| 6fc67e4 | Jerome Kelleher | 25 August 2018, 14:31:20 UTC | Merge pull request #595 from mcveanlab/CHANGELOG-0.6.1 CHANGELOG updates for version 0.6.1. | 25 August 2018, 14:31:20 UTC |
| 2dba5ec | Jerome Kelleher | 24 August 2018, 14:41:24 UTC | CHANGELOG updates for version 0.6.1. | 25 August 2018, 12:20:57 UTC |
| 8a8102c | Jerome Kelleher | 25 August 2018, 11:15:50 UTC | Merge pull request #597 from mcveanlab/demography-bug Statistical check for conservation of migration events. | 25 August 2018, 11:15:50 UTC |
| 18c6c23 | Jerome Kelleher | 25 August 2018, 10:45:59 UTC | Fixed verification test for simulate_from with demography. Closes #596. | 25 August 2018, 10:46:43 UTC |
| 1423f6d | Jerome Kelleher | 25 August 2018, 09:50:33 UTC | Tidy-ups and unit tests for demography. | 25 August 2018, 09:50:33 UTC |
| cde052a | Jerome Kelleher | 24 August 2018, 16:44:02 UTC | Stats test showing simulate_from demography bug. | 25 August 2018, 08:57:24 UTC |
| 1081f5f | Jerome Kelleher | 24 August 2018, 16:46:19 UTC | Merge pull request #591 from mcveanlab/document-flags Document flags reserved and unreserved status. | 24 August 2018, 16:46:19 UTC |
| d40f784 | Jerome Kelleher | 24 August 2018, 13:09:06 UTC | Document flags reserved and unreserved status. | 24 August 2018, 14:58:39 UTC |
| 0d22393 | Jerome Kelleher | 24 August 2018, 14:57:49 UTC | Merge pull request #592 from mcveanlab/fix-verification Fix matplotlib backend problem. | 24 August 2018, 14:57:49 UTC |
| d28a8c5 | Jerome Kelleher | 24 August 2018, 14:21:09 UTC | Fixed problem with JSON encoding. Closes #593 | 24 August 2018, 14:24:38 UTC |
| 6690025 | Jerome Kelleher | 24 August 2018, 13:22:43 UTC | Fix matplotlib backend problem. | 24 August 2018, 13:22:43 UTC |
| 152aa4d | Jerome Kelleher | 24 August 2018, 12:54:41 UTC | Merge pull request #581 from mcveanlab/finish-simulate-from Finish simulate from | 24 August 2018, 12:54:41 UTC |
| 1a4115a | Jerome Kelleher | 24 August 2018, 12:27:04 UTC | Updates from review. | 24 August 2018, 12:27:40 UTC |
| af677d0 | Jerome Kelleher | 23 August 2018, 15:13:53 UTC | More documentations for simulate_from. | 24 August 2018, 12:27:40 UTC |
| 8836503 | Jerome Kelleher | 22 August 2018, 20:01:24 UTC | First pass at tutorial for simulate_from. | 24 August 2018, 12:27:40 UTC |
| 3bc89af | Jerome Kelleher | 22 August 2018, 18:30:08 UTC | Tidy up algorithm code. | 24 August 2018, 12:27:39 UTC |
| 23f998f | Jerome Kelleher | 22 August 2018, 18:16:16 UTC | Removed simplify from simulate from code path. | 24 August 2018, 12:27:39 UTC |
| 37d344a | Jerome Kelleher | 20 August 2018, 20:58:13 UTC | Added discrete loci to WF and fixed up tests. | 24 August 2018, 12:27:39 UTC |
| ffe85c8 | Jerome Kelleher | 20 August 2018, 19:10:20 UTC | Fixed up tests. | 24 August 2018, 12:27:39 UTC |
| a06822e | Jerome Kelleher | 19 August 2018, 20:32:09 UTC | Working-ish versions of most things. | 24 August 2018, 12:27:39 UTC |
| 30e7fc0 | Jerome Kelleher | 19 August 2018, 17:40:09 UTC | (Re)implemented initial conditions using tree roots. | 24 August 2018, 12:27:39 UTC |
