTC | enable coverage data for _msprimemodule.c | 12 October 2020, 11:02:19 UTC |
| ed4935a | Ben Jeffery | 12 October 2020, 10:16:25 UTC | Merge pull request #1245 from benjeffery/doc-fix Fix doc build on non-PRs | 12 October 2020, 10:16:25 UTC |
| e2ce755 | Ben Jeffery | 12 October 2020, 10:07:38 UTC | Fix doc build on non-PRs | 12 October 2020, 10:07:38 UTC |
| 597eb80 | Ben Jeffery | 12 October 2020, 09:33:52 UTC | Merge pull request #1239 from tskit-dev/refactor-docs Refactor docs | 12 October 2020, 09:33:52 UTC |
| 50def05 | Ben Jeffery | 05 October 2020, 13:21:41 UTC | Autodoc deploy | 12 October 2020, 09:23:28 UTC |
| f44f491 | Jerome Kelleher | 01 October 2020, 17:21:17 UTC | Move docs build to GitHub workflow. | 12 October 2020, 09:23:28 UTC |
| 3808cea | Jerome Kelleher | 28 September 2020, 14:25:20 UTC | Initial docs refactoring. Uses jupyter-sphinx for online example chunks. | 12 October 2020, 09:23:28 UTC |
| 88236ab | mergify[bot] | 07 October 2020, 10:26:18 UTC | Merge pull request #1237 from castedo/4G_fast_search Halve number of machine instruction running in bottleneck function | 07 October 2020, 10:26:18 UTC |
| c879d73 | Castedo Ellerman | 22 September 2020, 12:30:00 UTC | fast_search_t binary search perf boost - lookup table for faster cached binary searches - speed up search for index of chromosome position of rate map - to address perf issue in msprime #1159 - greatly reduce machine instructions per rate_map_position_to_mass call | 07 October 2020, 01:15:36 UTC |
| 570a018 | mergify[bot] | 30 September 2020, 22:14:04 UTC | Merge pull request #1236 from JereKoskela/multiple-merger Beta coalescent timescale typo correction | 30 September 2020, 22:14:04 UTC |
| f48b384 | Jere Koskela | 30 September 2020, 17:46:30 UTC | Birkner et al (2018) reference added | 30 September 2020, 17:46:30 UTC |
| 1b7c32f | Jere Koskela | 30 September 2020, 16:51:00 UTC | Beta coalescent timescale typo | 30 September 2020, 16:51:00 UTC |
| 626bfc6 | mergify[bot] | 30 September 2020, 13:17:54 UTC | Merge pull request #1234 from mcveanlab/update-benchmarks Update benchmarks | 30 September 2020, 13:17:54 UTC |
| 018d2af | Jerome Kelleher | 30 September 2020, 12:14:15 UTC | Update DTWF long sequence length benchmark. Closes #1218 | 30 September 2020, 12:14:15 UTC |
| 541af32 | Jerome Kelleher | 30 September 2020, 11:58:31 UTC | Add benchmark for gene conversion. Closes #821 | 30 September 2020, 11:58:31 UTC |
| 0337990 | mergify[bot] | 30 September 2020, 10:15:09 UTC | Merge pull request #1232 from benjeffery/pytest-config Add pytest.ini | 30 September 2020, 10:15:09 UTC |
| 39c460a | Ben Jeffery | 30 September 2020, 10:04:45 UTC | Add pytest.ini | 30 September 2020, 10:04:45 UTC |
| a0f0fa8 | mergify[bot] | 30 September 2020, 09:02:08 UTC | Merge pull request #1203 from mcveanlab/bug_assert_macro Proposal for bug_assert macro | 30 September 2020, 09:02:08 UTC |
| abd05ea | Jerome Kelleher | 29 September 2020, 17:21:05 UTC | Use tsk_bug_assert macro. Closes #1192 | 30 September 2020, 08:55:05 UTC |
| ac1e897 | Jerome Kelleher | 29 September 2020, 15:52:52 UTC | Udate tskit to C_0.99.7 | 30 September 2020, 08:54:12 UTC |
| 12b4787 | Jerome Kelleher | 24 September 2020, 08:39:20 UTC | Proposal for bug_assert macro | 30 September 2020, 08:54:08 UTC |
| 15551e0 | mergify[bot] | 30 September 2020, 08:45:28 UTC | Merge pull request #1196 from fbaumdicker/speed_up_gc_left Speed up gc left | 30 September 2020, 08:45:28 UTC |
| 0537bdb | Franz Baumdicker | 15 September 2020, 00:58:50 UTC | remove gc_left dependency on right segment end and speed up gene conversion | 30 September 2020, 08:39:10 UTC |
| 1975026 | mergify[bot] | 30 September 2020, 07:14:41 UTC | Merge pull request #1229 from benjeffery/pytest Switch tests from nose to pytest | 30 September 2020, 07:14:41 UTC |
| 1fb37a1 | Ben Jeffery | 30 September 2020, 01:03:18 UTC | Fix warnings | 30 September 2020, 01:27:23 UTC |
| 6d86e18 | Ben Jeffery | 30 September 2020, 00:01:23 UTC | Switch tests from nose to pytest | 30 September 2020, 01:27:18 UTC |
| f40825e | mergify[bot] | 29 September 2020, 15:38:48 UTC | Merge pull request #1223 from castedo/pr/strict_upper_bound Add and use strict upper bound binary search function | 29 September 2020, 15:38:48 UTC |
| 37e6c8e | Castedo Ellerman | 27 September 2020, 10:04:26 UTC | Add and use strict upper bound binary search function - add function for strict upper bound binary search - use strict upper bound search in rate_map_mass_to_position - streamline rate_map_mass_to_position to run a little faster - rename binary search functions to be consistent - expand binary search unit tests to include new variant - add extreme cases to unit test for rate_map_mass_to_position | 29 September 2020, 15:27:19 UTC |
| 23d3b6b | mergify[bot] | 29 September 2020, 10:06:56 UTC | Merge pull request #1219 from mcveanlab/dev-docs-refresh Refesh development docs. | 29 September 2020, 10:06:56 UTC |
| 155c8a5 | Jerome Kelleher | 28 September 2020, 11:04:17 UTC | Refesh development docs. - Update the makefile to be more obvious and add clang-format target - Make it more difficult to mess up with clang-format by adding format-off in files we don't format. - Fix compile bug that somehow slipped through the net. - Make a pass through dev docs to refresh. Closes #1122 Closes #1208 | 29 September 2020, 10:00:17 UTC |
| b5c561c | mergify[bot] | 29 September 2020, 08:39:51 UTC | Merge pull request #1224 from JereKoskela/multiple-merger Multiple merger | 29 September 2020, 08:39:51 UTC |
