Removing Python 2 support

This release removes support for Python 2, adds more flexible tree access and a new tskit command line interface.

New features

• Remove support for Python 2 (:user:hugovk). See :issue:137 and :pr:140.
• More flexible tree API (:pr:121). Adds TreeSequence.at and TreeSequence.at_index methods to find specific trees, and efficient support for backwards traversal using reversed(ts.trees()).
• Add initial tskit CLI (:issue:80)
• Add tskit info CLI command (:issue:66)
• Enable drawing SVG trees with coloured edges (:user:hyanwong; :issue:149).
• Add Tree.is_descendant method (:issue:120)
• Add Tree.copy method (:issue:122)

Bugfixes

• Fixes to the low-level C API (:issue:132 and :issue:157)

C API Bugfixes

Bugfix release. Changes:


• Fix incorrect errors on tbl_collection_dump (#132)
  - Catch table overflows (#157)

Feature update

Minor feature update. Using the C API 0.99.1.

New features

• Add interface for setting TableCollection.sequence_length: #107
• Add support for building and dropping TableCollection indexes: #108

Draft C API release

Draft of the C API. The tables API should be quite mature and well documented. Changes will only be made if serious problems occur. The tree sequence and tree APIs are more provisional and are subject to changes.

Changes:

• Change the _tbl_ abbreviation to _table_ to improve readability. Hence, we now have, e.g., tsk_node_table_t etc.
• Change tsk_tbl_size_t to tsk_size_t.
• Standardise public API to use tsk_size_t and tsk_id_t as appropriate.
• Add tsk_flags_t typedef and consistently use this as the type used to encode bitwise flags. To avoid confusion, functions now have an options parameter.
• Rename tsk_table_collection_position_t to tsk_bookmark_t.
• Rename tsk_table_collection_reset_position to tsk_table_collection_truncate and tsk_table_collection_record_position to tsk_table_collection_record_num_rows.
• Generalise tsk_table_collection_sort to take a bookmark as start argument.
• Relax restriction that nodes in the samples argument to simplify must currently be marked as samples. (#72)
• Allow tsk_table_collection_simplify to take a NULL samples argument to specify "all samples in the current tables".
• Add support for building as a meson subproject.

Bugfix release

Bugfixes

• Fix missing provenance schema: #81

Bugfix release

Bugfix release.

Bugfixes

• Fix memory leak in table collection. #76

Initial alpha release of tskit C API

Initial alpha version of the tskit C API tagged. Version 0.99.x represents the series of releases leading to version 1.0.0 which will be the first stable release. After 1.0.0, semver rules regarding API/ABI breakage will apply; however, in the 0.99.x series arbitrary changes may happen.

Bugfix release

Fix broken packaging for 0.1.0 release.

Initial release

Initial release after separation from msprime 0.6.2. Code that reads tree sequence
files and processes them should be able to work without changes.

Breaking changes

• Removal of the previously deprecated sort_tables, simplify_tables
  and load_tables functions. All code should change to using corresponding
  TableCollection methods.

Initial Python release for bootstrapping

This is the initial release of tskit used to bootstrap the separation of tskit and msprime.