| a1cec66 | Jerome Kelleher | 31 May 2019, 16:45:15 UTC | Merge pull request #768 from mcveanlab/beta-final Final updates for 0.7.1b1 release | 31 May 2019, 16:45:15 UTC |
| e78e500 | Jerome Kelleher | 31 May 2019, 16:40:25 UTC | Add changelog heading file. | 31 May 2019, 16:40:25 UTC |
| a98e07f | Jerome Kelleher | 31 May 2019, 16:33:38 UTC | Updated changelog for beta release. | 31 May 2019, 16:33:38 UTC |
| 3bb00cd | Jerome Kelleher | 31 May 2019, 16:32:58 UTC | Work-around falling over verification tests. | 31 May 2019, 16:32:58 UTC |
| 661a443 | Jerome Kelleher | 31 May 2019, 16:29:46 UTC | Added CHANGELOG formatting. Closes #718 | 31 May 2019, 16:30:31 UTC |
| 21b8087 | Jerome Kelleher | 31 May 2019, 16:04:44 UTC | Added guidance for Python 2.7 users. Closes #751 | 31 May 2019, 16:04:44 UTC |
| 08f9021 | Jerome Kelleher | 31 May 2019, 15:45:32 UTC | Removed growth_rate in DTWF random tests. Closes #628 | 31 May 2019, 15:46:53 UTC |
| d9be64c | Jerome Kelleher | 31 May 2019, 15:39:25 UTC | Merge pull request #754 from mcveanlab/model-docs Model docs | 31 May 2019, 15:39:25 UTC |
| ac67b5f | Jerome Kelleher | 24 May 2019, 15:20:23 UTC | Added model_factory and generalise. | 31 May 2019, 15:30:47 UTC |
| e1244e6 | Jerome Kelleher | 23 May 2019, 17:03:31 UTC | Change model.population_size to reference_size. Also fix segfault bug in out-of-memory conditions with large numbers of populations and labels. | 31 May 2019, 14:40:24 UTC |
| f047f73 | Jerome Kelleher | 13 May 2019, 15:59:22 UTC | Document models and model change events. Closes #734 | 31 May 2019, 14:40:24 UTC |
| 891af8a | Jerome Kelleher | 13 May 2019, 15:41:11 UTC | Removed simulate() signature from documentation. Closes #620 | 31 May 2019, 14:40:24 UTC |
| 347a46e | Jerome Kelleher | 31 May 2019, 14:38:16 UTC | Merge pull request #765 from mcveanlab/max-time-redux Implement end_time for simulations. | 31 May 2019, 14:38:16 UTC |
| 36bbd3e | Jerome Kelleher | 31 May 2019, 11:21:22 UTC | Added end_time semantics to simulate. Closes #564. | 31 May 2019, 14:31:05 UTC |
| aa2d538 | Jerome Kelleher | 31 May 2019, 08:07:29 UTC | Merge pull request #764 from mcveanlab/minor-updates-0.7.1 Minor updates 0.7.1 | 31 May 2019, 08:07:29 UTC |
| a496477 | Jerome Kelleher | 31 May 2019, 07:56:45 UTC | Update reason for exclusing py37 on appveyor. | 31 May 2019, 08:01:17 UTC |
| 36b1344 | Jerome Kelleher | 31 May 2019, 07:44:17 UTC | Added checks for well formed RST to CI. Closes #452 | 31 May 2019, 07:53:26 UTC |
| c700779 | Jerome Kelleher | 31 May 2019, 07:40:32 UTC | Add compiler checks to CI. Closes #462 | 31 May 2019, 07:40:32 UTC |
| 677c489 | Jerome Kelleher | 31 May 2019, 07:30:20 UTC | Fix compiler warning. Closes #740 | 31 May 2019, 07:30:20 UTC |
| 23198fb | Jerome Kelleher | 23 May 2019, 06:57:14 UTC | Merge pull request #758 from mcveanlab/c-trajectory Simulate trajectories in C | 23 May 2019, 06:57:14 UTC |
| 015d2d5 | Jerome Kelleher | 22 May 2019, 16:40:33 UTC | Rule out events during sweeps & Python tests. | 22 May 2019, 19:46:33 UTC |
| b40889f | Jerome Kelleher | 22 May 2019, 15:11:58 UTC | C tests for running genic selection sweep. | 22 May 2019, 19:39:00 UTC |
