| 2b7948e | Jerome Kelleher | 22 February 2019, 11:57:19 UTC | Merge pull request #712 from mcveanlab/0.7.0-final 0.7.0 final | 22 February 2019, 11:57:19 UTC |
| 21812ff | Jerome Kelleher | 22 February 2019, 11:49:20 UTC | Updated changelog for release 0.7.0 | 22 February 2019, 11:49:20 UTC |
| d2c342b | Jerome Kelleher | 22 February 2019, 11:37:56 UTC | Removed problematic type checks. Closes #695 | 22 February 2019, 11:37:56 UTC |
| cafcff8 | Jerome Kelleher | 08 February 2019, 11:04:51 UTC | Merge pull request #707 from tskit-dev/rtd-build-tskit Import tskit on RTD. | 08 February 2019, 11:04:51 UTC |
| 8b20507 | Jerome Kelleher | 08 February 2019, 10:58:52 UTC | Import tskit on RTD. Closes #706 | 08 February 2019, 10:58:52 UTC |
| a0f95e9 | Jerome Kelleher | 08 February 2019, 10:31:55 UTC | Merge pull request #705 from mcveanlab/docs-update Docs update | 08 February 2019, 10:31:55 UTC |
| 2eae5fe | Jerome Kelleher | 08 February 2019, 10:22:48 UTC | Add tskit to autodoc mock imports. Closes #703. | 08 February 2019, 10:23:53 UTC |
| 686ebe0 | Jerome Kelleher | 08 February 2019, 10:18:18 UTC | Added documentation for record_full_arg. Closes #693 | 08 February 2019, 10:23:54 UTC |
| 7f9a83d | Jerome Kelleher | 07 February 2019, 18:51:07 UTC | Merge pull request #700 from andrewkern/master single_sweep model take 3 | 07 February 2019, 18:51:07 UTC |
| 24252c8 | andrewkern | 05 February 2019, 18:49:46 UTC | single_sweep model back to working; minimal case implemented | 07 February 2019, 18:47:22 UTC |
| 0b29022 | Jerome Kelleher | 07 February 2019, 11:36:07 UTC | Merge pull request #702 from mcveanlab/tskit-docs-updates Tskit docs updates | 07 February 2019, 11:36:07 UTC |
| 759b92c | Jerome Kelleher | 07 February 2019, 11:26:36 UTC | Minor docs fixes. | 07 February 2019, 11:27:22 UTC |
| e054c48 | Jerome Kelleher | 07 February 2019, 09:59:13 UTC | Tidied up README. Closes #685. | 07 February 2019, 11:27:22 UTC |
| c39d282 | Jerome Kelleher | 07 February 2019, 11:22:07 UTC | Merge pull request #698 from mcveanlab/tskit-0.99.1 Tskit 0.99.1 | 07 February 2019, 11:22:07 UTC |
| 1590b76 | Jerome Kelleher | 07 February 2019, 11:16:25 UTC | Enable failing test from version mismatch. | 07 February 2019, 11:16:25 UTC |
| d020c8f | Jerome Kelleher | 07 February 2019, 10:28:26 UTC | Remove 32-bit appveyor builds & update config. | 07 February 2019, 11:12:07 UTC |
| fc514cd | Jerome Kelleher | 07 February 2019, 10:13:07 UTC | Added tskit to conda packages. | 07 February 2019, 10:13:07 UTC |
| 578b8c1 | Jerome Kelleher | 05 February 2019, 20:47:16 UTC | Basic changes for tskit C_0.99.1. | 07 February 2019, 10:02:14 UTC |
| 860898d | Jerome Kelleher | 05 February 2019, 20:14:02 UTC | Added soft links for submodule directories | 07 February 2019, 09:47:17 UTC |
| 8896996 | Jerome Kelleher | 05 February 2019, 20:12:52 UTC | Checked out kastore at release 1.0.1. | 07 February 2019, 09:47:06 UTC |
| 4701414 | Jerome Kelleher | 05 February 2019, 20:12:13 UTC | Added kastore submodule. | 07 February 2019, 09:47:06 UTC |
