C API 0.99.11

Features

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

• Added a tsk_table_collection_canonicalse method, that allows checking for equality between
  tables that are equivalent up to reordering (@petrelharp, @mufernando, #1108).

• Removed a previous requirement on tsk_table_collection_union, allowing for unioning of
  new information both above and below shared history (@petrelharp, @mufernando, #1108).

• Support migrations in tsk_table_collection_sort. (@jeromekelleher,
  #22, #117, #1131).

Breaking changes

• Method tsk_individual_table_add_row has an extra arguments parents and parents_length.

• Add an options argument to tsk_table_collection_subset (@petrelharp, #1108),
  to allow for retaining the order of populations.

• Mutation error codes have changed

Changes

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

• File minor version change to support individual parents

C API 0.99.10

Minor change to internal APIs

C API 0.99.9

Minor Feature Release

Features

• Add TSK_KEEP_UNARY_IN_INDIVIDUALS flag to simplify, which allows the user to
  keep unary nodes only if they belong to a tabled individual. This is useful for
  simplification in forwards simulations (@hyanwong, #1113, #1119).

Python 0.3.4

Minor bugfix release.

Bugfixes

• Reinstate the unused zlib_compression option to tskit.dump, as msprime < 1.0 still uses it (@jeromekelleher, #1067).

Python 0.3.3

Minor feature release

Features

• Add TreeSequence.genetic_relatedness for calculating genetic relatedness between
  pairs of sets of nodes (@brieuclehmann, #1021, #1023, #974, #973, #898).

• Expose TreeSequence.coiterate() method to allow iteration over 2 sequences
  simultaneously, aiding comparison of trees from two sequences
  (@jeromekelleher, @hyanwong, #1021, #1022).

• tskit is now supported on, and has wheels for, python3.9
  (@benjeffery, #982, #907).

• Tree.newick() now has extra option include_branch_lengths to allow branch
  lengths to be omitted (@hyanwong, #931).

• Added Tree.generate_star static method to create star-topologies (@hyanwong,
  #934).

• Added Tree.generate_comb and Tree.generate_balanced methods to create
  example trees. (@jeromekelleher, #1026).

• Added equals method to TreeSequence, TableCollection and each of the tables which
  provides more flexible equality comparisons, for example, allowing
  users to ignore metadata or provenance in the comparison
  (@mufernando, @jeromekelleher, #896, #897,
  #913, #917).

• Added __eq__ to TreeSequence
  (@benjeffery, #1011, #1020).

• ts.dump and tskit.load now support reading and writing file objects such as
  FIFOs and sockets (@benjeffery, #657, #909).

• Added tskit.write_ms for writing to MS format
  (@saurabhbelsare, #727, #854).

• Added TableCollection.indexes for access to the edge insertion/removal order indexes
  (@benjeffery, #4, #916).

• The dictionary representation of a TableCollection now contains its index
  (@benjeffery, #870, #921).

• Added TreeSequence._repr_html_ for use in jupyter notebooks
  (@benjeffery, #872, #923).

• Added TreeSequence.__str__ to display a summary for terminal usage
  (@benjeffery, #938, #985).

• Added TableCollection.dump and TableCollection.load. This allows table
  collections that are not valid tree sequences to be manipulated
  (@benjeffery, #14, #986).

• Added nbytes method to tables, TableCollection and TreeSequence which
  reports the size in bytes of those objects
  (@jeromekelleher, @benjeffery, #54, #871).

• Added TableCollection.clear to clear data table rows and optionally
  provenances, table schemas and tree-sequence level metadata and schema
  (@benjeffery, #929, #1001).

Bugfixes

• LightWeightTableCollection.asdict and TableCollection.asdict now return copies
  of arrays (@benjeffery, #1025, #1029).

• The map_mutations method previously used the Fitch parsimony method, but this
  does not produce parsimonious results on non-binary trees. We now now use the
  Hartigan parsimony algorithm, which does (@jeromekelleher,
  #987, #1030).

• The flag argument to tables' add_row was treating the value as signed
  (@benjeffery, #1027, #1031).

Breaking changes

• The argument to ts.dump and tskit.load has been renamed file from path.
• All arguments to Tree.newick() except precision are now keyword-only.
• Renamed ts.trait_regression to ts.trait_linear_model.

C API 0.99.8

Minor feature release

New features

• Add tsk_treeseq_genetic_relatedness for calculating genetic relatedness between
  pairs of sets of nodes (@brieuclehmann, #1021, #1023, #974, #973, #898).

• Exposed tsk_table_collection_set_indexes to the API
  (@benjeffery, #870, #921).

Breaking changes

• Added an options argument to tsk_table_collection_equals
  and table equality methods to allow for more flexible equality criteria
  (e.g., ignore top-level metadata and schema or provenance tables).
  Existing code should add an extra final parameter 0 to retain the
  current behaviour (@mufernando, @jeromekelleher,
  #896, #897, #913, #917).

• Changed default behaviour of tsk_table_collection_clear to not clear
  provenances and added options argument to optionally clear provenances
  and schemas (@benjeffery, #929, #1001).

• Renamed tsk_treeseq_trait_regression to tsk_treeseq_trait_linear_model.

Python 0.3.2

Minor feature release

Breaking changes

• Change several methods (simplify(), trees(), Tree()) so most parameters
  are keyword only, not positional. This allows reordering of parameters, so
  that deprecated parameters can be moved, and the parameter order in similar functions,
  e.g. TableCollection.simplify and TreeSequence.simplify() can be made
  consistent (@hyanwong, #374, #846, #851)

Features

• Tree accessor functions (e.g. ts.first(), ts.at() pass extra parameters such as
  sample_indexes to the underlying Tree constructor; also root_threshold can
  be specified when calling ts.trees() (@hyanwong, #847, #848)

• Genomic intervals returned by python functions are now namedtuples, allowing .left
.right and .span usage (@hyanwong, #784, #786, #811)

• Added include_terminal parameter to edge diffs iterator, to output the last edges
  at the end of a tree sequence (@hyanwong, #783, #787)

• #832 - Add metadata_bytes method to allow access to raw
  TableCollection metadata (@benjeffery, #842)

• New tree.is_isolated(u) method (@hyanwong, #443).

• tskit.is_unknown_time can now check arrays. (@benjeffery, #857).

C API 0.99.7

Minor feature release

• Added TSK_INCLUDE_TERMINAL option to tsk_diff_iter_init to output the last edges
  at the end of a tree sequence (@hyanwong, #783, #787)

• Added tsk_bug_assert for assertions that should be compiled into release binaries
  (@benjeffery, #860)

Python 0.3.1

Minor bugfix release

Bugfixes

• #823 - Fix mutation time error when using simplify(keep_input_roots=True) (@petrelharp, #823).

• #821 - Fix mutation rows with unknown time never being equal (@petrelharp, #822).

C API 0.99.6

Bugfixes

• #823 - Fix mutation time error when using tsk_table_collection_simplify with TSK_KEEP_INPUT_ROOTS (@petrelharp, #823).