Python 1.0.0b3

Breaking Changes

• TreeSequence.tables now returns a zero-copy immutable view of the tables.
  To get a mutable copy, use TreeSequence.dump_tables().
  (@benjeffery, #3288, #760)

• For a tree seqeunce to be valid mutation parents in the table collection
  must be correct and consistent with the topology of the tree at each mutation site.
  TableCollection.tree_sequence() will raise a _tskit.LibraryError if this
  is not the case.
  (@benjeffery, #2729, #2732, #3212).

• Drop Python 3.9 support, require Python >= 3.10 (#3267, @benjeffery)

Features

• TreeSequence.map_to_vcf_model now also returns the transformed positions and
  contig length. (@benjeffery, #3174, #3173)

• draw_svg() methods now associate tree branches with edge IDs
  (@hyanwong, #3193, #557)

• draw_svg() methods now allow the y-axis to be placed on the right-hand side
  using y_axis="right" (@hyanwong, #3201)

• Add contig_id and isolated_as_missing to VcfModelMapping
  (@benjeffery, #3219, #3177)

• Add TreeSequence.mutations_edge which returns the edge ID for each mutation's
  edge. (@benjeffery, #3226, #3189)

• Add TreeSequence.sites_ancestral_state, TreeSequence.mutations_derived_state and
  TreeSequence.mutations_inherited_state properties to return the ancestral state of sites,
  derived state of mutations and inherited state of mutations as NumPy arrays of
  the new numpy 2.0 StringDType.
  (@benjeffery, #3228, #2632, #3276, #2631)

• Tskit now distributes with a requirement of numpy version 2 or greater. However, you can still use
  tskit with numpy 1.X by building tskit from source with numpy 1.X using pip install tskit --no-binary tskit.
  With numpy 1.X, any use of the new StringDType properties will result in a RuntimeError.
  If you try to use another python module that was compiled against numpy 1.X with numpy 2.X you may see
  the error "A module that was compiled using NumPy 1.x cannot be run in NumPy 2.0.0 as it may crash.".
  If no newer version of the module is available you will have to use the Numpy 1.X build as above.

• Add Mutation.inherited_state property which returns the inherited state
  for a single mutation. (@benjeffery, #3277, #2631)

Bugfixes

• In some tables with mutations out-of-order TableCollection.sort did not re-order
  the mutations so they formed a valid TreeSequence. TableCollection.sort and
  TableCollection.canonicalise now sort mutations by site, then time (if known),
  then the mutation's node's time, then number of descendant mutations
  (ensuring that parent mutations occur before children), then node, then
  their original order in the tables. (@benjeffery, #3257, #3253)

• Fix bug in TreeSequence.pair_coalescence_counts when span_normalise=True
  and a window breakpoint falls within an internal missing interval.
  (@nspope, #3176, #3175)

• Fix metadata schemas that are equal but have different byte representations not being equal
  when using TableCollection.assert_equals and Table.assert_equals.
  (@benjeffery, #3246, #3244)

• k-way statistics no longer require k sample sets, allowing in particular
  "self" comparisons for TreeSequence.genetic_relatedness. This changes the
  error code returned in some situations.
  (@andrewkern, @petrelharp, #3235, #3055)

• Fix UnboundLocalError in draw_svg() when using numeric max_time
  values with mutations over roots.
  (@benjeffery, #3274, #3273)

• Prevent iterating over a TopologyCounter
  (@benjeffery , #3202, #1462)

Breaking changes

• ltrim, rtrim, trim and shift raise an error if used on a tree sequence
  containing a reference sequence (@hyanwong, #3210, #2091)