| 8a39c40 | Jerome Kelleher | 05 December 2019, 15:26:05 UTC | Merge pull request #841 from mcveanlab/release-0.7.4 Update CHANGELOG for 0.7.4. | 05 December 2019, 15:26:05 UTC |
| 24e7f54 | Jerome Kelleher | 05 December 2019, 15:17:56 UTC | Update CHANGELOG for 0.7.4. | 05 December 2019, 15:17:56 UTC |
| cca1795 | Jerome Kelleher | 05 December 2019, 15:13:01 UTC | Merge pull request #840 from mcveanlab/fix-memory-leak Fix memory leak in low-level module. | 05 December 2019, 15:13:01 UTC |
| 22cc6c5 | Jerome Kelleher | 05 December 2019, 14:53:30 UTC | Fix memory leak in low-level module. The census-event string was not decrefed and we therefore leaked memory. | 05 December 2019, 14:53:30 UTC |
| 48b8da2 | Jerome Kelleher | 05 December 2019, 10:58:59 UTC | Merge pull request #838 from mcveanlab/fix-mutation-bug Fixed memory allocation error in mutgen. | 05 December 2019, 10:58:59 UTC |
| 8e57d9c | Jerome Kelleher | 04 December 2019, 20:23:00 UTC | Fixed memory allocation error in mutgen. Closes #806 | 05 December 2019, 10:55:46 UTC |
| c5e6a54 | Jerome Kelleher | 05 December 2019, 10:51:33 UTC | Merge pull request #837 from mcveanlab/mspms-length-error Test case for mspms incorrect length output. | 05 December 2019, 10:51:33 UTC |
| 5d8d29a | Jerome Kelleher | 04 December 2019, 17:22:02 UTC | Fix incorrect mspms tree length bug. Closes #836. | 05 December 2019, 09:46:35 UTC |
| 8e7a424 | Jerome Kelleher | 04 December 2019, 14:46:55 UTC | Test case for mspms incorrect length output. | 05 December 2019, 09:46:35 UTC |
| eed0aea | Jerome Kelleher | 05 December 2019, 08:32:32 UTC | Merge pull request #833 from mcveanlab/fix-recomb-overflow Fix problem in very-low recombination DTWF. | 05 December 2019, 08:32:32 UTC |
| e995344 | Jerome Kelleher | 26 November 2019, 11:33:09 UTC | Fix problem in very-low recombination DTWF. Closes #831. | 05 December 2019, 08:21:37 UTC |
| 0e8ae35 | Jerome Kelleher | 26 November 2019, 16:54:23 UTC | Merge pull request #832 from hyanwong/mathjax Update Doxyfile | 26 November 2019, 16:54:23 UTC |
| 05ac0f8 | Yan Wong | 22 November 2019, 11:58:15 UTC | Doxyfile is left over from a previous version. Delete it | 26 November 2019, 14:45:55 UTC |
| a3197ef | Jerome Kelleher | 12 November 2019, 08:42:56 UTC | Merge pull request #830 from petrelharp/doctweak clarify migration matrix; closes #828 | 12 November 2019, 08:42:56 UTC |
| 08bf018 | peter | 12 November 2019, 07:08:12 UTC | clarify migration matrix; closes #828 | 12 November 2019, 07:08:12 UTC |
| 61867d2 | Jerome Kelleher | 11 November 2019, 19:26:55 UTC | Merge pull request #829 from mcveanlab/better-errors Improved low-level error reporting on bad inputs. | 11 November 2019, 19:26:55 UTC |
| 0452d45 | Jerome Kelleher | 11 November 2019, 11:12:00 UTC | Improved low-level error reporting on bad inputs. | 11 November 2019, 11:12:00 UTC |
| ab92765 | Jerome Kelleher | 08 October 2019, 17:21:41 UTC | Merge pull request #822 from agladstein/container_docs improved container docs. closes #809 | 08 October 2019, 17:21:41 UTC |
| 61277d2 | Ariella Gladstein | 08 October 2019, 16:47:48 UTC | added info about release tags | 08 October 2019, 16:47:48 UTC |
| dd02e98 | Ariella Gladstein | 08 October 2019, 16:30:10 UTC | improved container docs. closes #809 | 08 October 2019, 16:30:10 UTC |
| 60b3c7d | Jerome Kelleher | 26 September 2019, 08:29:43 UTC | Merge pull request #799 from gtsambos/census Add census event(s) to msprime simulation | 26 September 2019, 08:29:43 UTC |
| 1a137ee | Jerome Kelleher | 26 September 2019, 07:50:51 UTC | Merge pull request #815 from mcveanlab/unpin-gsl Unpin GSL on Appveyor. | 26 September 2019, 07:50:51 UTC |
| 9a5586a | Georgia Tsambos | 16 September 2019, 02:39:10 UTC | Added to tests of census_events to increase code coverage. | 26 September 2019, 02:33:16 UTC |
| 6a3ba93 | Jerome Kelleher | 25 September 2019, 19:27:31 UTC | Unpin GSL on Appveyor. | 25 September 2019, 19:27:31 UTC |
| b0ae177 | Jerome Kelleher | 25 September 2019, 19:25:26 UTC | Merge pull request #814 from hyanwong/appveyor-update Appveyor update | 25 September 2019, 19:25:26 UTC |
