| a3e95c4 | Jerome Kelleher | 30 July 2019, 14:38:08 UTC | Merge pull request #794 from mcveanlab/release-notes-0.7.2 Release notes for 0.7.2. | 30 July 2019, 14:38:08 UTC |
| 49cd0a6 | Jerome Kelleher | 30 July 2019, 14:30:25 UTC | Release notes for 0.7.2. | 30 July 2019, 14:30:25 UTC |
| 91f022a | Jerome Kelleher | 26 July 2019, 14:04:03 UTC | Merge pull request #791 from marianne-aspbury/massmigration_debugger Update MassMigration descriptions in simulations.py | 26 July 2019, 14:04:03 UTC |
| 696d3f6 | marianne-aspbury | 23 July 2019, 09:03:47 UTC | Update MassMigration descriptions | 26 July 2019, 09:22:57 UTC |
| 3526df0 | Jerome Kelleher | 14 July 2019, 15:34:23 UTC | Merge pull request #782 from mcveanlab/improve-historical-samples Improve handling of sampling events and tests. | 14 July 2019, 15:34:23 UTC |
| 7465e16 | Jerome Kelleher | 09 July 2019, 20:00:45 UTC | Improve handling of sampling events and tests. | 14 July 2019, 15:29:18 UTC |
| 397cec1 | Jerome Kelleher | 14 July 2019, 15:16:12 UTC | Merge pull request #763 from andrewkern/more_discoal_verify added a few more tests to verify.py | 14 July 2019, 15:16:12 UTC |
| fed4db3 | andrewkern | 24 May 2019, 19:14:00 UTC | added a few more tests to verify.py | 14 July 2019, 15:08:00 UTC |
| 53a462b | Jerome Kelleher | 14 July 2019, 15:07:29 UTC | Merge pull request #785 from molpopgen/zero_coalescence_time Zero coalescence time | 14 July 2019, 15:07:29 UTC |
| 08fbc8c | Jerome Kelleher | 14 July 2019, 14:58:10 UTC | Moved nextafter into coalescence time calculation. Closes #783 | 14 July 2019, 14:59:12 UTC |
| 02a8db9 | molpopgen | 12 July 2019, 21:52:39 UTC | flake8 fixes | 14 July 2019, 14:59:12 UTC |
| c22c2d2 | molpopgen | 12 July 2019, 21:45:10 UTC | Forgot self in _ancient_sample_test. | 14 July 2019, 14:59:12 UTC |
| 692997c | molpopgen | 12 July 2019, 21:35:11 UTC | Add test based on code from @dl42. | 14 July 2019, 14:59:12 UTC |
| 1293e8c | molpopgen | 12 July 2019, 21:30:22 UTC | Check for waiting times of zero and increment current time via nextafter. Candidate fix for #783. | 14 July 2019, 14:59:12 UTC |
| 60df371 | Jerome Kelleher | 14 July 2019, 14:25:52 UTC | Merge pull request #781 from fbaumdicker/geneconversion adds gene conversion (python version) | 14 July 2019, 14:25:52 UTC |
| 27f769a | Franz Baumdicker | 09 July 2019, 18:24:27 UTC | added function to cut right gene conversion break | 09 July 2019, 18:24:27 UTC |
| a8d8088 | Franz Baumdicker | 05 July 2019, 12:41:03 UTC | change variable name from l to tl | 05 July 2019, 12:41:03 UTC |
| 5fce217 | Franz Baumdicker | 05 July 2019, 10:26:37 UTC | adds gene conversion (python version) | 05 July 2019, 10:26:37 UTC |
| 1f940bf | Jerome Kelleher | 02 July 2019, 07:38:57 UTC | Merge pull request #770 from JereKoskela/likelihood Likelihood | 02 July 2019, 07:38:57 UTC |
| 420ca2a | JereKoskela | 27 June 2019, 10:49:16 UTC | Tree traversal for mutation likelihood | 01 July 2019, 18:22:01 UTC |
| 756e2d8 | JereKoskela | 22 June 2019, 08:16:48 UTC | Added checks for zero mutation rate | 01 July 2019, 18:21:47 UTC |
| 076481a | JereKoskela | 21 June 2019, 18:07:52 UTC | Added tests for likelihood evaluation | 01 July 2019, 18:21:14 UTC |
