| 5860d93 | mergify[bot] | 12 November 2021, 18:08:17 UTC | Merge pull request #1912 from jeromekelleher/v1.0.3-final-updates Update changelog for release | 12 November 2021, 18:08:17 UTC |
| c559464 | Jerome Kelleher | 12 November 2021, 17:42:31 UTC | Update changelog for release | 12 November 2021, 17:57:33 UTC |
| 5c58c87 | Jerome Kelleher | 12 November 2021, 17:38:04 UTC | Merge pull request #1909 from jeromekelleher/cache-pop-table-v2 Improve performance in the lots-of-simulations case | 12 November 2021, 17:38:04 UTC |
| d838347 | Jerome Kelleher | 12 November 2021, 15:41:49 UTC | Improve performance in the lots-of-simulations case | 12 November 2021, 16:11:35 UTC |
| 2dbf702 | Jerome Kelleher | 12 November 2021, 12:40:52 UTC | Merge pull request #1904 from jeromekelleher/remove-provenance-parameter-fanciness Do not use inspect to generate provenance. | 12 November 2021, 12:40:52 UTC |
| 561266a | Jerome Kelleher | 11 November 2021, 19:51:32 UTC | Do not use inspect to generate provenance. Closes #1899 | 12 November 2021, 12:14:57 UTC |
| 813f6c5 | mergify[bot] | 12 November 2021, 08:40:23 UTC | Merge pull request #1906 from petrelharp/print_rates g not f, closes #1905 | 12 November 2021, 08:40:23 UTC |
| cb0ab60 | peter | 12 November 2021, 05:38:27 UTC | g not f, closes #1905 | 12 November 2021, 08:29:58 UTC |
| cdc5d99 | mergify[bot] | 12 November 2021, 08:28:01 UTC | Merge pull request #1907 from petrelharp/updatelink Update intersphinx for stdpopsim | 12 November 2021, 08:28:01 UTC |
| e9e39d4 | peter | 12 November 2021, 06:08:27 UTC | update stdpopsim rtd link | 12 November 2021, 06:13:10 UTC |
| 4897722 | Jerome Kelleher | 10 November 2021, 10:42:52 UTC | Merge pull request #1895 from jeromekelleher/fix-full-arg-simplify Fix bug in full_arg with missing genome | 10 November 2021, 10:42:52 UTC |
| b95b9b0 | Jerome Kelleher | 09 November 2021, 12:23:31 UTC | Fix bug in full_arg with missing genome Closes #1893 | 09 November 2021, 12:26:15 UTC |
| f47a4ab | mergify[bot] | 09 November 2021, 11:52:39 UTC | Merge pull request #1894 from hyanwong/time-scale-svg Change tree_height_scale to time_scale in docs | 09 November 2021, 11:52:39 UTC |
| 433fa0a | Yan Wong | 09 November 2021, 11:07:13 UTC | Change tree_height_scale to time_scale in docs Fixes #1859 | 09 November 2021, 11:11:20 UTC |
| 6b772c2 | mergify[bot] | 08 November 2021, 22:28:06 UTC | Merge pull request #1892 from tskit-dev/dependabot/pip/requirements/CI-tests-pip/hypothesis-6.24.2 Bump hypothesis from 6.24.0 to 6.24.2 in /requirements/CI-tests-pip | 08 November 2021, 22:28:06 UTC |
| d809669 | dependabot[bot] | 08 November 2021, 22:06:50 UTC | Bump hypothesis from 6.24.0 to 6.24.2 in /requirements/CI-tests-pip Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.24.0 to 6.24.2. - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.24.0...hypothesis-python-6.24.2) --- updated-dependencies: - dependency-name: hypothesis dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 08 November 2021, 22:19:59 UTC |
| ad52a10 | mergify[bot] | 08 November 2021, 22:16:01 UTC | Merge pull request #1891 from tskit-dev/dependabot/pip/requirements/CI-complete/pytest-xdist-2.4.0 Bump pytest-xdist from 2.3.0 to 2.4.0 in /requirements/CI-complete | 08 November 2021, 22:16:01 UTC |
| 9fbd9a1 | dependabot[bot] | 08 November 2021, 22:06:46 UTC | Bump pytest-xdist from 2.3.0 to 2.4.0 in /requirements/CI-complete Bumps [pytest-xdist](https://github.com/pytest-dev/pytest-xdist) from 2.3.0 to 2.4.0. - [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/v2.3.0...v2.4.0) --- updated-dependencies: - dependency-name: pytest-xdist dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> | 08 November 2021, 22:06:46 UTC |
