| becc7b9 | Yan Wong | 09 December 2022, 18:50:12 UTC | Update docs/mutations.md Co-authored-by: Peter Ralph <petrel.harp@gmail.com> | 09 December 2022, 19:02:47 UTC |
| 7fbcdce | Yan Wong | 08 December 2022, 20:36:55 UTC | Clarify "transition matrix" in docs And remove duplicated doc text. Fixes #2140 | 09 December 2022, 19:02:47 UTC |
| 4e479ef | Yan Wong | 06 December 2022, 14:32:06 UTC | Use state_independent in docs Switch a few mentions of parent independence to state independence | 07 December 2022, 04:28:37 UTC |
| a932851 | Gertjan Bisschop | 05 December 2022, 10:55:56 UTC | first pass store unary | 05 December 2022, 17:56:38 UTC |
| 0d06a0f | Ben Jeffery | 05 December 2022, 15:34:09 UTC | Fix doc build | 05 December 2022, 17:46:08 UTC |
| 0cef092 | Yan Wong | 16 November 2022, 11:15:58 UTC | Check for tree seqs without recombination nodes Fixes #2123 | 16 November 2022, 16:25:35 UTC |
| 777a529 | Ben Jeffery | 16 November 2022, 14:58:50 UTC | Fix and update lint | 16 November 2022, 16:02:20 UTC |
| f3d31a5 | Jerome Kelleher | 21 October 2022, 08:10:28 UTC | Merge pull request #2109 from petrelharp/small_fix small docfix | 21 October 2022, 08:10:28 UTC |
| 5e9b5c3 | peter | 28 September 2022, 21:23:10 UTC | small docfix | 20 October 2022, 13:21:39 UTC |
| 83fd84d | andrewkern | 20 October 2022, 05:09:49 UTC | changed default value for min allele length to 1 | 20 October 2022, 08:39:43 UTC |
| 4e10f8b | Jere Koskela | 15 October 2022, 10:52:20 UTC | Check for valid input in ARG likelihood | 18 October 2022, 12:16:15 UTC |
| 360dfec | Ben Jeffery | 15 October 2022, 21:15:25 UTC | Update tskit requirement for Tree.num_children_array | 17 October 2022, 07:19:24 UTC |
| a4c892c | Ben Jeffery | 28 September 2022, 13:48:33 UTC | Add tskit-book-theme to dev requirements | 29 September 2022, 11:27:35 UTC |
| a944c8e | Ben Jeffery | 29 September 2022, 09:53:03 UTC | Add kastore to CI deps | 29 September 2022, 11:08:51 UTC |
| f8aaf83 | Ben Jeffery | 05 August 2022, 20:32:07 UTC | New doc design | 13 September 2022, 12:21:57 UTC |
| e08b94f | Georgia Tsambos | 26 July 2022, 06:35:31 UTC | time travel error message has been updated to mention census events | 26 July 2022, 08:36:38 UTC |
| 4e5672a | Ben Jeffery | 14 July 2022, 22:27:59 UTC | Merge pull request #2090 from benjeffery/logo Use new logo | 14 July 2022, 22:27:59 UTC |
| a93880e | Ben Jeffery | 14 July 2022, 13:53:35 UTC | Use new logo | 14 July 2022, 22:23:07 UTC |
| 0f42d0b | andrewkern | 01 July 2022, 05:09:21 UTC | adding ms2ms.pl script for verification editing ms2ms.pl to play nice added a simple analytical verification of microsats removing ms2ms.pl for now further work on verification figured out scaling | 07 July 2022, 09:10:44 UTC |
| f904d78 | Aaron Ragsdale | 01 July 2022, 05:22:57 UTC | Multiple chromosomes with pedigrees docs | 04 July 2022, 16:41:42 UTC |
| 12bce27 | Jerome Kelleher | 01 July 2022, 08:49:00 UTC | Minor docs cleanup | 01 July 2022, 08:57:26 UTC |