| 1bad798 | Jerome Kelleher | 19 August 2018, 16:28:07 UTC | Version of algorithm using root edges. This mostly works, but there are a lot of subtle issues. Seems like using the tree roots is actually the way to go all right (but with the extra information). | 24 August 2018, 12:27:39 UTC |
| ee7743d | Jerome Kelleher | 19 August 2018, 11:33:53 UTC | Added default samples to TableCollection.simplify. | 24 August 2018, 12:27:39 UTC |
| 61fc060 | Jerome Kelleher | 18 August 2018, 16:58:32 UTC | Factored out segment_overlapper from simplify. | 24 August 2018, 12:27:39 UTC |
| 309b0f1 | Jerome Kelleher | 18 August 2018, 16:07:36 UTC | New algorithm that avoids tree iteration. | 24 August 2018, 12:27:39 UTC |
| cd1b635 | Jerome Kelleher | 18 August 2018, 12:08:04 UTC | Statistically correct* algorithm for simulate from. * Must all simplify on the resulting tree sequence to get rid of unary edges. | 24 August 2018, 12:27:39 UTC |
| f67d570 | Jerome Kelleher | 24 August 2018, 12:05:46 UTC | Merge pull request #583 from mcveanlab/provenance-schema Initial version of provenance schema. | 24 August 2018, 12:05:46 UTC |
| 077affc | Jerome Kelleher | 24 August 2018, 11:11:37 UTC | Added documentation for validate_provenance. | 24 August 2018, 11:19:14 UTC |
| 8f1318c | Jerome Kelleher | 21 August 2018, 20:33:51 UTC | Added schema_version and documentation. | 24 August 2018, 11:19:14 UTC |
| 21c496a | Jerome Kelleher | 21 August 2018, 16:34:02 UTC | Initial version of provenance schema. | 24 August 2018, 11:19:11 UTC |
| 6798905 | Jerome Kelleher | 24 August 2018, 10:24:47 UTC | Merge pull request #588 from shajoezhu/stats_check_for_xi_dirac update xi-dirac checks | 24 August 2018, 10:24:47 UTC |
| df10e60 | Joe Zhu | 23 August 2018, 18:18:03 UTC | update xi-dirac checks | 23 August 2018, 18:18:03 UTC |
| 65d5d35 | Jerome Kelleher | 23 August 2018, 10:20:35 UTC | Merge pull request #587 from mcveanlab/xi-dirac-checks Statistical checks for Xi coalescent. | 23 August 2018, 10:20:35 UTC |
| cb79adf | Jerome Kelleher | 23 August 2018, 09:51:30 UTC | Statistical checks for Xi coalescent. - Tidied up Hudson comparisons - Added framework for checking expected SFS. | 23 August 2018, 10:01:56 UTC |
| f548b34 | Jerome Kelleher | 23 August 2018, 09:07:43 UTC | Merge pull request #585 from mcveanlab/mutate-interval Add start_time and end_time to mutate. | 23 August 2018, 09:07:43 UTC |
| 9ab030a | Jerome Kelleher | 22 August 2018, 14:50:17 UTC | Add start_time and end_time to mutate. Closes #508. | 23 August 2018, 08:23:29 UTC |
| 635fa39 | Jerome Kelleher | 22 August 2018, 15:36:12 UTC | Merge pull request #586 from mcveanlab/misc-docs Miscellaneous doc fixes. | 22 August 2018, 15:36:12 UTC |
| fae96d5 | Jerome Kelleher | 22 August 2018, 14:59:41 UTC | Miscellaneous doc fixes. Closes #578 Closes #565 Closes #566 | 22 August 2018, 15:14:25 UTC |
| b8fc236 | Jerome Kelleher | 21 August 2018, 18:34:57 UTC | Merge pull request #584 from petrelharp/error_msg clarified error | 21 August 2018, 18:34:57 UTC |
| 5a51808 | peter | 21 August 2018, 17:44:54 UTC | clarified error | 21 August 2018, 17:59:03 UTC |