| e00bb39 | mergify[bot] | 01 November 2021, 22:23:48 UTC | Merge pull request #1884 from tskit-dev/dependabot/pip/requirements/CI-complete/numpy-1.21.3 Bump numpy from 1.21.2 to 1.21.3 in /requirements/CI-complete | 01 November 2021, 22:23:48 UTC |
| 6e5dc75 | dependabot[bot] | 01 November 2021, 22:06:16 UTC | Bump numpy from 1.21.2 to 1.21.3 in /requirements/CI-complete Bumps [numpy](https://github.com/numpy/numpy) from 1.21.2 to 1.21.3. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/HOWTO_RELEASE.rst.txt) - [Commits](https://github.com/numpy/numpy/compare/v1.21.2...v1.21.3) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 01 November 2021, 22:15:20 UTC |
| 8a76e10 | mergify[bot] | 01 November 2021, 22:12:28 UTC | Merge pull request #1883 from tskit-dev/dependabot/pip/requirements/CI-tests-pip/numpy-1.21.3 Bump numpy from 1.21.2 to 1.21.3 in /requirements/CI-tests-pip | 01 November 2021, 22:12:28 UTC |
| 7453f20 | dependabot[bot] | 01 November 2021, 22:06:00 UTC | Bump numpy from 1.21.2 to 1.21.3 in /requirements/CI-tests-pip Bumps [numpy](https://github.com/numpy/numpy) from 1.21.2 to 1.21.3. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/HOWTO_RELEASE.rst.txt) - [Commits](https://github.com/numpy/numpy/compare/v1.21.2...v1.21.3) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 01 November 2021, 22:06:00 UTC |
| 4536bcd | mergify[bot] | 25 October 2021, 22:26:29 UTC | Merge pull request #1880 from tskit-dev/dependabot/pip/requirements/CI-tests-pip/hypothesis-6.24.0 Bump hypothesis from 6.23.2 to 6.24.0 in /requirements/CI-tests-pip | 25 October 2021, 22:26:29 UTC |
| 3372c78 | dependabot[bot] | 25 October 2021, 22:06:15 UTC | Bump hypothesis from 6.23.2 to 6.24.0 in /requirements/CI-tests-pip Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.23.2 to 6.24.0. - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.23.2...hypothesis-python-6.24.0) --- updated-dependencies: - dependency-name: hypothesis dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> | 25 October 2021, 22:16:31 UTC |
| d8e6232 | mergify[bot] | 25 October 2021, 22:16:23 UTC | Merge pull request #1881 from tskit-dev/dependabot/pip/requirements/CI-complete/pytest-6.2.5 Bump pytest from 6.2.4 to 6.2.5 in /requirements/CI-complete | 25 October 2021, 22:16:23 UTC |
| 34f59c2 | dependabot[bot] | 25 October 2021, 22:06:23 UTC | Bump pytest from 6.2.4 to 6.2.5 in /requirements/CI-complete Bumps [pytest](https://github.com/pytest-dev/pytest) from 6.2.4 to 6.2.5. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/6.2.4...6.2.5) --- updated-dependencies: - dependency-name: pytest dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 25 October 2021, 22:06:23 UTC |
| 36139f2 | mergify[bot] | 18 October 2021, 22:23:20 UTC | Merge pull request #1874 from tskit-dev/dependabot/pip/requirements/CI-tests-pip/jsonschema-lt-5.0 Update jsonschema requirement from <4.0 to <5.0 in /requirements/CI-tests-pip | 18 October 2021, 22:23:20 UTC |
| bd114c1 | dependabot[bot] | 18 October 2021, 22:06:58 UTC | Update jsonschema requirement in /requirements/CI-tests-pip Updates the requirements on [jsonschema](https://github.com/Julian/jsonschema) to permit the latest version. - [Release notes](https://github.com/Julian/jsonschema/releases) - [Changelog](https://github.com/Julian/jsonschema/blob/main/CHANGELOG.rst) - [Commits](https://github.com/Julian/jsonschema/compare/v0.1...v4.1.0) --- updated-dependencies: - dependency-name: jsonschema dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> | 18 October 2021, 22:16:49 UTC |
