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Rejig changelog
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python/CHANGELOG.rst

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- Add ``TreeSequence.mutations_inherited_state`` which returns the inherited state
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for each mutation. (:user:`benjeffery`, :pr:`3276`, :issue:`2631`)
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- Add ``TreeSequence.sites_ancestral_state`` and ``TreeSequence.mutations_derived_state`` properties
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to return the ancestral state of sites and derived state of mutations as NumPy arrays of
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the new numpy 2.0 StringDType.
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(:user:`benjeffery`, :pr:`3228`, :issue:`2632`)
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- Tskit now distributes with a requirement of numpy version 2 or greater. However, you can still use
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tskit with numpy 1.X by building tskit from source with numpy 1.X using ``pip install tskit --no-binary tskit``.
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With numpy 1.X, any use of the new StringDType properties will result in a ``RuntimeError``.
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If you try to use another python module that was compiled against numpy 1.X with numpy 2.X you may see
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the error "A module that was compiled using NumPy 1.x cannot be run in NumPy 2.0.0 as it may crash.".
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If no newer version of the module is available you will have to use the Numpy 1.X build as above.
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**Bugfixes**
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- In some tables with mutations out-of-order `TableCollection.sort` did not re-order
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- ``ltrim``, ``rtrim``, ``trim`` and ``shift`` raise an error if used on a tree sequence
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containing a reference sequence (:user:`hyanwong`, :pr:`3210`, :issue:`2091`)
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- Add ``TreeSequence.sites_ancestral_state`` and ``TreeSequence.mutations_derived_state`` properties
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to return the ancestral state of sites and derived state of mutations as NumPy arrays of
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the new numpy 2.0 StringDType.
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This requires numpy version 2 or greater, as such this is now the minimum version stated in tskit's
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dependencies. If you try to use another python module that was compiled against numpy 1.X you may see
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the error "A module that was compiled using NumPy 1.x cannot be run in NumPy 2.0.0 as it may crash.".
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If no newer version of the module is avaliable you can still use it with tskit and numpy 1.X by
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building tskit from source with numpy 1.X using ``pip install tskit --no-binary tskit``. However
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any use of the new properties will result in a ``RuntimeError``.
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(:user:`benjeffery`, :pr:`3228`, :issue:`2632`)
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--------------------
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[0.6.4] - 2025-05-21
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--------------------

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