| e4e4355 | JereKoskela | 21 June 2019, 18:07:22 UTC | Added python likelihood evaluation | 01 July 2019, 18:21:14 UTC |
| b7b0963 | JereKoskela | 04 June 2019, 13:24:00 UTC | Implementation of ARG likelihood | 01 July 2019, 18:20:28 UTC |
| fc8ad0b | Jerome Kelleher | 28 June 2019, 07:49:14 UTC | Merge pull request #779 from petrelharp/coaltime Coalescence time calculation | 28 June 2019, 07:49:14 UTC |
| 4857612 | peter | 20 June 2019, 18:19:20 UTC | add mean coalescence time and allow coalescence rates to be computed at t=0 Use logging to provide debug info. | 27 June 2019, 16:09:12 UTC |
| 8852b59 | Jerome Kelleher | 18 June 2019, 21:23:36 UTC | Merge pull request #777 from mcveanlab/reinstate-add Add back in COPY to Dockerfile. | 18 June 2019, 21:23:36 UTC |
| ce46064 | Jerome Kelleher | 18 June 2019, 21:20:57 UTC | Add back in COPY to Dockerfile. | 18 June 2019, 21:22:16 UTC |
| d3963d1 | Jerome Kelleher | 18 June 2019, 21:06:44 UTC | Merge pull request #776 from mcveanlab/try-remove-copy-clone Remove ADD and git submodule update. | 18 June 2019, 21:06:44 UTC |
| 9348463 | Jerome Kelleher | 18 June 2019, 21:04:48 UTC | Remove ADD and git submodule update. | 18 June 2019, 21:04:48 UTC |
| 003cbe5 | Jerome Kelleher | 18 June 2019, 20:12:17 UTC | Merge pull request #775 from agladstein/master Fixed bug in docker build | 18 June 2019, 20:12:17 UTC |
| 22078ff | Ariella Gladstein | 18 June 2019, 20:05:37 UTC | Fixed bug in docker build | 18 June 2019, 20:05:37 UTC |
| 7f4acc2 | Jerome Kelleher | 18 June 2019, 12:15:48 UTC | Merge pull request #661 from agladstein/master Initial Ubuntu 18.04 Dockerfile with working msprime, and development… | 18 June 2019, 12:15:48 UTC |
| 9acbf11 | Ariella Gladstein | 18 December 2018, 20:45:08 UTC | Initial Ubuntu 18.04 Dockerfile with working msprime, and development docs for Docker | 18 June 2019, 12:11:50 UTC |
| eecf9c2 | Jerome Kelleher | 13 June 2019, 07:14:58 UTC | Merge pull request #774 from DomNelson/dtwf_slim_single_locus_test Increase SLiM generations to 10x first coalescence time | 13 June 2019, 07:14:58 UTC |
| 4377995 | DomNelson | 12 June 2019, 21:19:51 UTC | Increase SLiM generations to 10x first coalescence time | 12 June 2019, 21:19:51 UTC |
| 21783d1 | Jerome Kelleher | 08 June 2019, 10:09:09 UTC | Merge pull request #773 from mcveanlab/release-0.7.1-final Final updates for 0.7.1 | 08 June 2019, 10:09:09 UTC |
| d87eeb3 | Jerome Kelleher | 08 June 2019, 09:56:51 UTC | Changelog for 0.7.1. | 08 June 2019, 09:59:04 UTC |
| b7c33c4 | Jerome Kelleher | 08 June 2019, 09:38:43 UTC | Raise an error on ModelChanges in debugger. Closes #448 | 08 June 2019, 09:59:04 UTC |
| 8b01919 | Jerome Kelleher | 08 June 2019, 09:32:18 UTC | Added metadata to Populations. Closes #772. | 08 June 2019, 09:59:02 UTC |
| c843b2d | Jerome Kelleher | 07 June 2019, 07:14:13 UTC | Merge pull request #769 from DomNelson/dtwf_statistical_tests Streamline DTWF tests and update test requirements | 07 June 2019, 07:14:13 UTC |
| d62c830 | DomNelson | 03 June 2019, 19:25:11 UTC | Streamline DTWF tests and update test requirements | 06 June 2019, 19:02:17 UTC |
| 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 |