| e319213 | mergify[bot] | 18 October 2021, 22:14:24 UTC | Merge pull request #1872 from tskit-dev/dependabot/pip/requirements/CI-docs/newick-1.3.1 Bump newick from 1.3.0 to 1.3.1 in /requirements/CI-docs | 18 October 2021, 22:14:24 UTC |
| 1547a0b | dependabot[bot] | 18 October 2021, 22:06:47 UTC | Bump newick from 1.3.0 to 1.3.1 in /requirements/CI-docs Bumps [newick](https://github.com/dlce-eva/python-newick) from 1.3.0 to 1.3.1. - [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/v1.3.0...v1.3.1) --- updated-dependencies: - dependency-name: newick dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 18 October 2021, 22:06:47 UTC |
| abf6d0e | mergify[bot] | 11 October 2021, 22:39:06 UTC | Merge pull request #1871 from tskit-dev/dependabot/pip/requirements/CI-complete/hypothesis-6.23.2 Bump hypothesis from 6.23.0 to 6.23.2 in /requirements/CI-complete | 11 October 2021, 22:39:06 UTC |
| f3c9f5c | dependabot[bot] | 11 October 2021, 22:31:51 UTC | Bump hypothesis from 6.23.0 to 6.23.2 in /requirements/CI-complete Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.23.0 to 6.23.2. - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.23.0...hypothesis-python-6.23.2) --- updated-dependencies: - dependency-name: hypothesis dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 11 October 2021, 22:31:51 UTC |
| 9119c0a | mergify[bot] | 11 October 2021, 22:31:27 UTC | Merge pull request #1852 from tskit-dev/dependabot/pip/requirements/CI-complete/pytest-cov-3.0.0 Bump pytest-cov from 2.12.1 to 3.0.0 in /requirements/CI-complete | 11 October 2021, 22:31:27 UTC |
| a0599ff | dependabot[bot] | 11 October 2021, 22:07:54 UTC | Bump pytest-cov from 2.12.1 to 3.0.0 in /requirements/CI-complete Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 2.12.1 to 3.0.0. - [Release notes](https://github.com/pytest-dev/pytest-cov/releases) - [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest-cov/compare/v2.12.1...v3.0.0) --- updated-dependencies: - dependency-name: pytest-cov dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> | 11 October 2021, 22:19:34 UTC |
| 85b828a | mergify[bot] | 11 October 2021, 22:18:28 UTC | Merge pull request #1870 from tskit-dev/dependabot/pip/requirements/CI-tests-pip/hypothesis-6.23.2 Bump hypothesis from 6.17.3 to 6.23.2 in /requirements/CI-tests-pip | 11 October 2021, 22:18:28 UTC |
| 1ddcb47 | dependabot[bot] | 11 October 2021, 22:08:04 UTC | Bump hypothesis from 6.17.3 to 6.23.2 in /requirements/CI-tests-pip Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.17.3 to 6.23.2. - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.17.3...hypothesis-python-6.23.2) --- updated-dependencies: - dependency-name: hypothesis dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> | 11 October 2021, 22:08:04 UTC |
| 9b92701 | Jerome Kelleher | 07 October 2021, 18:57:13 UTC | Merge pull request #1858 from jeromekelleher/validate-ped-sim Validate ped sim | 07 October 2021, 18:57:13 UTC |
| 449a5f8 | Jerome Kelleher | 06 October 2021, 10:58:57 UTC | Initial verification checks for wf_ped | 07 October 2021, 18:47:12 UTC |
| 6a17b6f | mergify[bot] | 07 October 2021, 10:00:27 UTC | Merge pull request #1861 from jeromekelleher/pin-jsonschema Pin to jsonschema<4 to workaround breakage | 07 October 2021, 10:00:27 UTC |
| ee85431 | Jerome Kelleher | 06 October 2021, 15:58:54 UTC | Pin to jsonschema<4 to workaround breakage Closes #1860 | 07 October 2021, 09:01:13 UTC |
| ef31dd1 | Jerome Kelleher | 06 October 2021, 09:11:16 UTC | Merge pull request #1846 from jeromekelleher/more-pedigrees Refactor and simplify simulation through pedigrees | 06 October 2021, 09:11:16 UTC |
| 8704c45 | Jerome Kelleher | 20 September 2021, 11:18:30 UTC | Low-level changes for production pedigree sims Closes #1843 Closes #1089 Closes #1575 | 06 October 2021, 08:50:30 UTC |
