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20 changes: 12 additions & 8 deletions CHANGELOG.md
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@@ -1,6 +1,10 @@
# Changelog

## [0.2.6] - XXXXXXXXXX
## [0.2.6] - 2026-03-06

Maintenance release.

- Python >= 3.11 is required.


## [0.2.5] - 2026-02-03
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- The algorithm now operates completely in unscaled time (in units of generations) under
the hood, which means that `tsdate.build_prior_grid` now requires the parameter
`Ne`.
- Users now have access to the marginal posterior distributions on node age by running
- Users now have access to the marginal posterior distributions on node age by running
`tsdate.get_dates`, though this is undocumented for now.

**Bugfixes**
Expand All @@ -234,14 +238,14 @@

**Features**

- Two new methods, `tsdate.sites_time_from_ts` and `tsdate.add_sampledata_times`,
- Two new methods, `tsdate.sites_time_from_ts` and `tsdate.add_sampledata_times`,
support inference of tree sequences from non-contemporaneous samples.
- New tutorial on inferring tree sequences from modern and historic/ancient samples
- New tutorial on inferring tree sequences from modern and historic/ancient samples
explains how to use these functions in conjunction with `tsinfer`.
- `tsdate.preprocess_ts` supports dating inferred tree sequences which include large,
uninformative stretches (i.e. centromeres and telomeres). Simply run this function
- `tsdate.preprocess_ts` supports dating inferred tree sequences which include large,
uninformative stretches (i.e. centromeres and telomeres). Simply run this function
on the tree sequence before dating it.
- `ignore_outside` is a new parameter in the outside pass which tells `tsdate` to
- `ignore_outside` is a new parameter in the outside pass which tells `tsdate` to
ignore edges from oldest root (these edges are often of low quality in `tsinfer`
inferred tree sequences)
- Development environment is now equivalent to other `tskit-dev` projects
Expand All @@ -251,7 +255,7 @@

- Improve user experience with more progress bars and logging.
- Slightly change traversal method in outside and outside maximization algorithms,
this should only affect inference on inferred tree sequences with large numbers
this should only affect inference on inferred tree sequences with large numbers
of nodes at the same frequency.
- Improve reporting of current project version
- Use appdirs for default caching location
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4 changes: 2 additions & 2 deletions docs/_config.yml
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title: Tsdate manual
author: Tskit Developers
copyright: "2023"
copyright: "2026"
only_build_toc_files: true
logo: tsdate_logo.svg
favicon: favicon.ico
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[ "py:class", "dtype=int8" ],
[ "py:class", "iter" ],
[ "py:class", "string" ],
]
]
7 changes: 2 additions & 5 deletions docs/installation.md
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Expand Up @@ -20,10 +20,7 @@ kernelspec:

To install `tsdate` simply run:

$ python3 -m pip install tsdate --user

Python 3.8, or a more recent version, is required. The software has been tested
on MacOSX and Linux.
$ python -m pip install tsdate

Once installed, `tsdate`'s {ref}`Command Line Interface (CLI) <sec_cli>` can be accessed via:

Expand Down Expand Up @@ -55,4 +52,4 @@ tens of seconds. To speed up loading time, you can set the environment variable

The compiled code is not cached by default as it can be problematic when
e.g. running the same installation on different CPU types in a cluster,
and can occassionally lead to unexpected crashes.
and can occassionally lead to unexpected crashes.
1 change: 1 addition & 0 deletions pyproject.toml
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Expand Up @@ -115,6 +115,7 @@ include-package-data = true

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

[tool.pytest.ini_options]
testpaths = ["tests"]
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