Python version of alignments with missingness (#3317)

Author: benjeffery

c/CHANGELOG.rst

@@ -1,3 +1,12 @@
+----------
+Unreleased
+----------
+
+- ``tsk_variant_init`` and associated variant decoding methods now
+  fully support TSK_ISOLATED_NOT_MISSING not being set for internal nodes.
+  (:user:`benjeffery`, :pr:`3313`)
+
+
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 [1.2.0] - 2025-09-24
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python/CHANGELOG.rst

@@ -1,3 +1,20 @@
+----------
+Unreleased
+----------
+
+**Features**
+
+- ``TreeSequence.variants``, ``.genotype_matrix``, ``.haplotypes``, and ``.alignments`` methods
+  now fully support ``isolated_as_missing`` behaviour with internal nodes.
+  (:user:`benjeffery`, :pr:`3313`, :pr:`3317`, :issue:`1896`)
+
+**Breaking Changes**
+
+- The ``reference_sequence`` argument to ``TreeSequence.alignments`` is now required
+  to be the same length as the tree sequence. Previously it was required to be the length
+  of the requested interval.
+  (:user:`benjeffery`, :pr:`3317`)
+
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 [1.0.0b3] - 2025-10-15
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