| 41369c8 | mergify[bot] | 29 September 2021, 11:05:15 UTC | Merge pull request #1850 from tskit-dev/dependabot/pip/requirements/CI-tests-pip/pytest-xdist-2.4.0 Bump pytest-xdist from 2.3.0 to 2.4.0 in /requirements/CI-tests-pip | 29 September 2021, 11:05:15 UTC |
| c7b9496 | dependabot[bot] | 27 September 2021, 22:16:25 UTC | Bump pytest-xdist from 2.3.0 to 2.4.0 in /requirements/CI-tests-pip Bumps [pytest-xdist](https://github.com/pytest-dev/pytest-xdist) from 2.3.0 to 2.4.0. - [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/v2.3.0...v2.4.0) --- updated-dependencies: - dependency-name: pytest-xdist dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> | 29 September 2021, 10:51:27 UTC |
| 65c01a3 | mergify[bot] | 27 September 2021, 22:23:48 UTC | Merge pull request #1849 from tskit-dev/dependabot/pip/requirements/CI-complete/hypothesis-6.23.0 Bump hypothesis from 6.21.1 to 6.23.0 in /requirements/CI-complete | 27 September 2021, 22:23:48 UTC |
| 4d4f04c | dependabot[bot] | 27 September 2021, 22:15:48 UTC | Bump hypothesis from 6.21.1 to 6.23.0 in /requirements/CI-complete Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.21.1 to 6.23.0. - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.21.1...hypothesis-python-6.23.0) --- updated-dependencies: - dependency-name: hypothesis dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> | 27 September 2021, 22:15:48 UTC |
| 11b8dde | mergify[bot] | 20 September 2021, 22:30:07 UTC | Merge pull request #1847 from tskit-dev/dependabot/pip/requirements/CI-tests-pip/pytest-6.2.5 Bump pytest from 6.2.4 to 6.2.5 in /requirements/CI-tests-pip | 20 September 2021, 22:30:07 UTC |
| 60f4e93 | dependabot[bot] | 20 September 2021, 22:07:14 UTC | Bump pytest from 6.2.4 to 6.2.5 in /requirements/CI-tests-pip Bumps [pytest](https://github.com/pytest-dev/pytest) from 6.2.4 to 6.2.5. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/6.2.4...6.2.5) --- updated-dependencies: - dependency-name: pytest dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 20 September 2021, 22:16:45 UTC |
| fb8e90c | mergify[bot] | 20 September 2021, 22:16:37 UTC | Merge pull request #1848 from tskit-dev/dependabot/pip/requirements/CI-complete/pytest-xdist-2.3.0 Bump pytest-xdist from 2.2.1 to 2.3.0 in /requirements/CI-complete | 20 September 2021, 22:16:37 UTC |
| 96e42e4 | dependabot[bot] | 20 September 2021, 22:07:14 UTC | Bump pytest-xdist from 2.2.1 to 2.3.0 in /requirements/CI-complete Bumps [pytest-xdist](https://github.com/pytest-dev/pytest-xdist) from 2.2.1 to 2.3.0. - [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/v2.2.1...v2.3.0) --- 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 September 2021, 22:07:14 UTC |
| 5f7ed09 | mergify[bot] | 20 September 2021, 09:20:11 UTC | Merge pull request #1819 from nikbaya/pedigree-tests Added tests for simulating through pedigrees | 20 September 2021, 09:20:11 UTC |
| c0e85a4 | Jerome Kelleher | 20 September 2021, 09:06:11 UTC | Bump circleCI cache key | 20 September 2021, 09:06:11 UTC |
| 3de41e3 | Jerome Kelleher | 19 September 2021, 14:11:13 UTC | Skip problematic tests and cleanup | 19 September 2021, 18:59:13 UTC |
| cdd70e3 | Nik Baya | 25 August 2021, 09:21:20 UTC | Added tests for simulating through pedigrees Added test_unrelated Increased num_generations for test_deep Added new assert to check number of nodes is unchanged after simulating through pedigree Added more pedigree tests Added tests for: - Parents with mixed "generations" - Inbreeding siblings - Half-sibs - Inbreeding half-sibs - Oedipus (offspring and their parent being parents) Added pedigree tests from algorithms.py Fixes error of extra nodes being added to pedigree Cleaned up print statements used for debugging Skipped tests that fail due to trying to add an edge between nodes with the same time Removed print statements from debugging | 19 September 2021, 18:59:13 UTC |