| a22d342 | andrewkern | 28 June 2022, 21:28:21 UTC | clean up of microsatellite documentation and defaults added documentation example; added test coverage had to swap params for a happy codecov jerome's comments included | 01 July 2022, 08:57:26 UTC |
| 4937d88 | Jerome Kelleher | 28 June 2022, 10:24:25 UTC | Merge pull request #2079 from jeromekelleher/tweak-microsats Review interface and documentation. | 28 June 2022, 10:24:25 UTC |
| 787210a | Jerome Kelleher | 27 June 2022, 11:19:54 UTC | Review interface and documentation. Closes #2074 Apply suggestions from code review Co-authored-by: Andrew Kern <adkern@uoregon.edu> | 28 June 2022, 10:00:19 UTC |
| d70abaa | Ben Jeffery | 26 May 2022, 18:37:17 UTC | Update to tskit 1.0.0 | 27 June 2022, 19:32:33 UTC |
| f717961 | andrewkern | 14 June 2022, 06:34:09 UTC | microsat model added implemented generalized model of microsatellite evolution better doi for TPM more microsatellite model stuff and some documentation rescaled things at Peter's suggestion Update docs/mutations.md simple commits from review Co-authored-by: Jerome Kelleher <jk@well.ox.ac.uk> refactored design to include MicrosatMutationModel class Update msprime/mutations.py Co-authored-by: Peter Ralph <petrel.harp@gmail.com> Peter's docstring suggestions included added tests of transition matrix; further clean up to docs one last test added another example to the docs edited CHANGELOG Apply suggestions from code review suggestions from @petrelharp Co-authored-by: Peter Ralph <petrel.harp@gmail.com> further tests and cleanup from code review linting wasn't installed... weird insertion throwing a bug fixed doc bug introduced during code review found bug in rescaling test of betas in trans mat parameterize testing added test of internal allele beta ratios add vscode to gitignore comments from peter tests on tests Apply suggestions from code review Co-authored-by: Peter Ralph <petrel.harp@gmail.com> changed bounds on u to be open interval better doc string on defaults for TPM and EL2 models further doc string edits further doc string edits; part 2 | 24 June 2022, 22:33:22 UTC |
| dafdcfe | peter | 09 June 2022, 19:01:15 UTC | note about census nodes (closes #2065) | 10 June 2022, 14:20:15 UTC |
| c11a2f1 | Ben Jeffery | 19 May 2022, 01:14:36 UTC | Merge pull request #2058 from tskit-dev/test Fix linux wheel building and testing | 19 May 2022, 01:14:36 UTC |
| 8c1b8a6 | Ben Jeffery | 18 May 2022, 23:56:02 UTC | Fix linux wheel building and testing | 19 May 2022, 00:57:42 UTC |
| 8ffb29d | Jerome Kelleher | 18 May 2022, 15:26:59 UTC | Merge pull request #2056 from jeromekelleher/release-1.2 Update Changelog for 1.2.0 | 18 May 2022, 15:26:59 UTC |
| 6385ec3 | Jerome Kelleher | 18 May 2022, 15:06:03 UTC | Update Changelog for 1.2.0 Closes #2040 | 18 May 2022, 15:11:35 UTC |
| 09403d0 | Peter Ralph | 16 May 2022, 23:40:17 UTC | Merge pull request #2054 from petrelharp/hapmap_clarification clarification to read_hapmap docs | 16 May 2022, 23:40:17 UTC |
| 8f60e04 | peter | 16 May 2022, 22:13:30 UTC | clarification to read_hapmap docs | 16 May 2022, 22:16:38 UTC |
| cb6807b | Ben Jeffery | 15 May 2022, 08:21:40 UTC | Merge pull request #2052 from benjeffery/py3.10 Python 3.10 test and wheels | 15 May 2022, 08:21:40 UTC |