| 483ee5b | Jerome Kelleher | 05 February 2019, 20:11:11 UTC | Moved tskit submodule to new location. | 07 February 2019, 09:47:03 UTC |
| 301fa10 | Jerome Kelleher | 06 February 2019, 13:16:17 UTC | Merge pull request #699 from JereKoskela/full_arg_migration_test Full arg migration test | 06 February 2019, 13:16:17 UTC |
| 0493956 | JereKoskela | 06 February 2019, 12:10:08 UTC | Fixed defrag check for full arg | 06 February 2019, 12:10:08 UTC |
| c62d35f | JereKoskela | 06 February 2019, 12:09:04 UTC | Fixed migration flags | 06 February 2019, 12:09:04 UTC |
| a5b1bc3 | JereKoskela | 06 February 2019, 10:35:40 UTC | Compare full ard and migrations Added a test which compares the stored list of migration events with stored migration edges, and verifies that the two coincide | 06 February 2019, 10:35:40 UTC |
| 5499f02 | JereKoskela | 06 February 2019, 10:33:13 UTC | Fixed labels and defrag for full arg Added a migration label to migration nodes under full arg storage, and fixed an issue where the segment chain wasn't getting defragmented often enough under full arg storage. | 06 February 2019, 10:33:13 UTC |
| c086457 | Jerome Kelleher | 05 February 2019, 10:32:00 UTC | Merge pull request #696 from mcveanlab/fix-tests Minimal changes to fix tests | 05 February 2019, 10:32:00 UTC |
| eb5b2a3 | Jerome Kelleher | 05 February 2019, 10:06:33 UTC | Fixed lint issue from new version of flake8. | 05 February 2019, 10:06:33 UTC |
| a829ce5 | Jerome Kelleher | 05 February 2019, 10:01:26 UTC | Cleanup stray printf. | 05 February 2019, 10:01:26 UTC |
| 77ea0fb | Jerome Kelleher | 05 February 2019, 09:58:42 UTC | Skip problematic test for conflicting C versions. | 05 February 2019, 09:58:42 UTC |
| 0e4c8d8 | Jerome Kelleher | 30 January 2019, 11:39:58 UTC | Merge pull request #665 from JereKoskela/likelihood_evaluation Full ARG recording. | 30 January 2019, 11:39:58 UTC |
| 908c733 | JereKoskela | 30 January 2019, 10:52:56 UTC | Cleaned up print statement Removed a stray printf from msp_merge_ancestors | 30 January 2019, 10:52:56 UTC |
| 42dcd16 | Jerome Kelleher | 29 January 2019, 16:55:45 UTC | Add ARG recording check. | 29 January 2019, 16:55:45 UTC |
| f7fa596 | Jerome Kelleher | 29 January 2019, 16:47:51 UTC | Fixed bug in merge_ancestors. Disabled ARG recording for multiple merger coalescents as there is a problem with 'cancelling' events in this context. It can be done easily enough, but doesn't seem worth doing right now. | 29 January 2019, 16:47:51 UTC |
| ab1d3e0 | Jerome Kelleher | 29 January 2019, 14:40:01 UTC | Simplified arg recording code. | 29 January 2019, 15:49:08 UTC |
| ca6c144 | JereKoskela | 26 January 2019, 12:04:46 UTC | Test coverage for store_full_arg | 26 January 2019, 12:04:46 UTC |
| 7684ea3 | JereKoskela | 26 January 2019, 12:04:13 UTC | Added full_arg support to msp_merge_ancestors | 26 January 2019, 12:04:13 UTC |
| fe63c62 | Jerome Kelleher | 17 January 2019, 20:55:13 UTC | Added flags for CA and RE nodes in the ARG. | 17 January 2019, 21:12:25 UTC |