| 5a990dd | Jerome Kelleher | 19 September 2021, 18:55:59 UTC | Merge pull request #1844 from jeromekelleher/check-circle Remove system pip. | 19 September 2021, 18:55:59 UTC |
| 8f280a5 | Jerome Kelleher | 19 September 2021, 18:32:26 UTC | Remove system pip. | 19 September 2021, 18:32:26 UTC |
| abe6116 | mergify[bot] | 15 September 2021, 14:02:12 UTC | Merge pull request #1841 from benjeffery/update_circle Update circle CI image | 15 September 2021, 14:02:12 UTC |
| 6a9c603 | Ben Jeffery | 15 September 2021, 10:10:12 UTC | Update circle CI image | 15 September 2021, 10:57:02 UTC |
| 8d394c2 | mergify[bot] | 14 September 2021, 13:59:48 UTC | Merge pull request #1837 from tskit-dev/dependabot/pip/requirements/CI-docs/daiquiri-3.0.1 Bump daiquiri from 3.0.0 to 3.0.1 in /requirements/CI-docs | 14 September 2021, 13:59:48 UTC |
| 9f1b3a9 | dependabot[bot] | 13 September 2021, 22:07:11 UTC | Bump daiquiri from 3.0.0 to 3.0.1 in /requirements/CI-docs Bumps [daiquiri](https://github.com/jd/daiquiri) from 3.0.0 to 3.0.1. - [Release notes](https://github.com/jd/daiquiri/releases) - [Commits](https://github.com/jd/daiquiri/compare/3.0.0...3.0.1) --- updated-dependencies: - dependency-name: daiquiri dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 14 September 2021, 13:34:29 UTC |
| 2060a4a | mergify[bot] | 14 September 2021, 13:34:19 UTC | Merge pull request #1836 from tskit-dev/dependabot/pip/requirements/CI-complete/hypothesis-6.21.1 Bump hypothesis from 6.17.3 to 6.21.1 in /requirements/CI-complete | 14 September 2021, 13:34:19 UTC |
| e3c2a82 | dependabot[bot] | 13 September 2021, 22:07:08 UTC | Bump hypothesis from 6.17.3 to 6.21.1 in /requirements/CI-complete Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.17.3 to 6.21.1. - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.17.3...hypothesis-python-6.21.1) --- updated-dependencies: - dependency-name: hypothesis dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> | 14 September 2021, 13:14:06 UTC |
| fa78042 | mergify[bot] | 13 September 2021, 22:18:04 UTC | Merge pull request #1838 from tskit-dev/dependabot/pip/requirements/CI-tests-pip/numpy-1.21.2 Bump numpy from 1.21.0 to 1.21.2 in /requirements/CI-tests-pip | 13 September 2021, 22:18:04 UTC |
| df711af | dependabot[bot] | 13 September 2021, 22:07:12 UTC | Bump numpy from 1.21.0 to 1.21.2 in /requirements/CI-tests-pip Bumps [numpy](https://github.com/numpy/numpy) from 1.21.0 to 1.21.2. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/HOWTO_RELEASE.rst.txt) - [Commits](https://github.com/numpy/numpy/compare/v1.21.0...v1.21.2) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 13 September 2021, 22:07:12 UTC |
| fda727e | mergify[bot] | 07 September 2021, 10:19:34 UTC | Merge pull request #1832 from tskit-dev/dependabot/pip/requirements/CI-complete/daiquiri-3.0.1 Bump daiquiri from 3.0.0 to 3.0.1 in /requirements/CI-complete | 07 September 2021, 10:19:34 UTC |
| cd38354 | dependabot[bot] | 06 September 2021, 22:06:16 UTC | Bump daiquiri from 3.0.0 to 3.0.1 in /requirements/CI-complete Bumps [daiquiri](https://github.com/jd/daiquiri) from 3.0.0 to 3.0.1. - [Release notes](https://github.com/jd/daiquiri/releases) - [Commits](https://github.com/jd/daiquiri/compare/3.0.0...3.0.1) --- updated-dependencies: - dependency-name: daiquiri dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 07 September 2021, 10:12:41 UTC |
