Python 0.5.3

Fixes

• The Variant object can now be initialized with 64 bit numpy ints as
  returned e.g. from np.where (@hyanwong, #2518, #2514)

• Fix tree.mrca for the case of a tree with multiple roots.
  (@benjeffery, #2533, #2521)

Features

• The ts.nodes method now takes an order parameter so that nodes
  can be visited in time order (@hyanwong, #2471, #2370)

• Add samples argument to TreeSequence.genotype_matrix.
  Default is None, where all the sample nodes are selected.
  (@szhan, #2493, #678)

• ts.draw and the draw_svg methods now have an optional omit_sites
  parameter, aiding drawing large trees with many sites and mutations
  (@hyanwong, #2519, #2516)

Breaking Changes

• Single statistics computed with TreeSequence.general_stat are now
  returned as numpy scalars if windows=None, AND; samples is a single
  list or None (for a 1-way stat), OR indexes is None or a single list of
  length k (instead of a list of length-k lists).
  (@gtsambos, #2417, #2308)

• Accessor methods such as ts.edge(n) and ts.node(n) now allow negative
  indexes (@hyanwong, #2478, #1008)

• ts.subset() produces valid tree sequences even if nodes are shuffled
  out of time order (@hyanwong, #2479, #2473), and the
  same for tables.subset() (@hyanwong, #2489). This involves
  sorting the returned tables, potentially changing the returned edge order.

Performance improvements

• TreeSequence.link_ancestors no longer continues to process edges once all
  of the sample and ancestral nodes have been accounted for, improving memory
  overhead and overall performance
  (@gtsambos, #2456, #2442)