| 6b4b5c8 | Jerome Kelleher | 17 January 2019, 20:35:50 UTC | Added basic plumbing for record_full_arg. | 17 January 2019, 20:35:50 UTC |
| a93dc3b | Jerome Kelleher | 16 January 2019, 14:20:16 UTC | Merge pull request #688 from mcveanlab/bump-c-coverage Minor tweaks to bump up test coverage. | 16 January 2019, 14:20:16 UTC |
| de2f439 | Jerome Kelleher | 16 January 2019, 13:57:34 UTC | Minor tweaks to bump up test coverage. | 16 January 2019, 13:57:34 UTC |
| 482cde5 | JereKoskela | 16 January 2019, 10:46:13 UTC | Likelihood evaluation implementation in C | 16 January 2019, 13:30:06 UTC |
| 7a8fc28 | JereKoskela | 21 December 2018, 10:33:18 UTC | While loop cosmetics Shortened some while loops in store_edges_left and store_edges_right, and tidied whitespace. | 16 January 2019, 13:11:42 UTC |
| e2f8818 | JereKoskela | 20 December 2018, 20:12:24 UTC | Add files via upload Fixed issue where nodes with multiple segments caused missing edges in the ARG. | 16 January 2019, 13:11:42 UTC |
| 9ee48cc | Jerome Kelleher | 20 December 2018, 17:35:57 UTC | Added command line arg for full-arg. | 16 January 2019, 13:11:42 UTC |
| 61e8676 | JereKoskela | 20 December 2018, 16:09:17 UTC | Polished full ARG output | 16 January 2019, 13:11:42 UTC |
| 6812a99 | JereKoskela | 19 December 2018, 17:54:28 UTC | Added basic support for outputting full args | 16 January 2019, 13:11:42 UTC |
| 43d7c1e | Jerome Kelleher | 16 January 2019, 12:51:44 UTC | Merge pull request #687 from mcveanlab/meson-initial Meson initial | 16 January 2019, 12:51:44 UTC |
| b65d9c8 | Jerome Kelleher | 16 January 2019, 12:29:40 UTC | Updated dev docs to use meson. | 16 January 2019, 12:40:06 UTC |
| 95fa342 | Jerome Kelleher | 16 January 2019, 11:31:14 UTC | Run gcov within build directory. | 16 January 2019, 11:56:58 UTC |
| 8fdfc31 | Jerome Kelleher | 14 January 2019, 17:26:36 UTC | Update circle config to use meson. | 14 January 2019, 17:29:18 UTC |
| 86497ba | Jerome Kelleher | 14 January 2019, 17:11:58 UTC | Change to meson.build for lib development. | 14 January 2019, 17:11:58 UTC |
| b8d7d14 | Jerome Kelleher | 14 January 2019, 15:44:32 UTC | Merge pull request #686 from mcveanlab/release-0.7.0a1 Update changelog for 0.7.0a1 release. | 14 January 2019, 15:44:32 UTC |
| 458708f | Jerome Kelleher | 14 January 2019, 15:14:49 UTC | Update changelog for 0.7.0a1 release. | 14 January 2019, 15:16:38 UTC |
| 9a259ba | Jerome Kelleher | 14 January 2019, 15:03:42 UTC | Merge pull request #683 from mcveanlab/tskit-updates Tskit updates | 14 January 2019, 15:03:42 UTC |
| 30e9d48 | Jerome Kelleher | 14 January 2019, 14:39:06 UTC | Trimmed back requirements. Closes #681. | 14 January 2019, 14:53:28 UTC |
| d0d97f4 | Jerome Kelleher | 14 January 2019, 14:38:41 UTC | Added Py37 and dropped Py33 from metadata. | 14 January 2019, 14:42:12 UTC |
| 403a786 | Jerome Kelleher | 14 January 2019, 14:06:02 UTC | Update PyPI page. | 14 January 2019, 14:42:08 UTC |