| 37bd48d | Jerome Kelleher | 07 September 2021, 07:50:01 UTC | Merge pull request #1829 from jeromekelleher/c-api-0.99.14 C api 0.99.14 | 07 September 2021, 07:50:01 UTC |
| 609d46c | mergify[bot] | 06 September 2021, 22:20:30 UTC | Merge pull request #1831 from tskit-dev/dependabot/pip/requirements/CI-tests-pip/daiquiri-3.0.1 Bump daiquiri from 3.0.0 to 3.0.1 in /requirements/CI-tests-pip | 06 September 2021, 22:20:30 UTC |
| 1cd60cc | dependabot[bot] | 06 September 2021, 22:06:15 UTC | Bump daiquiri from 3.0.0 to 3.0.1 in /requirements/CI-tests-pip Bumps [daiquiri](https://github.com/jd/daiquiri) from 3.0.0 to 3.0.1. - [Release notes](https://github.com/jd/daiquiri/releases) - [Commits](https://github.com/jd/daiquiri/compare/3.0.0...3.0.1) --- updated-dependencies: - dependency-name: daiquiri dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 06 September 2021, 22:14:05 UTC |
| ed6a1ac | mergify[bot] | 06 September 2021, 22:12:59 UTC | Merge pull request #1830 from tskit-dev/dependabot/pip/requirements/CI-docs/sphinx-argparse-0.3.1 Bump sphinx-argparse from 0.2.5 to 0.3.1 in /requirements/CI-docs | 06 September 2021, 22:12:59 UTC |
| f5e110b | dependabot[bot] | 06 September 2021, 22:06:10 UTC | Bump sphinx-argparse from 0.2.5 to 0.3.1 in /requirements/CI-docs Bumps [sphinx-argparse]() from 0.2.5 to 0.3.1. --- updated-dependencies: - dependency-name: sphinx-argparse dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> | 06 September 2021, 22:06:10 UTC |
| 0cc7c4b | Jerome Kelleher | 06 September 2021, 18:40:15 UTC | Fix compiler warnings with 64 bit tsk_size_t | 06 September 2021, 18:40:15 UTC |
| c576ffa | Jerome Kelleher | 06 September 2021, 18:29:37 UTC | Update to tskit C 0.99.14 Closes #1828 | 06 September 2021, 18:29:37 UTC |
| 8c79d22 | mergify[bot] | 30 August 2021, 22:40:08 UTC | Merge pull request #1826 from tskit-dev/dependabot/pip/requirements/CI-docs/jupyter-book-0.11.3 Bump jupyter-book from 0.11.2 to 0.11.3 in /requirements/CI-docs | 30 August 2021, 22:40:08 UTC |
| 90b5c4c | dependabot[bot] | 30 August 2021, 22:06:54 UTC | Bump jupyter-book from 0.11.2 to 0.11.3 in /requirements/CI-docs Bumps [jupyter-book](https://github.com/executablebooks/jupyter-book) from 0.11.2 to 0.11.3. - [Release notes](https://github.com/executablebooks/jupyter-book/releases) - [Changelog](https://github.com/executablebooks/jupyter-book/blob/master/CHANGELOG.md) - [Commits](https://github.com/executablebooks/jupyter-book/compare/v0.11.2...v0.11.3) --- updated-dependencies: - dependency-name: jupyter-book dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 30 August 2021, 22:25:11 UTC |
| 4623a13 | mergify[bot] | 30 August 2021, 22:25:01 UTC | Merge pull request #1824 from tskit-dev/dependabot/pip/requirements/CI-tests-pip/hypothesis-6.17.3 Bump hypothesis from 6.15.0 to 6.17.3 in /requirements/CI-tests-pip | 30 August 2021, 22:25:01 UTC |
| 316ae07 | dependabot[bot] | 30 August 2021, 22:06:41 UTC | Bump hypothesis from 6.15.0 to 6.17.3 in /requirements/CI-tests-pip Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.15.0 to 6.17.3. - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.15.0...hypothesis-python-6.17.3) --- updated-dependencies: - dependency-name: hypothesis dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> | 30 August 2021, 22:15:14 UTC |
| 357f676 | mergify[bot] | 30 August 2021, 22:14:12 UTC | Merge pull request #1825 from tskit-dev/dependabot/pip/requirements/CI-complete/hypothesis-6.17.3 Bump hypothesis from 6.14.5 to 6.17.3 in /requirements/CI-complete | 30 August 2021, 22:14:12 UTC |