| 58ba833 | Jerome Kelleher | 21 August 2018, 13:46:47 UTC | Merge pull request #582 from shajoezhu/xi_dirac_Vs_hybridLambda checking dirac_compute_coalescence_rate in pairwise coalescent case | 21 August 2018, 13:46:47 UTC |
| 09a4273 | Jerome Kelleher | 21 August 2018, 13:24:41 UTC | Fixed seed for problematic test case. | 21 August 2018, 13:24:41 UTC |
| d9c970d | Joe Zhu | 20 August 2018, 12:04:48 UTC | checking dirac_compute_coalescence_rate in pairwise coalescent case | 21 August 2018, 12:53:44 UTC |
| 8cab3e9 | Jerome Kelleher | 20 August 2018, 16:40:49 UTC | Merge pull request #580 from mcveanlab/genotypes-perf Genotypes perf | 20 August 2018, 16:40:49 UTC |
| d9d62f1 | Jerome Kelleher | 20 August 2018, 15:33:32 UTC | Added samples option to ts.variants(). | 20 August 2018, 16:17:06 UTC |
| 8214d63 | Jerome Kelleher | 20 August 2018, 13:46:47 UTC | Added samples list to vargen C API. Also changed to left_sample, etc throughout. | 20 August 2018, 16:17:06 UTC |
| 706e2ce | Jerome Kelleher | 20 August 2018, 12:08:24 UTC | Settled on next being undefined for rightmost samples. | 20 August 2018, 16:17:06 UTC |
| 0cc2489 | Jerome Kelleher | 17 August 2018, 16:19:43 UTC | Partially working C implementation. | 20 August 2018, 16:17:06 UTC |
| cb53237 | Jerome Kelleher | 17 August 2018, 13:44:47 UTC | Working version of algorithm with tracked_samples. | 20 August 2018, 16:17:06 UTC |
| 19b21b7 | Jerome Kelleher | 17 August 2018, 13:09:53 UTC | Minimal change to use integer pointers. | 20 August 2018, 16:17:06 UTC |
| f49ec2e | Jerome Kelleher | 16 August 2018, 15:28:38 UTC | Initial work on removing pointers for sample lists. | 20 August 2018, 16:17:06 UTC |
| f109731 | Jerome Kelleher | 20 August 2018, 07:49:04 UTC | Merge pull request #555 from petrelharp/more_table_input text input/output and tables | 20 August 2018, 07:49:04 UTC |
| 1bb9d1d | peter | 10 July 2018, 00:19:08 UTC | text input and minor fixing added tests and input | 19 August 2018, 06:12:34 UTC |
| 36888eb | Jerome Kelleher | 17 August 2018, 19:03:48 UTC | Merge pull request #561 from petrelharp/docdocgoose More doc fixing | 17 August 2018, 19:03:48 UTC |
| 598f359 | peter | 12 July 2018, 16:46:52 UTC | another minor doc fix headers better minor edits | 17 August 2018, 18:17:10 UTC |
| 9dc7a7d | Jerome Kelleher | 15 August 2018, 18:20:49 UTC | Merge pull request #577 from mcveanlab/pickle-bug Pickle support for TableCollection. | 15 August 2018, 18:20:49 UTC |
| d659344 | Jerome Kelleher | 15 August 2018, 16:39:41 UTC | Pickle support for TableCollection. Closes #574. | 15 August 2018, 17:49:02 UTC |
| ec717bf | Jerome Kelleher | 15 August 2018, 16:40:42 UTC | Merge pull request #575 from mcveanlab/ts-uuid-2 Add file_uuid to tree sequence object. | 15 August 2018, 16:40:42 UTC |
| b391523 | Jerome Kelleher | 15 August 2018, 15:53:39 UTC | Added file_uuid to TreeSequence. Closes #536. | 15 August 2018, 15:58:05 UTC |
| 3325167 | Jerome Kelleher | 15 August 2018, 12:53:24 UTC | Add file_uuid to TableCollection. | 15 August 2018, 15:58:00 UTC |