| 18f6424 | Jerome Kelleher | 22 May 2019, 14:11:25 UTC | Basic tests for genic selection trajectory. | 22 May 2019, 19:38:59 UTC |
| 74940dd | Jerome Kelleher | 15 May 2019, 19:30:07 UTC | Basic outline for C trajectory simulation. | 22 May 2019, 19:38:59 UTC |
| d1957b0 | Jerome Kelleher | 22 May 2019, 19:30:47 UTC | Merge pull request #732 from DomNelson/wf_docs Add to docs: WF model, multiple chromosomes, and hybrid simulations #447 | 22 May 2019, 19:30:47 UTC |
| efbad63 | DomNelson | 17 April 2019, 22:51:03 UTC | Add to docs: WF model, multiple chromosomes, and hybrid simulations | 22 May 2019, 14:55:46 UTC |
| 4f4a1d2 | Jerome Kelleher | 22 May 2019, 10:31:04 UTC | Merge pull request #761 from DomNelson/wf_API_docs Add docstring to DTWF class describing model details #447 | 22 May 2019, 10:31:04 UTC |
| 8311413 | Dominic Nelson | 15 May 2019, 18:50:12 UTC | Add docstring to DTWF class describing model details | 20 May 2019, 22:40:12 UTC |
| 1bb881b | Jerome Kelleher | 20 May 2019, 21:16:52 UTC | Merge pull request #742 from jgallowa07/master Add pop size and coalescent rate trajectories to demography debugger | 20 May 2019, 21:16:52 UTC |
| 164535b | Jerome Kelleher | 20 May 2019, 19:46:23 UTC | Style cleanups. | 20 May 2019, 19:49:12 UTC |
| 760020c | jgallowa07 | 01 May 2019, 21:52:55 UTC | Fixed logic for double step validation | 16 May 2019, 17:29:07 UTC |
| 1389eb6 | Jerome Kelleher | 16 May 2019, 08:16:33 UTC | Merge pull request #760 from mcveanlab/fix-test-failure Fix intermittent random test failure. | 16 May 2019, 08:16:33 UTC |
| b460380 | Jerome Kelleher | 16 May 2019, 08:02:52 UTC | Fix intermittent random test failure. | 16 May 2019, 08:02:52 UTC |
| 84e7b88 | Jerome Kelleher | 16 May 2019, 07:37:03 UTC | Merge pull request #759 from DomNelson/dtwf_fix_simultaneous_historical_samples Allow multiple historical samples per generation in DTWF | 16 May 2019, 07:37:03 UTC |
| d747f48 | Dominic Nelson | 15 May 2019, 19:32:14 UTC | Allow multiple historical samples per generation in DTWF | 15 May 2019, 19:59:27 UTC |
| 170eafc | Jerome Kelleher | 15 May 2019, 19:46:34 UTC | Merge pull request #757 from DomNelson/dtwf_non_integer_demographic_events Add DTWF support for demographic events between generations - fixes #750 | 15 May 2019, 19:46:34 UTC |
| 61959cf | Jerome Kelleher | 15 May 2019, 18:44:31 UTC | Tweaks to Python tests. | 15 May 2019, 18:45:02 UTC |
| 1d97415 | DomNelson | 14 May 2019, 15:45:41 UTC | Add support for demographic events between generations | 15 May 2019, 18:45:02 UTC |
| c6e9a21 | Jerome Kelleher | 15 May 2019, 16:04:25 UTC | Merge pull request #756 from andrewkern/discoal_verify adding discoal checks to verifaction.py | 15 May 2019, 16:04:25 UTC |
| 869d97b | andrewkern | 13 May 2019, 22:44:24 UTC | adding discoal checks to verifaction.py | 15 May 2019, 15:24:07 UTC |
| 884a962 | Jerome Kelleher | 13 May 2019, 14:23:28 UTC | Merge pull request #752 from DomNelson/dtwf_unsupported_bottleneck Add error code for unsupported DTWF bottlenecks - Fixes #747 | 13 May 2019, 14:23:28 UTC |
| ecbd119 | Jerome Kelleher | 13 May 2019, 14:14:19 UTC | Fixup Python tests for DTWF bottlenecks. | 13 May 2019, 14:14:19 UTC |