| 5a0d8f5 | Ben Jeffery | 15 May 2022, 01:00:26 UTC | Python 3.10 test and wheels | 15 May 2022, 01:00:26 UTC |
| e686efb | peter | 12 April 2022, 13:25:59 UTC | log2 docs fixup | 03 May 2022, 08:54:14 UTC |
| 1296c93 | Graham Gower | 01 May 2022, 09:48:22 UTC | Fix non-MassMigration edge case in from_old_style() Closes #2047. | 03 May 2022, 08:41:56 UTC |
| f4c858b | Ben Jeffery | 22 April 2022, 10:15:51 UTC | Update to use the build module instead of setup.py directly This means that our build dependancies are explicity listed and we don't have to do tricks to get numpy to work. | 22 April 2022, 11:16:09 UTC |
| 4905ea0 | Ben Jeffery | 22 April 2022, 10:15:26 UTC | Fix setuptools_scm not working with a shallow git clone in docker | 22 April 2022, 11:16:09 UTC |
| ef42e6f | Jerome Kelleher | 19 April 2022, 13:54:02 UTC | Merge pull request #2042 from jeromekelleher/final-pedigree-docs Finish pedigrees and demography | 19 April 2022, 13:54:02 UTC |
| 32a2e0b | Jerome Kelleher | 19 April 2022, 11:35:53 UTC | Finish pedigrees and demography Closes #2009 | 19 April 2022, 11:35:53 UTC |
| 4af2ba5 | Jerome Kelleher | 19 April 2022, 09:38:47 UTC | Merge pull request #2039 from jeromekelleher/more-pedigree-docs Complete the pedigree utilities docs | 19 April 2022, 09:38:47 UTC |
| ac86cd5 | Jerome Kelleher | 13 April 2022, 14:26:54 UTC | Complete the pedigree utilities and API docs Closes #2007 Closes #2008 Closes #1919 | 19 April 2022, 09:04:31 UTC |
| b9580e4 | Jerome Kelleher | 13 April 2022, 12:27:32 UTC | Clamp recomb rates to >= 0 in sweep model. Closes #1966 | 19 April 2022, 08:55:44 UTC |
| 246aa67 | Jerome Kelleher | 13 April 2022, 11:31:07 UTC | Merge pull request #2034 from jeromekelleher/change-to-dot Change missing data string to "." in pedigree. | 13 April 2022, 11:31:07 UTC |
| bb3f142 | Jerome Kelleher | 12 April 2022, 14:20:01 UTC | Change missing data string to "." in pedigree. Closes #2032 | 13 April 2022, 11:16:57 UTC |
| a822772 | Jerome Kelleher | 12 April 2022, 15:58:17 UTC | Merge pull request #2036 from jeromekelleher/1.2-infrastructure-updates Small doc and infrastructure updates | 12 April 2022, 15:58:17 UTC |
| af6ceb8 | Jerome Kelleher | 12 April 2022, 14:55:10 UTC | Fix changelog formatting Closes #2006 | 12 April 2022, 14:55:10 UTC |
| fa58df5 | Jerome Kelleher | 12 April 2022, 14:51:20 UTC | Add citation info for msprime 1.0 Closes #2035 | 12 April 2022, 14:51:20 UTC |
| db22545 | Ben Jeffery | 31 March 2022, 22:16:40 UTC | Update pre-commit | 04 April 2022, 08:07:22 UTC |
| cfa2481 | Jerome Kelleher | 04 April 2022, 07:52:31 UTC | Merge pull request #2027 from benjeffery/ci-check Fix tests for Python 3.9.12 | 04 April 2022, 07:52:31 UTC |
| 6ac33c2 | Ben Jeffery | 03 April 2022, 22:34:44 UTC | Fix stdout tests for Python 3.9.12 | 04 April 2022, 01:19:26 UTC |
| 9843e21 | Gregor Gorjanc | 24 February 2022, 22:51:09 UTC | Minor tweaks to Ancestry and Pedigree docs | 25 February 2022, 12:31:36 UTC |
