| 35fa41b | Ben Jeffery | 17 March 2021, 13:34:13 UTC | Redirect RTD | 17 March 2021, 13:53:27 UTC |
| 7371acd | Jerome Kelleher | 13 January 2021, 16:15:08 UTC | Merge pull request #1360 from mcveanlab/samples-update Finalise sampling for sim_ancestry | 13 January 2021, 16:15:08 UTC |
| 9b6d403 | Jerome Kelleher | 13 January 2021, 15:40:53 UTC | Add private method to make seeds deterministic Improve documentation for sampling. | 13 January 2021, 15:42:19 UTC |
| 6cb6619 | Jerome Kelleher | 12 January 2021, 14:36:40 UTC | Change to use SampleSets | 13 January 2021, 15:42:07 UTC |
| ffd27ff | Jerome Kelleher | 11 January 2021, 17:05:23 UTC | Improve error checking and testing. | 11 January 2021, 17:05:23 UTC |
| fd23bf9 | Jerome Kelleher | 11 January 2021, 12:21:09 UTC | Finalise samples API. Removes the Demography.sample() method in favour of a more expressive samples argument in sim_ancestry. | 11 January 2021, 12:21:09 UTC |
| 9ff6368 | Jerome Kelleher | 07 January 2021, 15:52:41 UTC | Change max_time to math.inf Makes logs more readable. | 07 January 2021, 15:52:41 UTC |
| cb603c9 | mergify[bot] | 05 January 2021, 07:27:54 UTC | Merge pull request #1199 from petrelharp/slim_mutation_metadata add time to slim metadata | 05 January 2021, 07:27:54 UTC |
| 38af646 | peter | 19 September 2020, 07:16:49 UTC | added time to slim metadata: closes #1188 | 05 January 2021, 04:37:27 UTC |
| be482ae | mergify[bot] | 04 January 2021, 11:10:42 UTC | Merge pull request #1359 from benjeffery/pin-sphinx Pin sphinx due to error | 04 January 2021, 11:10:42 UTC |
| f5b2701 | Ben Jeffery | 04 January 2021, 10:11:29 UTC | Pin sphinx due to error | 04 January 2021, 11:06:36 UTC |
| 2eb665a | Jerome Kelleher | 18 December 2020, 16:01:38 UTC | Merge pull request #1340 from mcveanlab/species-tree-refactor Use recent features in species tree parsing code. | 18 December 2020, 16:01:38 UTC |
| 63c9850 | Jerome Kelleher | 17 December 2020, 23:21:33 UTC | Add growth_rate and initial_size to species tree. | 18 December 2020, 15:52:11 UTC |
| 9bc2766 | Jerome Kelleher | 16 December 2020, 23:36:44 UTC | Change species trees to use one population per node. Closes #1072 | 17 December 2020, 23:22:14 UTC |
| 9c61835 | Jerome Kelleher | 16 December 2020, 22:24:07 UTC | Make species tree parsers part of Demography class. Closes #958 | 17 December 2020, 23:22:14 UTC |
| 8b5749c | mergify[bot] | 17 December 2020, 21:35:33 UTC | Merge pull request #1342 from petrelharp/adjust_p minor improvements to mutation verification | 17 December 2020, 21:35:33 UTC |
| 4359be2 | peter | 17 December 2020, 17:57:51 UTC | minor improvements to mutation verification | 17 December 2020, 21:28:35 UTC |
| 0af0623 | mergify[bot] | 17 December 2020, 17:50:26 UTC | Merge pull request #1341 from petrelharp/adjust_p move to verification | 17 December 2020, 17:50:26 UTC |
| 9342e83 | peter | 17 December 2020, 06:41:22 UTC | move statistical tests of mutation to verification | 17 December 2020, 17:46:35 UTC |
| 8e64e66 | Jerome Kelleher | 16 December 2020, 21:26:18 UTC | Merge pull request #1336 from mcveanlab/demography-updates Updates demography factory methods. | 16 December 2020, 21:26:18 UTC |
| 151bdc6 | Jerome Kelleher | 15 December 2020, 01:51:25 UTC | Rename simple_model to isolated_model Change parameter semantics of island_model and stepping_stone_model to follow the same pattern as isolated_model. Closes #1333 | 16 December 2020, 21:19:20 UTC |
| 8732aae | mergify[bot] | 16 December 2020, 09:17:03 UTC | Merge pull request #1339 from petrelharp/adjust_p adjust p-thresholds | 16 December 2020, 09:17:03 UTC |
| 0459ff2 | peter | 16 December 2020, 06:41:15 UTC | adjust p-thresholds | 16 December 2020, 06:41:15 UTC |
| c12837f | mergify[bot] | 15 December 2020, 14:07:48 UTC | Merge pull request #1337 from hyanwong/remove-map-len Remove __len__ and size() from RateMap | 15 December 2020, 14:07:48 UTC |