| b24d187 | Jerome Kelleher | 13 May 2019, 14:08:08 UTC | Remove add-time errors for bottlenecks. | 13 May 2019, 14:08:08 UTC |
| 8db58b8 | DomNelson | 12 May 2019, 18:37:21 UTC | Add error code for unsupported DTWF bottlenecks Also fix infinite loop in demography debugger | 13 May 2019, 12:35:19 UTC |
| 6de2adb | Jerome Kelleher | 13 May 2019, 12:35:08 UTC | Merge pull request #749 from DomNelson/dtwf_pop_size Round DTWF pop size, and set model earlier in demographic tests. Fixes #739 | 13 May 2019, 12:35:08 UTC |
| 32b7aaa | Jerome Kelleher | 13 May 2019, 12:25:49 UTC | Change to catch zeros size at runtime only. | 13 May 2019, 12:27:54 UTC |
| cbcaf5f | DomNelson | 09 May 2019, 20:39:04 UTC | Round DTWF pop size, set model earlier in demography tests. Fixes #739 Previously used ceil to avoid zero population size in DTWF, but this only let badly-specified models run without errors. A more descriptive error is now thrown. Appropriately resizing populations in tests then led to time travel errors in bottleneck events. These should not have been possible to specify in DTWF (they are only supported in the Hudson model), so model is now set earlier to catch this. | 13 May 2019, 12:26:14 UTC |
| 352257b | Jerome Kelleher | 12 May 2019, 14:15:01 UTC | Merge pull request #745 from mcveanlab/sweeps-python-c Sweeps python c | 12 May 2019, 14:15:01 UTC |
| 609a319 | Jerome Kelleher | 09 May 2019, 12:42:42 UTC | Worked around non-rentrancy of single_sweep. | 09 May 2019, 12:46:42 UTC |
| b3c2ead | Jerome Kelleher | 09 May 2019, 11:07:57 UTC | Added basic interface for num_labels and sweeps. | 09 May 2019, 11:07:57 UTC |
| 7c546da | Jerome Kelleher | 08 May 2019, 19:24:48 UTC | Low-level interface for sweeps. | 09 May 2019, 09:37:51 UTC |
| 242d48a | Jerome Kelleher | 08 May 2019, 17:02:12 UTC | Changed sweep locus to position. | 09 May 2019, 09:37:51 UTC |
| 5f28829 | Jerome Kelleher | 08 May 2019, 16:34:22 UTC | Fix some compiler warnings. | 09 May 2019, 09:37:51 UTC |
| c4213ee | Jerome Kelleher | 09 May 2019, 09:35:13 UTC | Merge pull request #738 from mcveanlab/test-model-changes Closing down model loopholes | 09 May 2019, 09:35:13 UTC |
| 398d695 | Jerome Kelleher | 09 May 2019, 09:17:30 UTC | Updated demography and simulate_from tests for DTWF. | 09 May 2019, 09:26:41 UTC |
| f49155b | Jerome Kelleher | 29 April 2019, 16:06:54 UTC | Various improvements to simulation model code. - store_full_arg is always an error for anything but Hudson. - Remove ban on bottlenecks for various models. - Add very basic support for model in demography debugger. | 09 May 2019, 08:00:10 UTC |
| 0f24990 | Jerome Kelleher | 29 April 2019, 15:06:48 UTC | Turn on mistakenly disabled tests. | 09 May 2019, 08:00:10 UTC |
| 3452c00 | Jerome Kelleher | 09 May 2019, 07:56:53 UTC | Merge pull request #737 from DomNelson/dtwf_c_demography_tests Add demographic tests in C for DTWF - fixes #626 | 09 May 2019, 07:56:53 UTC |
| e446bf7 | Jerome Kelleher | 09 May 2019, 07:43:42 UTC | Fixed some memory leaks. Also removed assertion on integer event times. | 09 May 2019, 07:44:13 UTC |