| dfde2c8 | dependabot[bot] | 30 August 2021, 22:06:44 UTC | Bump hypothesis from 6.14.5 to 6.17.3 in /requirements/CI-complete Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.14.5 to 6.17.3. - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.14.5...hypothesis-python-6.17.3) --- updated-dependencies: - dependency-name: hypothesis dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> | 30 August 2021, 22:06:44 UTC |
| 53b2a19 | mergify[bot] | 23 August 2021, 22:22:11 UTC | Merge pull request #1817 from tskit-dev/dependabot/pip/requirements/CI-tests-pip/hypothesis-6.15.0 Bump hypothesis from 6.14.5 to 6.15.0 in /requirements/CI-tests-pip | 23 August 2021, 22:22:11 UTC |
| b653340 | dependabot[bot] | 23 August 2021, 22:05:32 UTC | Bump hypothesis from 6.14.5 to 6.15.0 in /requirements/CI-tests-pip Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.14.5 to 6.15.0. - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.14.5...hypothesis-python-6.15.0) --- updated-dependencies: - dependency-name: hypothesis dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> | 23 August 2021, 22:15:42 UTC |
| bc1ec86 | mergify[bot] | 23 August 2021, 22:13:18 UTC | Merge pull request #1818 from tskit-dev/dependabot/pip/requirements/CI-complete/scipy-1.7.1 Bump scipy from 1.7.0 to 1.7.1 in /requirements/CI-complete | 23 August 2021, 22:13:18 UTC |
| 6ef584b | dependabot[bot] | 23 August 2021, 22:05:32 UTC | Bump scipy from 1.7.0 to 1.7.1 in /requirements/CI-complete Bumps [scipy](https://github.com/scipy/scipy) from 1.7.0 to 1.7.1. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](https://github.com/scipy/scipy/compare/v1.7.0...v1.7.1) --- updated-dependencies: - dependency-name: scipy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 23 August 2021, 22:05:32 UTC |
| 2495616 | mergify[bot] | 19 August 2021, 08:58:31 UTC | Merge pull request #1807 from nikbaya/merge-ancestors Pass node to merge ancestors in pedigree climb | 19 August 2021, 08:58:31 UTC |
| 3324ea4 | Nik Baya | 12 August 2021, 09:35:11 UTC | Pass node to merge ancestors in pedigree climb Remove parent > child assert Make msp_store_node return node id Get node from ts using node id from individual Swap ret and new_node_id from msp_store_node Check if more nodes are added when DTWF pedigree model is run Codecov check Run clang-format Check that number of nodes is unchanged after msp_run is called | 19 August 2021, 08:52:32 UTC |
| 06853a9 | mergify[bot] | 18 August 2021, 18:07:27 UTC | Merge pull request #1814 from petrelharp/unskip remove skipif windows on ooa test, closes #1629 | 18 August 2021, 18:07:27 UTC |
| 4140a2c | peter | 18 August 2021, 17:21:34 UTC | remove skipif windows on ooa test, closes #1629 | 18 August 2021, 17:21:54 UTC |
| b13e7d9 | mergify[bot] | 16 August 2021, 22:31:33 UTC | Merge pull request #1811 from tskit-dev/dependabot/pip/requirements/CI-docs/matplotlib-3.4.3 Bump matplotlib from 3.4.2 to 3.4.3 in /requirements/CI-docs | 16 August 2021, 22:31:33 UTC |
| 1613c44 | dependabot[bot] | 16 August 2021, 22:06:51 UTC | Bump matplotlib from 3.4.2 to 3.4.3 in /requirements/CI-docs Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.4.2 to 3.4.3. - [Release notes](https://github.com/matplotlib/matplotlib/releases) - [Commits](https://github.com/matplotlib/matplotlib/compare/v3.4.2...v3.4.3) --- updated-dependencies: - dependency-name: matplotlib dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 16 August 2021, 22:23:08 UTC |
| d4b7895 | mergify[bot] | 16 August 2021, 22:21:34 UTC | Merge pull request #1810 from tskit-dev/dependabot/pip/requirements/CI-tests-pip/tskit-0.3.7 Bump tskit from 0.3.6 to 0.3.7 in /requirements/CI-tests-pip | 16 August 2021, 22:21:34 UTC |