| a6af5d7 | Jerome Kelleher | 15 August 2018, 15:07:34 UTC | Merge pull request #573 from mcveanlab/system-random-seeds Seeds generated explictly using generator. | 15 August 2018, 15:07:34 UTC |
| 2c5893d | Jerome Kelleher | 15 August 2018, 12:29:56 UTC | Seeds generated explictly using generator. Closes #534. Seeds are now generated uniquely across muliple processes also. | 15 August 2018, 13:44:50 UTC |
| 970de93 | Jerome Kelleher | 15 August 2018, 12:08:45 UTC | Merge pull request #571 from mcveanlab/catch-zero-branches Detect when simulations produce bad node times. | 15 August 2018, 12:08:45 UTC |
| 4add776 | Jerome Kelleher | 14 August 2018, 17:27:04 UTC | Detect when simulations produce bad node times. Closes #87 Closes #570 | 15 August 2018, 10:15:35 UTC |
| d74eacd | Jerome Kelleher | 15 August 2018, 10:05:22 UTC | Merge pull request #541 from mcveanlab/simulate_from Simulate from | 15 August 2018, 10:05:22 UTC |
| 8e50152 | Jerome Kelleher | 14 August 2018, 15:40:55 UTC | Added some statistical tests. | 14 August 2018, 15:40:55 UTC |
| 08f1df6 | Jerome Kelleher | 14 August 2018, 13:58:53 UTC | Fixed up some dev makefile issues. | 14 August 2018, 13:58:53 UTC |
| baf3845 | Jerome Kelleher | 14 August 2018, 13:53:50 UTC | Fix memory leak in tests. | 14 August 2018, 13:53:50 UTC |
| 4dc6f52 | Jerome Kelleher | 14 August 2018, 13:43:55 UTC | Fixed up rebasing issues. | 14 August 2018, 13:43:55 UTC |
| 28ad2e3 | Jerome Kelleher | 07 August 2018, 19:13:56 UTC | Clarify remaining corner cases. | 14 August 2018, 13:39:58 UTC |
| 728bd90 | Jerome Kelleher | 06 August 2018, 20:13:40 UTC | Identify cases where coordinate mapping fails. | 14 August 2018, 13:39:58 UTC |
| 6fefd2f | Jerome Kelleher | 05 August 2018, 16:54:41 UTC | Fix some errors in handling zero recombination rates. | 14 August 2018, 13:39:58 UTC |
| 6fd6298 | Jerome Kelleher | 04 August 2018, 17:23:29 UTC | Narrowed problems down to zero recombination case. | 14 August 2018, 13:39:56 UTC |
| a2f874b | Jerome Kelleher | 04 August 2018, 15:17:41 UTC | Added physical_to_discrete_genetic to recomb map. | 14 August 2018, 13:39:27 UTC |
| 2d2002b | Jerome Kelleher | 04 August 2018, 11:26:01 UTC | Moved recombination map tests to own file. | 14 August 2018, 13:39:27 UTC |
| 0bba152 | Jerome Kelleher | 01 August 2018, 19:45:34 UTC | Identified problem with recombination map. simulate_from will currently only run if the recomb_map has a single locus. | 14 August 2018, 13:39:27 UTC |
| f1f63e3 | Jerome Kelleher | 29 July 2018, 16:21:31 UTC | Added initial framework for tests on SLiM output. | 14 August 2018, 13:39:27 UTC |
| b36e8a0 | Jerome Kelleher | 29 July 2018, 15:24:39 UTC | Don't allow generating mutations with non-zero start_time. | 14 August 2018, 13:39:27 UTC |
| 32f5c9f | Jerome Kelleher | 29 July 2018, 15:12:57 UTC | Added various tests for demography. Identified issue with L != 1 for single locus simulation. | 14 August 2018, 13:39:27 UTC |
| 72729c2 | Jerome Kelleher | 29 July 2018, 12:44:15 UTC | Tests for handling multiple populations. | 14 August 2018, 13:39:27 UTC |