| 1a8e105 | DomNelson | 08 May 2019, 02:25:02 UTC | Fixes to historical samples in DTWF simulations and C demography tests DTWF historical samples are now added after parent selection so that times of nodes and parents cannot be the same. Also, historical sampling events are now added to demography debugging (all models) which previously led to an error in overlap counts if any demographic events occurred after historical sample times. | 09 May 2019, 07:44:13 UTC |
| 4ba0623 | Jerome Kelleher | 08 May 2019, 16:27:28 UTC | Merge pull request #744 from andrewkern/single_sweep_model single_sweep prototype implemented in C | 08 May 2019, 16:27:28 UTC |
| ab0e671 | andrewkern | 07 May 2019, 22:04:26 UTC | took out the sweep_dt parameter, calculating on the fly from trajectories | 08 May 2019, 16:20:23 UTC |
| 412ab10 | Jerome Kelleher | 07 May 2019, 15:48:07 UTC | Add tests for error conditions. | 07 May 2019, 15:52:09 UTC |
| 1cf210f | andrewkern | 03 May 2019, 18:42:14 UTC | single_sweep prototype implemented in C | 07 May 2019, 13:53:21 UTC |
| 5d9ad1c | Jerome Kelleher | 01 May 2019, 20:22:04 UTC | Merge pull request #741 from andrewkern/dev_doc_patch quick patch to the development docs | 01 May 2019, 20:22:04 UTC |
| 99ed854 | andrewkern | 01 May 2019, 18:09:26 UTC | quick patch to the development docs | 01 May 2019, 18:09:26 UTC |
| e4a29bf | Jerome Kelleher | 19 April 2019, 09:04:46 UTC | Merge pull request #736 from mcveanlab/model-change-event Fix bug in DWTF ancient samples | 19 April 2019, 09:04:46 UTC |
| fa1c8ef | Jerome Kelleher | 18 April 2019, 08:44:51 UTC | Fixed bug in historical sampling for DTWF. Closes #443 | 18 April 2019, 08:49:03 UTC |
| 9172ed5 | Jerome Kelleher | 17 April 2019, 19:39:23 UTC | Added tests for DWTF historical samples in C. Closes #625 | 18 April 2019, 08:46:11 UTC |
| ab943b8 | Jerome Kelleher | 17 April 2019, 19:27:50 UTC | Added some unit tests for model switching. | 18 April 2019, 08:46:11 UTC |
| af225c3 | Jerome Kelleher | 17 April 2019, 07:53:47 UTC | Merge pull request #735 from mufernando/master Update tutorial.rst | 17 April 2019, 07:53:47 UTC |
| 029c6bb | Murillo Fernando Rodrigues | 16 April 2019, 23:06:38 UTC | Update tutorial.rst | 16 April 2019, 23:06:38 UTC |
| 560f0a7 | Jerome Kelleher | 14 April 2019, 16:09:21 UTC | Merge pull request #733 from DomNelson/performance Remove unnecessary and costly sanity checks | 14 April 2019, 16:09:21 UTC |
| b2fc946 | Dominic Nelson | 12 April 2019, 14:56:40 UTC | Remove unnecessary and costly sanity checks | 14 April 2019, 16:00:03 UTC |
| 3ddd247 | Jerome Kelleher | 12 April 2019, 08:32:50 UTC | Merge pull request #731 from mcveanlab/fix-lint-failure Fix lint failure from new version of flake8. | 12 April 2019, 08:32:50 UTC |
| 17b1f43 | Jerome Kelleher | 12 April 2019, 08:26:05 UTC | Fix lint failure from new version of flake8. | 12 April 2019, 08:26:05 UTC |
| e3f6b7f | Jerome Kelleher | 12 April 2019, 08:16:19 UTC | Merge pull request #726 from andrewkern/demog_output_tool added two helpful functions to the DemographyDebugger class | 12 April 2019, 08:16:19 UTC |
| fc47024 | Jerome Kelleher | 19 March 2019, 20:29:24 UTC | Merge pull request #729 from jgallowa07/mean_rr added mean recombination rate | 19 March 2019, 20:29:24 UTC |
