Python 0.3.5

Breaking changes

• tskit now requires Python 3.7 (@benjeffery, #1235)

Features

• SVG visualization plots mutations at the correct time, if it exists, and a y-axis,
  with label can be drawn. Both x- and y-axes can be plotted on trees as well as
  tree sequences (@hyanwong,#840, #580, #1236)

• SVG visualization now uses squares for sample nodes and red crosses for mutations,
  with the site/mutation positions marked on the x-axis. Additionally, an x-axis
  label can be set (@hyanwong,#1155, #1194, #1182, #1213)

• Add parents column to the individual table to allow recording of pedigrees
  (@ivan-krukov, @benjeffery, #852, #1125, #866, #1153, #1177, #1192 #1199).

• Added Tree.generate_random_binary static method to create random
  binary trees (@hyanwong, @jeromekelleher, #1037).

• Change the default behaviour of Tree.split_polytomies to generate
  the shortest possible branch lengths instead of a fixed epsilon of
  1e-10. (@jeromekelleher, #1089, #1090)

• Default value metadata in add_row functions is now schema-dependant, so that
  metadata={} is no longer needed as an argument when a schema is present
  (@benjeffery, #1084).

• default in metadata schemas is used to fill in missing values when encoding for
  the struct codec. (@benjeffery, #1073, #1116).

• Added canonical option to table collection sorting (@mufernando,
  @petrelharp, #705)

• Added various arguments to TreeSequence.subset, to allow for stable
  population indexing and lossless node reordering with subset.
  (@petrelharp, #1097)

Changes

• Allow mutations that have the same derived state as their parent mutation.
  (@benjeffery, #1180, #1233)

• File minor version change to support individual parents