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Various minor tweaks pre-release
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CHANGELOG.md

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# Changelog
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## [0.2.6] - XXXXXXXXXX
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## [0.2.6] - 2026-03-06
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Maintenance release.
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- Python >= 3.11 is required.
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## [0.2.5] - 2026-02-03
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- The algorithm now operates completely in unscaled time (in units of generations) under
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the hood, which means that `tsdate.build_prior_grid` now requires the parameter
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`Ne`.
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- Users now have access to the marginal posterior distributions on node age by running
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- Users now have access to the marginal posterior distributions on node age by running
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`tsdate.get_dates`, though this is undocumented for now.
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**Bugfixes**
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**Features**
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- Two new methods, `tsdate.sites_time_from_ts` and `tsdate.add_sampledata_times`,
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- Two new methods, `tsdate.sites_time_from_ts` and `tsdate.add_sampledata_times`,
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support inference of tree sequences from non-contemporaneous samples.
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- New tutorial on inferring tree sequences from modern and historic/ancient samples
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- New tutorial on inferring tree sequences from modern and historic/ancient samples
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explains how to use these functions in conjunction with `tsinfer`.
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- `tsdate.preprocess_ts` supports dating inferred tree sequences which include large,
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uninformative stretches (i.e. centromeres and telomeres). Simply run this function
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- `tsdate.preprocess_ts` supports dating inferred tree sequences which include large,
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uninformative stretches (i.e. centromeres and telomeres). Simply run this function
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on the tree sequence before dating it.
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- `ignore_outside` is a new parameter in the outside pass which tells `tsdate` to
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- `ignore_outside` is a new parameter in the outside pass which tells `tsdate` to
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ignore edges from oldest root (these edges are often of low quality in `tsinfer`
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inferred tree sequences)
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- Development environment is now equivalent to other `tskit-dev` projects
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- Improve user experience with more progress bars and logging.
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- Slightly change traversal method in outside and outside maximization algorithms,
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this should only affect inference on inferred tree sequences with large numbers
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this should only affect inference on inferred tree sequences with large numbers
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of nodes at the same frequency.
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- Improve reporting of current project version
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- Use appdirs for default caching location

docs/_config.yml

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title: Tsdate manual
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author: Tskit Developers
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copyright: "2023"
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copyright: "2026"
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only_build_toc_files: true
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logo: tsdate_logo.svg
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favicon: favicon.ico
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[ "py:class", "dtype=int8" ],
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[ "py:class", "iter" ],
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[ "py:class", "string" ],
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]
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]

docs/installation.md

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To install `tsdate` simply run:
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$ python3 -m pip install tsdate --user
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Python 3.8, or a more recent version, is required. The software has been tested
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on MacOSX and Linux.
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$ python -m pip install tsdate
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Once installed, `tsdate`'s {ref}`Command Line Interface (CLI) <sec_cli>` can be accessed via:
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The compiled code is not cached by default as it can be problematic when
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e.g. running the same installation on different CPU types in a cluster,
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and can occassionally lead to unexpected crashes.
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and can occassionally lead to unexpected crashes.

pyproject.toml

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[tool.setuptools_scm]
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write_to = "tsdate/_version.py"
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local_scheme = "no-local-version"
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[tool.pytest.ini_options]
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testpaths = ["tests"]

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