Python 0.5.0

Major Feature Release

Breaking Changes

• The JSON metadata codec now interprets the empty string as an empty object. This means
  that applying a schema to an existing table will no longer necessitate modifying the
  existing rows. (@benjeffery, #2064, #2104)

• Remove the previously deprecated as_bytes argument to TreeSequence.variants.
  If you need genotypes in byte form this can be done following the code in the
  to_macs method on line 5573 of trees.py.
  This argument was initially deprecated more than 3 years ago when the code was part of
  msprime.
  (@benjeffery, #605, #2172)

• Arguments after ploidy in write_vcf marked as keyword only
  (@jeromekelleher, #2329, #2315).

• When metadata equal to b'' is printed to text or HTML tables it will render as
  an empty string rather than "b''". (@hyanwong, #2349, #2351)

Changes

• A min_time parameter in draw_svg enables the youngest node as the y axis min
  value, allowing negative times.
  (@hyanwong, #2197, #2215)

• VcfWriter.write now prints the site ID of variants in the ID field of the
  output VCF files.
  (@roohy, #2103, #2107)

• Make dumping of tables and tree sequences to disk a zero-copy operation.
  (@benjeffery, #2111, #2124)

• Add copy argument to TreeSequence.variants which if False reuses the
  returned Variant object for improved performance. Defaults to True.
  (@benjeffery, #605, #2172)

• tree.mrca now takes 2 or more arguments and gives the common ancestor of them all.
  (@savitakartik, #1340, #2121)

• Add a edge attribute to the Mutation class that gives the ID of the
  edge that the mutation falls on.
  (@jeromekelleher, #685, #2279).

• Add the TreeSequence.split_edges operation which inserts nodes into
  edges at a specific time.
  (@jeromekelleher, #2276, #2296).

• Add the TreeSequence.decapitate (and closely related
  TableCollection.delete_older) operation to remove topology and mutations
  older than a give time.
  (@jeromekelleher, #2236, #2302, #2331).

• Add the TreeSequence.individuals_time and TreeSequence.individuals_population
  methods to return arrays of per-individual times and populations, respectively.
  (@petrelharp, #1481, #2298).

• Add the sample_mask and site_mask to write_vcf to allow parts
  of an output VCF to be omitted or marked as missing data. Also add the
  as_vcf convenience function, to return VCF as a string.
  (@jeromekelleher, #2300).

• Add support for missing data to write_vcf, and add the isolated_as_missing
  argument. (@jeromekelleher, #2329, #447).

• Add Tree.num_children_array and Tree.num_children. Returns the counts of
  the number of child nodes for each or a single node in the tree respectively.
  (@GertjanBisschop, #2318, #2319, #2332)

• Add Tree.path_length.
  (@jeremyguez, #2249, #2259).

• Add B1 tree balance index.
  (@jeremyguez, @jeromekelleher, #2251, #2281, #2346).

• Add B2 tree balance index.
  (@jeremyguez, @jeromekelleher, #2252, #2353, #2354).

• Add Sackin tree imbalance index.
  (@jeremyguez, @jeromekelleher, #2246, #2258).

• Add Colless tree imbalance index.
  (@jeremyguez, @jeromekelleher, #2250, #2266, #2344).

• Add direction argument to TreeSequence.edge_diffs, allowing iteration
  over diffs in the reverse direction. NOTE: this comes with a ~10% performance
  regression as the implementation was moved from C to Python for simplicity
  and maintainability. Please open an issue if this affects your application.
  (@jeromekelleher, @benjeffery, #2120).

• Add Tree.edge_array and Tree.edge. Returns the edge id of the edge encoding
  the relationship of each node with its parent.
  (@GertjanBisschop, #2361, #2357)