Python 0.6.0

Breaking Changes

• The definition of TreeSequence.genetic_relatedness and
  TreeSequence.genetic_relatedness_weighted are changed
  to average over sample sets, rather than summing over them.
  For computation with diploid sample sets, this will change the result
  by a factor of four; for larger sample sets it will now produce
  sensible values that are comparable between sample sets of different sizes.
  The default for these methods is also changed to polarised=True,
  but the output is unchanged for centre=True (the default).
  See the documentation for these methods for more discussion.
  (@petrelharp, @mmosmond, #1623)

Bugfixes

• Fix to TreeSequence.genetic_relatedness with indexes=None and
  proportion=True. (@petrelharp, #2984, #1623)

• Fix to TreeSequence.general_stat when using non-strict summary functions
  in the presence of non-ancestral material (very rare).
  (@petrelharp, #2983, #1623)

• Printing tskit.MetadataSchema(schema=None) now shows "Null_schema" rather
  than None, to avoid confusion (@hyanwong, #2720)

• Limit output HTML when a tree sequence is displayed that has a large amount of metadata.
  (@benjeffery, #2999)

• Fix warning in draw_svg to use correct warnings module.
  (@duncanMR, #2870, #2871)

Features

• Add the centre option to TreeSequence.genetic_relatedness and
  TreeSequence.genetic_relatedness_weighted.
  (@petrelharp, @mmosmond, #1623)

• Edges now have an .interval attribute returning a tskit.Interval object.
  (@hyanwong, #2531)

• Variants now have a states() method that returns the genotypes as an
  (inefficient) array of strings, rather than integer indexes, to
  aid comparison of genetic variation (@hyanwong, #2617)

• Added distance_between that calculates the total distance between two nodes in a tree.
  (@Billyzhang1229, #2771)

• Added genetic_relatedness_matrix method to compute
  pairwise genetic relatedness between sample sets.
  (@jeromekelleher, @petrelharp, #2823)

• Add TreeSequence.extend_haplotypes method that extends ancestral haplotypes
  using recombination information, leading to unary nodes in many trees and
  fewer edges. (@petrelharp, @hfr1tz3, :user: nspope,
  @avabamf, #2651, #2938)

• Add Table.drop_metadata to make clearing metadata from tables easy.
  (@jeromekelleher, #2944)

• Add Interval.mid and Tree.mid properties to return the midpoint of the interval.
  (@currocam, #2960)

• Added genetic_relatedness_vector method to compute product of genetic relatedness
  matrix and weight vector.
  (@petrelharp, #2980)

• Added pair_coalescence_counts method to calculate coalescence events per node or time
  interval, pair_coalescence_quantiles method to estimate quantiles of pair
  coalescence times using empirical CDF inversion, and pair_coalescence_rates method to
  estimate instantaneous rates of pair coalescence within time intervals from the empirical CDF.
  (@nspope, #2915, #2976, #2985)

• Add provenance information to the HTML notebook representation of a tree sequence.
  (@benjeffery, #3001)

• The .draw_svg() methods can add annotated genomic regions (e.g. genes) to the
  x-axis. (@hyanwong, #3002)

• Added a node_titles and a mutation_titles parameter to .draw_svg() methods
  which assigns a string to node and mutation symbols, commonly shown on mouseover. This
  can reduce label clutter while retaining useful info (@hyanwong, #3007)

• Added (currently undocumented) use of the order parameter in Tree.draw_svg() to
  pass a subset of nodes, so subtrees can be visually collapsed. Additionally, an option
  pack_untracked_polytomies allows large polytomies involving untracked samples to
  be summarised as a dotted line (@hyanwong, #3011 #3010, #3012)

• Added a title parameter to .draw_svg() methods (@hyanwong, #3015)

• Add comma separation to all display numbers. (@benjeffery, #3017, #3018)

• Added Tree.ancestors(u) method. (@hyanwong, #2706, #3021)

• Add resources section to provenance schema. (@benjeffery, #3016)

• Add Tree.rf_distance method to calculate the unweighted Robinson-Foulds distance
  between two trees. (@Billyzhang1229, #995, #2643, #3032)