| ece4140 | Jerome Kelleher | 14 January 2019, 14:04:47 UTC | Removed unnecessary files from dist. | 14 January 2019, 14:04:47 UTC |
| af624da | Jerome Kelleher | 14 January 2019, 13:31:52 UTC | Update CI configurations. | 14 January 2019, 13:33:24 UTC |
| 48e9e08 | Jerome Kelleher | 14 January 2019, 13:28:17 UTC | Completed pass through docs. | 14 January 2019, 13:28:17 UTC |
| e36a352 | Jerome Kelleher | 14 January 2019, 13:15:57 UTC | Updated API docs to point to tskit. | 14 January 2019, 13:15:57 UTC |
| 10fb2cd | Jerome Kelleher | 14 January 2019, 12:26:28 UTC | Rejigged structure to remove tskit bits. | 14 January 2019, 12:26:28 UTC |
| 8bf4acd | Jerome Kelleher | 14 January 2019, 11:47:21 UTC | Removed some redundant files. | 14 January 2019, 11:47:21 UTC |
| 7b5a533 | Jerome Kelleher | 14 January 2019, 11:45:18 UTC | Cleaned up stress_lowlevel. | 14 January 2019, 11:45:18 UTC |
| 5e7f1e7 | Jerome Kelleher | 14 January 2019, 11:37:32 UTC | Update to tskit C 0.99.0. | 14 January 2019, 11:37:32 UTC |
| e3bb30b | Jerome Kelleher | 10 January 2019, 15:39:22 UTC | Merge pull request #680 from mcveanlab/remote-tskit Remove tskit | 10 January 2019, 15:39:22 UTC |
| 050f3f8 | Jerome Kelleher | 10 January 2019, 14:38:44 UTC | Updated build to remove tskit. Update CI setup temporarily to use pre-release tskit package. | 10 January 2019, 15:26:48 UTC |
| 03b891d | Jerome Kelleher | 10 January 2019, 14:29:10 UTC | Fixed up C code to compile. | 10 January 2019, 14:29:10 UTC |
| edbc596 | Jerome Kelleher | 10 January 2019, 14:13:55 UTC | Removed kastore submodule. | 10 January 2019, 14:13:55 UTC |
| 7c0c9e9 | Jerome Kelleher | 10 January 2019, 14:11:20 UTC | Removal of most tskit files. | 10 January 2019, 14:11:20 UTC |
| 2992140 | Jerome Kelleher | 10 January 2019, 12:09:05 UTC | Merge pull request #679 from mcveanlab/provenance-tskit Fixup provenance handling. | 10 January 2019, 12:09:05 UTC |
| e7fa6b9 | Jerome Kelleher | 10 January 2019, 11:55:18 UTC | Fixup provenance handling. Closes #667. | 10 January 2019, 11:55:18 UTC |
| 70e16a8 | Jerome Kelleher | 09 January 2019, 19:54:18 UTC | Merge pull request #677 from jgallowa07/doc-fix Doc Fix for SparseTree.num_nodes | 09 January 2019, 19:54:18 UTC |
| 20e9b0e | jgallowa07 | 08 January 2019, 18:57:37 UTC | Doc Fix for SparseTree.num_nodes | 09 January 2019, 19:40:19 UTC |
| d904f6b | Jerome Kelleher | 09 January 2019, 19:30:33 UTC | Merge pull request #676 from mcveanlab/tskit-final-c-api Tskit final c api | 09 January 2019, 19:30:33 UTC |
| 8fe16cb | Jerome Kelleher | 09 January 2019, 17:40:28 UTC | Fix line lengths. | 09 January 2019, 17:40:28 UTC |
| 73c0e99 | Jerome Kelleher | 09 January 2019, 17:32:08 UTC | Disable py36 on Appveyor due to upstream error. See github.com/tskit-dev/msprime/issues/678 | 09 January 2019, 17:34:22 UTC |
| 4d20e93 | Jerome Kelleher | 09 January 2019, 15:01:19 UTC | Removed dynamic kastore linkage. | 09 January 2019, 17:34:22 UTC |
