From 783b1c4ce6700c6a2643641cec2e70148d226f10 Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Thu, 5 Mar 2026 17:01:54 +0000 Subject: [PATCH] Various minor tweaks pre-release --- CHANGELOG.md | 20 ++++++++++++-------- docs/_config.yml | 4 ++-- docs/installation.md | 7 ++----- pyproject.toml | 1 + 4 files changed, 17 insertions(+), 15 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1616f4d1..ed54c7e3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 @@ -221,7 +225,7 @@ - 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** @@ -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 @@ -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 diff --git a/docs/_config.yml b/docs/_config.yml index 01292d84..a5987c5d 100644 --- a/docs/_config.yml +++ b/docs/_config.yml @@ -3,7 +3,7 @@ title: Tsdate manual author: Tskit Developers -copyright: "2023" +copyright: "2026" only_build_toc_files: true logo: tsdate_logo.svg favicon: favicon.ico @@ -87,4 +87,4 @@ sphinx: [ "py:class", "dtype=int8" ], [ "py:class", "iter" ], [ "py:class", "string" ], - ] \ No newline at end of file + ] diff --git a/docs/installation.md b/docs/installation.md index a8e50740..adc25f79 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -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) ` can be accessed via: @@ -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. \ No newline at end of file +and can occassionally lead to unexpected crashes. diff --git a/pyproject.toml b/pyproject.toml index a3c15121..6d4afccf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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"]