| 0ac31a0 | Jerome Kelleher | 23 February 2022, 20:11:19 UTC | Merge pull request #1925 from jeromekelleher/pedigree-text Some initial work on pedigree text input | 23 February 2022, 20:11:19 UTC |
| 29e8c06 | Jerome Kelleher | 07 January 2022, 17:14:59 UTC | Start on documenting pedigrees | 23 February 2022, 19:57:20 UTC |
| b3bb9e7 | Jerome Kelleher | 07 January 2022, 16:29:58 UTC | Change to parent0, parent1 for mother/father | 23 February 2022, 16:50:30 UTC |
| f722070 | Jerome Kelleher | 06 January 2022, 17:25:34 UTC | Rough working version | 23 February 2022, 16:50:20 UTC |
| 2078a1e | Jerome Kelleher | 06 January 2022, 16:46:24 UTC | Remove parse_fam from pedigrees | 23 February 2022, 16:50:20 UTC |
| 64fa93a | Jerome Kelleher | 21 November 2021, 19:35:40 UTC | Some initial work on pedigree text input | 23 February 2022, 16:50:20 UTC |
| f6fc608 | Jerome Kelleher | 10 February 2022, 13:51:29 UTC | Merge pull request #2005 from jeromekelleher/release-1.1.1 Update changelog for release 1.1.1 | 10 February 2022, 13:51:29 UTC |
| 831e26c | Jerome Kelleher | 10 February 2022, 13:42:44 UTC | Update changelog for release 1.1.1 | 10 February 2022, 13:42:44 UTC |
| 4bf9fbd | chriscrsmith | 07 February 2022, 21:22:07 UTC | msp_gsl_ran_flat() msp_gsl_ran_flat() incorporated comments from Jerome and Kevin incorporated additional edits from Jerome | 10 February 2022, 12:39:06 UTC |
| 1157768 | Jerome Kelleher | 10 February 2022, 12:21:20 UTC | Merge pull request #2004 from jeromekelleher/fix-circle-build Disable multithreaded tests | 10 February 2022, 12:21:20 UTC |
| e25cdd7 | Jerome Kelleher | 10 February 2022, 12:00:16 UTC | Disable multithreaded tests | 10 February 2022, 12:00:16 UTC |
| 0807f6d | peter | 23 January 2022, 15:30:40 UTC | RateMap docs | 25 January 2022, 17:34:35 UTC |
| 45fd7b8 | Jerome Kelleher | 24 January 2022, 12:16:33 UTC | Merge pull request #1992 from tskit-dev/revert-1982-full-arg Revert "Initial pass at single node recombination" | 24 January 2022, 12:16:33 UTC |
| 6496ffe | Jerome Kelleher | 24 January 2022, 10:28:51 UTC | Revert "Initial pass at single node recombination" This reverts commit e949c946bdf3ede80b6e0861ecd84284361ecbb3. | 24 January 2022, 10:28:51 UTC |
| 8d4f14e | Jerome Kelleher | 24 January 2022, 10:28:51 UTC | Revert "Skipping likelihood tests temporarily." This reverts commit 43070306b0d9233c854b264a1b2bdca6b996c26e. | 24 January 2022, 10:28:51 UTC |
| 4307030 | Jerome Kelleher | 19 January 2022, 10:10:55 UTC | Skipping likelihood tests temporarily. | 19 January 2022, 14:26:32 UTC |
| e949c94 | Jere Koskela | 17 January 2022, 13:44:31 UTC | Initial pass at single node recombination | 19 January 2022, 14:26:32 UTC |
| df31bc0 | Jerome Kelleher | 19 January 2022, 14:17:25 UTC | Merge pull request #1983 from jeromekelleher/remove-setuptools_scm-pin Remove ancient pinning | 19 January 2022, 14:17:25 UTC |
| 7c4fe73 | Jerome Kelleher | 19 January 2022, 13:54:42 UTC | Update rtype reference and pin sphinx 4.4 Closes #1988 | 19 January 2022, 14:04:38 UTC |
| eeb3855 | Jerome Kelleher | 19 January 2022, 10:30:53 UTC | Remove ancient pinning | 19 January 2022, 14:04:38 UTC |