| 8364cb2 | Jerome Kelleher | 09 January 2019, 14:53:13 UTC | Changed treeseq_load_tables to treeseq_alloc in C. Also change dump_tables to copy_tables. | 09 January 2019, 17:34:22 UTC |
| 2a61de1 | Jerome Kelleher | 09 January 2019, 13:54:03 UTC | Changed NULL_X to tskit.NULL in Python. | 09 January 2019, 17:34:22 UTC |
| e2f4a6f | Jerome Kelleher | 09 January 2019, 12:12:50 UTC | Changed to TSK_NULL in the C code. | 09 January 2019, 17:34:22 UTC |
| 9c95343 | Jerome Kelleher | 09 January 2019, 12:03:44 UTC | Clean up msprime C headers. | 09 January 2019, 17:34:22 UTC |
| 6af9f72 | Jerome Kelleher | 09 January 2019, 11:35:05 UTC | Rename SparseTree to Tree. | 09 January 2019, 17:34:22 UTC |
| fcb62fe | Jerome Kelleher | 09 January 2019, 11:24:12 UTC | Removed TSK_ALLOC_TABLES flag. | 09 January 2019, 17:34:22 UTC |
| 3c3e0d9 | Jerome Kelleher | 08 January 2019, 16:57:53 UTC | Automatic alloc for tsk_tbl_collection_load. | 09 January 2019, 17:34:22 UTC |
| 1e02a55 | Jerome Kelleher | 08 January 2019, 14:44:36 UTC | Remove increment sizes from x_tbl_alloc. Also remove redundant aspects of C API. | 09 January 2019, 17:34:22 UTC |
| 3b9bf10 | Peter Ralph | 09 January 2019, 17:03:07 UTC | Merge pull request #675 from petrelharp/ancestry_docs document mean_descendants | 09 January 2019, 17:03:07 UTC |
| d602302 | peter | 09 January 2019, 16:59:39 UTC | document mean descendants | 09 January 2019, 16:59:39 UTC |
| 7099578 | Jerome Kelleher | 08 January 2019, 14:44:22 UTC | Merge pull request #674 from mcveanlab/error-codes Update error codes for tskit. | 08 January 2019, 14:44:22 UTC |
| e595e75 | Jerome Kelleher | 08 January 2019, 13:30:58 UTC | Defined tskit exception hierarchy. | 08 January 2019, 14:17:18 UTC |
| 08b4d5e | Jerome Kelleher | 08 January 2019, 12:08:47 UTC | Mulitplex tskit errors in msprime. | 08 January 2019, 12:54:52 UTC |
| 68bbad2 | Jerome Kelleher | 08 January 2019, 10:58:14 UTC | Removed tskit errors from msprime. | 08 January 2019, 10:58:14 UTC |
| 59f2756 | Jerome Kelleher | 21 December 2018, 17:40:32 UTC | Update error codes for tskit. | 08 January 2019, 10:38:11 UTC |
| 1402eff | Jerome Kelleher | 21 December 2018, 15:13:30 UTC | Merge pull request #659 from mcveanlab/tables_from_dict Using dictionaries of arrays as the long-term interchange format. | 21 December 2018, 15:13:30 UTC |
| 2d21b44 | Jerome Kelleher | 14 December 2018, 15:33:54 UTC | Changed interchange to dict encoding of TableCollection. Also separated out tskit and msprime tests more fully. | 20 December 2018, 20:34:43 UTC |
| 844dfe1 | Jerome Kelleher | 13 December 2018, 10:49:57 UTC | Merge pull request #648 from mcveanlab/tskit-ll-module Split up low-level C modules for msprime and tskit | 13 December 2018, 10:49:57 UTC |
| 4c17c93 | Jerome Kelleher | 11 December 2018, 16:16:14 UTC | Split Python code and tests between tskit and msprime. | 13 December 2018, 10:20:32 UTC |
| 802d07c | Jerome Kelleher | 07 December 2018, 16:33:08 UTC | Partial separation of low-level msprime & tskit modules. | 13 December 2018, 10:16:30 UTC |