| 5b9b17a | Yan Wong | 25 September 2019, 15:50:11 UTC | Point MSP_CONDA_PREFIX to the venv | 25 September 2019, 15:50:11 UTC |
| 7ffbbfd | Jerome Kelleher | 11 September 2019, 19:18:33 UTC | Pin GSL to 2.4 to work around issues on conda. | 25 September 2019, 15:44:00 UTC |
| 984b7c3 | Jerome Kelleher | 02 September 2019, 09:54:41 UTC | Update appveyor configutation. | 25 September 2019, 15:43:42 UTC |
| 4d20c54 | Jerome Kelleher | 25 September 2019, 12:50:32 UTC | Merge pull request #813 from mcveanlab/likelihood-linkage Plumbing for the log likelihood C code. | 25 September 2019, 12:50:32 UTC |
| f39279d | Jerome Kelleher | 25 September 2019, 10:54:02 UTC | Fix memory alloc error & ban rates < 0. | 25 September 2019, 10:55:37 UTC |
| d94aba1 | Jerome Kelleher | 25 September 2019, 10:28:04 UTC | Plumbing for the log likelihood C code. | 25 September 2019, 10:28:04 UTC |
| d68a8cf | Jerome Kelleher | 25 September 2019, 08:45:52 UTC | Merge pull request #810 from JereKoskela/likelihood Basic C implementation of likelihood evaluation | 25 September 2019, 08:45:52 UTC |
| 1a3bada | JereKoskela | 24 September 2019, 14:15:21 UTC | Comments and cleanup | 24 September 2019, 14:15:21 UTC |
| 668a4ab | Jerome Kelleher | 17 September 2019, 15:23:10 UTC | Merge pull request #805 from gtsambos/mac-docs Updated developer docs with info for Mac users. | 17 September 2019, 15:23:10 UTC |
| 2d528d5 | Georgia Tsambos | 16 September 2019, 23:23:25 UTC | Minor changes to Mac dev docs incorporating @molpopgen's comments. | 16 September 2019, 23:23:25 UTC |
| be3d521 | Georgia Tsambos | 16 September 2019, 04:26:24 UTC | Changed order of rules in Makefile so that the default is to run without all the checks. | 16 September 2019, 04:26:24 UTC |
| 75d2925 | Georgia Tsambos | 05 September 2019, 00:17:18 UTC | Added some notes to developer docs about some common gotchas for Mac OS X users. | 16 September 2019, 04:25:08 UTC |
| 043b210 | JereKoskela | 15 September 2019, 15:23:41 UTC | Basic C implementation of likelihood evaluation | 15 September 2019, 15:47:19 UTC |
| 8f1b854 | Georgia Tsambos | 09 September 2019, 03:50:31 UTC | Added documentation and tutorial for census events. | 09 September 2019, 04:09:25 UTC |
| 0fc968b | Georgia Tsambos | 04 September 2019, 22:55:03 UTC | Updated Python tests of census events. | 09 September 2019, 04:09:25 UTC |
| 18d3c55 | Georgia Tsambos | 02 September 2019, 01:27:35 UTC | Added node flag for census events and altered other bits of code to use this flag Added API docstring for census events Modified tests of census events. Minor changes to C implementation of add_census_event. | 09 September 2019, 04:08:56 UTC |
| bcdb764 | Georgia Tsambos | 23 August 2019, 14:56:39 UTC | Added Python-C boilerplate for census events. Small start to making Python tests for census events. | 09 September 2019, 04:07:43 UTC |
| 432e59d | Georgia Tsambos | 20 August 2019, 14:48:51 UTC | Added C code for census event. Added C code for census events. Added placeholders for C functions to implement census_event. Added code for a single census node/edge. Added code to loopify msp_census_event. Updated C test for add_census_event. Added test of msp_print_census_event to improve code coverage. Changes to census_event due to Jerome's comments. Fixed bug in msp_census_event that was messing up edge table output. | 09 September 2019, 04:07:07 UTC |
| 8ce627f | Jerome Kelleher | 03 August 2019, 12:11:08 UTC | Merge pull request #797 from mcveanlab/0.7.3-release-notes Release notes. | 03 August 2019, 12:11:08 UTC |
| 801a3b9 | Jerome Kelleher | 03 August 2019, 12:04:33 UTC | Release notes. | 03 August 2019, 12:04:33 UTC |
| 37a18d1 | Jerome Kelleher | 03 August 2019, 12:01:27 UTC | Merge pull request #796 from mcveanlab/smc-full-arg Reinstates full-arg support for SMC. | 03 August 2019, 12:01:27 UTC |
| fbda32c | Jerome Kelleher | 03 August 2019, 11:54:37 UTC | Reinstates full-arg support for SMC. Closes #795 | 03 August 2019, 11:54:37 UTC |
| 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 |