| 8ae2704 | jgallowa07 | 18 March 2019, 19:00:45 UTC | fix requested changes | 19 March 2019, 16:34:08 UTC |
| 7325364 | Jerome Kelleher | 19 March 2019, 08:30:02 UTC | Tweaks to API and tests. | 19 March 2019, 08:46:27 UTC |
| 2b1d85a | andrewkern | 16 March 2019, 03:34:18 UTC | added two helpful functions to the DemographyDebugger class clean up style, added tests, minor bug fix pulling out code to be specialized later | 18 March 2019, 19:43:01 UTC |
| 0aa6727 | Jerome Kelleher | 17 March 2019, 12:52:09 UTC | Merge pull request #727 from tskit-dev/jeromekelleher-patch-1 Temporarily reduce project coverage C target | 17 March 2019, 12:52:09 UTC |
| c065b5a | Jerome Kelleher | 17 March 2019, 12:32:28 UTC | Temporarily reduce project coverage C target Until low-level code for models is implemented and tested | 17 March 2019, 12:44:53 UTC |
| 750b168 | Jerome Kelleher | 14 March 2019, 20:07:05 UTC | Merge pull request #722 from brianzhang01/patch-1 Fix typo in hyperlink | 14 March 2019, 20:07:05 UTC |
| 1e5ed2c | Brian Zhang | 14 March 2019, 16:45:24 UTC | Fix typo in hyperlink | 14 March 2019, 16:45:24 UTC |
| ac4ec03 | Jerome Kelleher | 09 March 2019, 11:40:51 UTC | Merge pull request #721 from hugovk/rm-2 Remove support for Python 2 | 09 March 2019, 11:40:51 UTC |
| 415057c | Jerome Kelleher | 09 March 2019, 11:29:10 UTC | Miscellaneous Py2 removal changes. | 09 March 2019, 11:29:10 UTC |
| 9deea44 | Jerome Kelleher | 09 March 2019, 11:11:06 UTC | Remove Python 2 from C module. | 09 March 2019, 11:11:06 UTC |
| a49df56 | Jerome Kelleher | 09 March 2019, 11:05:54 UTC | Added back explicit inheritence from object. | 09 March 2019, 11:05:54 UTC |
| d2dc1a5 | Hugo | 08 March 2019, 22:08:47 UTC | Add python_requires to help pip | 08 March 2019, 22:08:47 UTC |
| 49777a9 | Hugo | 08 March 2019, 22:05:09 UTC | The future is now | 08 March 2019, 22:05:09 UTC |
| dc71213 | Hugo | 08 March 2019, 22:01:49 UTC | Remove the Six compatibilty library | 08 March 2019, 22:01:49 UTC |
| a56b5e3 | Hugo | 08 March 2019, 21:59:54 UTC | Upgrade Python syntax with pyupgrade --py3-plus | 08 March 2019, 21:59:54 UTC |
| ba9eada | Hugo | 08 March 2019, 21:58:39 UTC | Drop support for legacy Python 2.7 | 08 March 2019, 21:58:39 UTC |
| 0113cd8 | Jerome Kelleher | 05 March 2019, 10:51:35 UTC | Merge pull request #720 from tskit-dev/docfix small docfix | 05 March 2019, 10:51:35 UTC |
| cce2ee6 | Jerome Kelleher | 05 March 2019, 09:59:37 UTC | Push up threshold to avoid random failures. | 05 March 2019, 10:38:14 UTC |
| b134945 | peter | 04 March 2019, 17:48:40 UTC | small docfix | 04 March 2019, 17:48:40 UTC |
| 362d41d | Jerome Kelleher | 04 March 2019, 11:32:36 UTC | Merge pull request #716 from tskit-dev/zero_recomb trailing zero recombination rate fix | 04 March 2019, 11:32:36 UTC |
| 873a212 | peter | 03 March 2019, 17:10:26 UTC | trailing zero recomb fix | 03 March 2019, 23:02:31 UTC |
| 7ebdf88 | Jerome Kelleher | 23 February 2019, 12:26:56 UTC | Merge pull request #713 from hyanwong/doc-change-issue-48 Update api.rst | 23 February 2019, 12:26:56 UTC |