| 77ce22f | Yan Wong | 15 December 2020, 13:25:26 UTC | Remove __len__ and size() from RateMap As suggested by @grahamgower, because it is unclear if we mean the number of rates or the number of positions. This will force users to do len(rate_map.rate) or len(rate_map.position) as appropriate. I'm assuming that len(ratemap) and ratemap.size() were never previously released - if so this should not affect backwards compatibility. | 15 December 2020, 13:25:26 UTC |
| 7dfafb7 | mergify[bot] | 15 December 2020, 12:56:49 UTC | Merge pull request #1335 from hyanwong/ratemap-improvements Improvements to RateMap | 15 December 2020, 12:56:49 UTC |
| d40cd30 | Yan Wong | 13 December 2020, 11:51:09 UTC | Improvements to RateMap | 15 December 2020, 09:25:47 UTC |
| 4bfd87e | mergify[bot] | 14 December 2020, 17:42:01 UTC | Merge pull request #1314 from mcveanlab/mutate-for-1.0 Updates to mutations API for 1.0 | 14 December 2020, 17:42:01 UTC |
| b17bc4c | Jerome Kelleher | 25 November 2020, 16:49:55 UTC | Convert mutation tests to use sim_ancestry. Also change default for discrete_genome in sim_mutations to True. | 14 December 2020, 16:58:24 UTC |
| 28755bc | Jerome Kelleher | 25 November 2020, 16:20:55 UTC | Add sim_mutations function and deprecate mutate() Revert mutate() to its behaviour at release 0.7.4 and document it as deprecated. Closes #1174 | 14 December 2020, 16:04:46 UTC |
| a365322 | Jerome Kelleher | 25 November 2020, 15:11:39 UTC | Rename "discrete" to "discrete_genome" in mutate() Closes #1235 | 14 December 2020, 16:04:46 UTC |
| f3c5dcc | Jerome Kelleher | 14 December 2020, 15:46:30 UTC | Merge pull request #1332 from mcveanlab/species-tree-fixes Disallow non ultrametric in parse_species_tree. | 14 December 2020, 15:46:30 UTC |
| 8726b8e | Jerome Kelleher | 09 December 2020, 23:55:46 UTC | Disallow non ultrametric in parse_species_tree. Closes #1328 | 10 December 2020, 00:01:29 UTC |
| 5ca4eb4 | Jerome Kelleher | 10 December 2020, 00:00:55 UTC | Merge pull request #1323 from cdquinto/how_to_doc How to doc | 10 December 2020, 00:00:55 UTC |
| b3bee4b | Consuelo Quinto | 30 November 2020, 20:35:43 UTC | added a section about how to add documentation | 09 December 2020, 23:37:03 UTC |
| 65fc33e | mergify[bot] | 03 December 2020, 12:31:53 UTC | Merge pull request #1330 from fbaumdicker/add_gc_documentation add documentation for gene conversion | 03 December 2020, 12:31:53 UTC |
| 6b4837f | Franz Baumdicker | 02 December 2020, 00:54:10 UTC | add documentation for gene conversion | 03 December 2020, 12:27:26 UTC |
| adcb144 | mergify[bot] | 02 December 2020, 17:05:36 UTC | Merge pull request #1324 from mcveanlab/add-tskit-version-test Add explicit test for tskit C version. | 02 December 2020, 17:05:36 UTC |
| 01d32fb | Jerome Kelleher | 30 November 2020, 23:46:51 UTC | Add explicit test for tskit C version. | 02 December 2020, 17:01:20 UTC |
| a9d82db | mergify[bot] | 01 December 2020, 23:23:40 UTC | Merge pull request #1316 from mcveanlab/demography-cleanups Demography metadata | 01 December 2020, 23:23:40 UTC |
| 2b7bc05 | Jerome Kelleher | 25 November 2020, 22:45:07 UTC | Add metadata schema to population and user_metadata. Closes #1017 | 01 December 2020, 23:16:46 UTC |
| 51eb9af | Jerome Kelleher | 25 November 2020, 22:23:10 UTC | Enforce valid Python idenifier for Population name. Closes #1073 | 01 December 2020, 23:16:46 UTC |
| d5c834c | mergify[bot] | 01 December 2020, 22:19:48 UTC | Merge pull request #1329 from hyanwong/conftest Add conftest and mark tests >5secs as slow | 01 December 2020, 22:19:48 UTC |
| 300a13e | Yan Wong | 01 December 2020, 19:17:43 UTC | Add conftest and mark tests >5secs as slow | 01 December 2020, 19:36:21 UTC |
| e9f9c89 | mergify[bot] | 30 November 2020, 23:39:04 UTC | Merge pull request #1322 from benjeffery/fix-submodule Revert accidental submodule change | 30 November 2020, 23:39:04 UTC |
| f01a08e | Ben Jeffery | 30 November 2020, 22:35:51 UTC | Revert accidental submodule change | 30 November 2020, 22:35:51 UTC |
| 525ee9e | Ben Jeffery | 30 November 2020, 20:36:22 UTC | Merge pull request #1321 from benjeffery/disable-docs Disable doc upload | 30 November 2020, 20:36:22 UTC |
| 7a91975 | Ben Jeffery | 30 November 2020, 20:35:06 UTC | Disable doc upload | 30 November 2020, 20:35:06 UTC |
| 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 |