| 833945f | molpopgen | 13 January 2022, 15:50:02 UTC | Pin meson | 14 January 2022, 12:15:29 UTC |
| 33bfc76 | Ben Jeffery | 14 January 2022, 12:06:43 UTC | Merge pull request #1980 from benjeffery/fix_mergify Update mergify config | 14 January 2022, 12:06:43 UTC |
| f682615 | Ben Jeffery | 14 January 2022, 11:26:54 UTC | Update mergify config | 14 January 2022, 11:26:54 UTC |
| 39e4d87 | Jerome Kelleher | 06 January 2022, 15:47:40 UTC | Merge pull request #1973 from benjeffery/remove-dependabot Remove dependabot | 06 January 2022, 15:47:40 UTC |
| d28adb2 | Ben Jeffery | 06 January 2022, 15:31:38 UTC | Remove dependabot | 06 January 2022, 15:31:38 UTC |
| ddbc3c0 | Jerome Kelleher | 06 January 2022, 15:19:42 UTC | Merge pull request #1971 from jeromekelleher/backwards-pedigree-sim Add backwards WF simulator for pedigrees | 06 January 2022, 15:19:42 UTC |
| b1b5a2d | Jerome Kelleher | 09 December 2021, 13:48:29 UTC | Add backwards WF simulator for pedigrees | 06 January 2022, 15:11:52 UTC |
| efd2495 | mergify[bot] | 05 January 2022, 16:13:33 UTC | Merge pull request #1769 from molpopgen/fix_multiple_sweeps_example Change multiple sweeps example to use complete sweeps. | 05 January 2022, 16:13:33 UTC |
| d948900 | Jerome Kelleher | 05 January 2022, 16:05:20 UTC | Change hard-coded 1e6 to Ne | 05 January 2022, 16:05:20 UTC |
| 34591ef | molpopgen | 13 July 2021, 18:16:40 UTC | Change start/end frequencies to be a complete sweep in example. | 05 January 2022, 15:59:56 UTC |
| 871af7b | mergify[bot] | 05 January 2022, 12:04:34 UTC | Merge pull request #1970 from jeromekelleher/fix-test-warnings Fix warnings from deprecated tskit API | 05 January 2022, 12:04:34 UTC |
| e0a043a | Jerome Kelleher | 05 January 2022, 11:33:28 UTC | Fix warnings from deprecated tskit API | 05 January 2022, 11:33:28 UTC |
| 83c6b7a | mergify[bot] | 27 December 2021, 22:13:48 UTC | Merge pull request #1968 from tskit-dev/dependabot/pip/requirements/CI-complete/newick-1.3.2 Bump newick from 1.3.1 to 1.3.2 in /requirements/CI-complete | 27 December 2021, 22:13:48 UTC |
| 76c49cb | dependabot[bot] | 27 December 2021, 22:06:40 UTC | Bump newick from 1.3.1 to 1.3.2 in /requirements/CI-complete Bumps [newick](https://github.com/dlce-eva/python-newick) from 1.3.1 to 1.3.2. - [Release notes](https://github.com/dlce-eva/python-newick/releases) - [Changelog](https://github.com/dlce-eva/python-newick/blob/master/CHANGELOG.md) - [Commits](https://github.com/dlce-eva/python-newick/compare/v1.3.1...v1.3.2) --- updated-dependencies: - dependency-name: newick dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 27 December 2021, 22:06:40 UTC |
| ddb25b6 | mergify[bot] | 20 December 2021, 22:25:07 UTC | Merge pull request #1962 from andrewkern/sweep_warn changing this doc string | 20 December 2021, 22:25:07 UTC |
| 7d2baa2 | andrewkern | 15 December 2021, 19:02:32 UTC | changing this doc string | 20 December 2021, 22:16:54 UTC |
| 30678bb | mergify[bot] | 20 December 2021, 22:15:27 UTC | Merge pull request #1963 from tskit-dev/dependabot/pip/requirements/CI-complete/pytest-xdist-2.5.0 Bump pytest-xdist from 2.4.0 to 2.5.0 in /requirements/CI-complete | 20 December 2021, 22:15:27 UTC |