| b4cd2dd | dependabot[bot] | 16 August 2021, 22:06:47 UTC | Bump tskit from 0.3.6 to 0.3.7 in /requirements/CI-tests-pip Bumps [tskit](https://github.com/tskit-dev/tskit) from 0.3.6 to 0.3.7. - [Release notes](https://github.com/tskit-dev/tskit/releases) - [Changelog](https://github.com/tskit-dev/tskit/blob/main/docs/convert_changelog.py) - [Commits](https://github.com/tskit-dev/tskit/compare/0.3.6...0.3.7) --- updated-dependencies: - dependency-name: tskit dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 16 August 2021, 22:14:52 UTC |
| 0686b2b | mergify[bot] | 16 August 2021, 22:13:06 UTC | Merge pull request #1809 from tskit-dev/dependabot/pip/requirements/CI-complete/numpy-1.21.2 Bump numpy from 1.21.1 to 1.21.2 in /requirements/CI-complete | 16 August 2021, 22:13:06 UTC |
| 5927534 | dependabot[bot] | 16 August 2021, 22:06:22 UTC | Bump numpy from 1.21.1 to 1.21.2 in /requirements/CI-complete Bumps [numpy](https://github.com/numpy/numpy) from 1.21.1 to 1.21.2. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/HOWTO_RELEASE.rst.txt) - [Commits](https://github.com/numpy/numpy/compare/v1.21.1...v1.21.2) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 16 August 2021, 22:06:22 UTC |
| 7a49bc6 | mergify[bot] | 11 August 2021, 18:53:35 UTC | Merge pull request #1802 from nikbaya/update-climb-pedigrees Update setup of WF pedigree model for table-based approach | 11 August 2021, 18:53:35 UTC |
| 37c0ba8 | Nik Baya | 05 August 2021, 15:58:30 UTC | Added nodes to individual_t Ran clang-format Initialise tree sequence in msp_set_simulation_model_wf_ped Converted msp error codes back into tsk error codes when testing for out of bounds individuals Move msp_set_pedigree into msp_set_simulation_model_wf_ped Assign nodes to pedigree individuals Run clang-format Replace tsk_individual_table_get_row with tsk_treeseq_get_individual in msp_set_simulation_model_wf_ped Assign nodes to pedigree individuals Run clang-format Use ind_obj.parents instead of ind_parents Change translation of tsk error to msp in out of bounds assert | 11 August 2021, 18:46:55 UTC |
| 48046a1 | mergify[bot] | 09 August 2021, 22:24:33 UTC | Merge pull request #1805 from tskit-dev/dependabot/pip/requirements/CI-tests-pip/scipy-1.7.1 Bump scipy from 1.6.3 to 1.7.1 in /requirements/CI-tests-pip | 09 August 2021, 22:24:33 UTC |
| c5ea5d1 | dependabot[bot] | 09 August 2021, 22:06:40 UTC | Bump scipy from 1.6.3 to 1.7.1 in /requirements/CI-tests-pip Bumps [scipy](https://github.com/scipy/scipy) from 1.6.3 to 1.7.1. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](https://github.com/scipy/scipy/compare/v1.6.3...v1.7.1) --- updated-dependencies: - dependency-name: scipy dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> | 09 August 2021, 22:18:15 UTC |
| 5338630 | mergify[bot] | 09 August 2021, 22:13:56 UTC | Merge pull request #1804 from tskit-dev/dependabot/pip/requirements/CI-complete/codecov-2.1.12 Bump codecov from 2.1.10 to 2.1.12 in /requirements/CI-complete | 09 August 2021, 22:13:56 UTC |
| ae7dd2c | dependabot[bot] | 09 August 2021, 22:06:32 UTC | Bump codecov from 2.1.10 to 2.1.12 in /requirements/CI-complete Bumps [codecov](https://github.com/codecov/codecov-python) from 2.1.10 to 2.1.12. - [Release notes](https://github.com/codecov/codecov-python/releases) - [Changelog](https://github.com/codecov/codecov-python/blob/master/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-python/compare/v2.1.10...v2.1.12) --- updated-dependencies: - dependency-name: codecov dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> | 09 August 2021, 22:06:32 UTC |
| bb31974 | mergify[bot] | 04 August 2021, 23:24:43 UTC | Merge pull request #1799 from tskit-dev/dependabot/pip/requirements/CI-complete/hypothesis-6.14.5 Bump hypothesis from 6.14.3 to 6.14.5 in /requirements/CI-complete | 04 August 2021, 23:24:43 UTC |
