Python 0.3.6

[benjeffery]

Minor feature release

Breaking changes

• Mutation.position and Mutation.index which were deprecated in 0.2.2 (Sep '19) have
  been removed.

Features

• Add direct, copy-free access to the arrays representing the quintuply-linked structure
  of Tree (e.g. left_child_array). Allows performant algorithms over the tree
  structure using, for example, numba
  (@jeromekelleher, #1299, #1320).

• Add fancy indexing to tables. E.g. table[6:86] returns a new table with the
  specified rows. Supports slices, index arrays and boolean masks
  (@benjeffery, #1221, #1348, #1342).

• Add Table.append method for adding rows from classes such as SiteTableRow and
  Site (@benjeffery, #1111, #1254).

• SVG visualization of a tree sequence can be restricted to displaying between left
  and right genomic coordinates using the x_lim parameter. The default settings
  now mean that if the left or right flanks of a tree sequence are entirely empty,
  these regions will not be plotted in the SVG (@hyanwong, #1288).

• SVG visualization of a single tree allows all mutations on an edge to be plotted
  via the all_edge_mutations param (@hyanwong,#1253, #1258).

• Entity classes such as Mutation, Node are now python dataclasses
  (@benjeffery, #1261).

• Metadata decoding for table row access is now lazy (@benjeffery, #1261).

• Add html notebook representation for Tree and change Tree.__str__ from dict
  representation to info table. (@benjeffery, #1269, #1304).

• Improve display of tables when printed, limiting lines set via
  tskit.set_print_options (@benjeffery,#1270, #1300).

• Add Table.assert_equals and TableCollection.assert_equals which give an exact
  report of any differences. (@benjeffery,#1076, #1328)

Changes

• In drawing methods max_tree_height and tree_height_scale have been deprecated
  in favour of max_time and time_scale
  (@benjeffery,#1262, #1331).

Fixes

• Tree sequences were not properly init'd after unpickling
  (@benjeffery, #1297, #1298)

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This discussion was created from the release Python 0.3.6.