| 94c284d | Jerome Kelleher | 28 July 2018, 18:53:03 UTC | Checks for demographic events occuring before start_time. | 14 August 2018, 13:39:25 UTC |
| 02d2427 | Jerome Kelleher | 28 July 2018, 18:10:17 UTC | Fixed issues with historical samples & start_time. | 14 August 2018, 13:38:39 UTC |
| 4fa27d0 | Jerome Kelleher | 28 July 2018, 15:30:57 UTC | Fixed bug in population handling. Also fixed a couple of minor bugs: - TableCollection.__str__ wasn't showing individuals. - Setting NodeTable.individuals nuked the population column. | 14 August 2018, 13:38:39 UTC |
| 04af6b5 | Jerome Kelleher | 28 July 2018, 14:08:15 UTC | Support mutations in from_ts simulate. Also remove support for mutation_generator in simulate, and make sure that we cannot specify mutation rate along with from_ts. | 14 August 2018, 13:38:39 UTC |
| 8ad03e1 | Jerome Kelleher | 28 July 2018, 11:59:06 UTC | Added start_time argument to simulate. | 14 August 2018, 13:38:36 UTC |
| a0561a0 | Jerome Kelleher | 28 July 2018, 10:43:28 UTC | Changed max_time to a hidden unsupported parameters. Implementing and verifying the semantics of max_time precisely and correctly is a little involved, so has been put off to some other time. | 14 August 2018, 13:37:44 UTC |
| 504ad35 | Jerome Kelleher | 22 July 2018, 19:43:45 UTC | Added basic max_time support for simulate. | 14 August 2018, 13:37:44 UTC |
| 97c4bcf | Jerome Kelleher | 22 July 2018, 16:37:02 UTC | Added Python interface to simulate_from. | 14 August 2018, 13:37:44 UTC |
| 0e29200 | Jerome Kelleher | 19 July 2018, 20:35:08 UTC | More C tests for simulate_from. | 14 August 2018, 13:37:42 UTC |
| 94f8461 | Jerome Kelleher | 16 July 2018, 20:12:09 UTC | C implementation of algorithm simulate-from algorithm. Not working for replication yet. | 14 August 2018, 13:36:51 UTC |
| 1f9eef7 | Jerome Kelleher | 16 July 2018, 16:27:04 UTC | Removed unmaintained max_memory from C API. | 14 August 2018, 13:36:50 UTC |
| d0ea154 | Jerome Kelleher | 15 July 2018, 20:21:41 UTC | Python changes for mandatory recomb_map. | 14 August 2018, 13:36:50 UTC |
| 0f6234c | Jerome Kelleher | 14 July 2018, 15:02:27 UTC | recomb_map now mandatory argument for simulator. | 14 August 2018, 13:36:48 UTC |
| f0149ec | Jerome Kelleher | 10 July 2018, 20:05:04 UTC | Python implemtation of simulate_from. | 14 August 2018, 13:34:27 UTC |
| 5c69cff | Jerome Kelleher | 10 July 2018, 17:45:10 UTC | Minimum changes to update algorithms.py for new API. | 14 August 2018, 13:34:26 UTC |
| 385a6bc | Jerome Kelleher | 21 June 2018, 15:55:19 UTC | Some infrastructure for simulate from. | 14 August 2018, 13:34:26 UTC |
| 073a7a3 | Jerome Kelleher | 21 June 2018, 15:33:25 UTC | Made recomb_map a property of the simulator. | 14 August 2018, 13:34:26 UTC |
| 8e35560 | Jerome Kelleher | 21 June 2018, 14:30:25 UTC | Updated low-level module to use tables. | 14 August 2018, 13:34:26 UTC |
| e3d27fa | Jerome Kelleher | 21 June 2018, 14:11:41 UTC | Changed edges to write to tables. | 14 August 2018, 13:34:26 UTC |
| 52af9aa | Jerome Kelleher | 21 June 2018, 13:46:34 UTC | Changed migrations to store into tables. | 14 August 2018, 13:34:26 UTC |