| f8eacd2 | dependabot[bot] | 20 December 2021, 22:07:16 UTC | Bump pytest-xdist from 2.4.0 to 2.5.0 in /requirements/CI-complete Bumps [pytest-xdist](https://github.com/pytest-dev/pytest-xdist) from 2.4.0 to 2.5.0. - [Release notes](https://github.com/pytest-dev/pytest-xdist/releases) - [Changelog](https://github.com/pytest-dev/pytest-xdist/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest-xdist/compare/v2.4.0...v2.5.0) --- updated-dependencies: - dependency-name: pytest-xdist dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> | 20 December 2021, 22:07:16 UTC |
| 066cf53 | mergify[bot] | 15 December 2021, 08:32:51 UTC | Merge pull request #1961 from petrelharp/docfix sim_ancestry not simulate | 15 December 2021, 08:32:51 UTC |
| f9ff373 | peter | 15 December 2021, 05:20:14 UTC | sim_ancestry not simulate | 15 December 2021, 06:20:41 UTC |
| 57ef4ee | Jerome Kelleher | 14 December 2021, 19:12:35 UTC | Merge pull request #1953 from jeromekelleher/time-units-and-refseq Time units and refseq | 14 December 2021, 19:12:35 UTC |
| 74b7018 | Jerome Kelleher | 13 December 2021, 15:35:19 UTC | Error if time_units is uncalibrated in sim_mutations Closes #1877 | 14 December 2021, 19:04:56 UTC |
| 88dcc54 | Jerome Kelleher | 13 December 2021, 15:16:42 UTC | Add tests to verify reference sequence untouched Also check that sim_mutations maintains time_units Closes #1951 | 14 December 2021, 19:04:56 UTC |
| 8f86bb9 | mergify[bot] | 14 December 2021, 14:02:06 UTC | Merge pull request #1958 from tskit-dev/dependabot/pip/requirements/CI-tests-conda/demes-0.2.1 Bump demes from 0.2.0 to 0.2.1 in /requirements/CI-tests-conda | 14 December 2021, 14:02:06 UTC |
| 0812d60 | dependabot[bot] | 13 December 2021, 22:07:20 UTC | Bump demes from 0.2.0 to 0.2.1 in /requirements/CI-tests-conda Bumps [demes](https://github.com/popsim-consortium/demes-python) from 0.2.0 to 0.2.1. - [Release notes](https://github.com/popsim-consortium/demes-python/releases) - [Changelog](https://github.com/popsim-consortium/demes-python/blob/main/CHANGELOG.md) - [Commits](https://github.com/popsim-consortium/demes-python/compare/0.2.0...0.2.1) --- updated-dependencies: - dependency-name: demes dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 14 December 2021, 13:51:47 UTC |
| 28a6484 | mergify[bot] | 13 December 2021, 22:47:34 UTC | Merge pull request #1959 from tskit-dev/dependabot/pip/requirements/CI-tests-pip/scipy-1.7.3 Bump scipy from 1.7.1 to 1.7.3 in /requirements/CI-tests-pip | 13 December 2021, 22:47:34 UTC |
| 2210354 | dependabot[bot] | 13 December 2021, 22:25:23 UTC | Bump scipy from 1.7.1 to 1.7.3 in /requirements/CI-tests-pip Bumps [scipy](https://github.com/scipy/scipy) from 1.7.1 to 1.7.3. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](https://github.com/scipy/scipy/compare/v1.7.1...v1.7.3) --- updated-dependencies: - dependency-name: scipy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 13 December 2021, 22:40:05 UTC |
