Changes in version 2026-04-07                      

Added (new features)

  - Added the following scalar getters to match tskit C/Python API
      - TreeSequence$discrete_genome() to query whether genome
        coordinates are discrete integer values.
      - TreeSequence$has_reference_sequence() to query whether a tree
        sequence contains a reference genome sequence.
      - TreeSequence$discrete_time() to query whether time values are
        discrete integer values.
      - TreeSequence$file_uuid() to query the UUID of the source .trees
        file.
      - TableCollection$has_reference_sequence() to query whether a
        table collection contains a reference genome sequence.
      - TableCollection$file_uuid() to query the UUID of the source
        .trees file.
      - TableCollection$sequence_length() to query the sequence length.
      - TableCollection$time_units() to query the time units.
      - TableCollection$has_index() to query whether edge indexes are
        present.
  - Added a public header and defaults for downstream use of C++
    functions in inst/include/RcppTskit_public.hpp, included by
    inst/include/RcppTskit.hpp.
  - Added TableCollection$build_index() to build indexes and
    TableCollection$drop_index() to drop indexes.
  - Added ``TableCollection$num_*()` getters for the number of rows in
    the tables.
  - Added rtsk_individual_table_add_row() and
    TableCollection$individual_table_add_row() to append individual rows
    from \code{R}, mirroring tsk_individual_table_add_row().
  - Added rtsk_node_table_add_row() and
    TableCollection$node_table_add_row() to append node rows from
    \code{R}, mirroring tsk_node_table_add_row().
  - Added rtsk_edge_table_add_row() and
    TableCollection$edge_table_add_row() to append edge rows from
    \code{R}, mirroring tsk_edge_table_add_row().
  - Added rtsk_site_table_add_row() and
    TableCollection$site_table_add_row() to append site rows from
    \code{R}, mirroring tsk_site_table_add_row().
  - Added rtsk_mutation_table_add_row() and
    TableCollection$mutation_table_add_row() to append mutation rows
    from \code{R}, mirroring tsk_mutation_table_add_row().
  - TODO

Changed

  - Renamed low-level C++ and R API names such that we map onto tskit C
    API, for example, RcppTskit functions are named rtsk_treeseq_load(),
    while tskit C name is tsk_treeseq_load(). This is an internal
    breaking change, but in a good direction now that the package is
    still young and in experimental mode.
  - Renamed TreeSequence and TableCollection external-pointer field from
    pointer to xptr.
  - Ensured TableCollection$tree_sequence() matches tskit Python API: it
    now builds indexes on the TableCollection, if indexes are not
    present.
  - We now use bit64::integer64 (signed 64 bit integer) instead of int
    aiming to approach tsk_size_t in tskit C (unsigned 64 bit integer);
    in low-level rtsk_treeseq_get_num_*() wrappers and
    count/metadata-length fields.
  - TODO

Maintenance

  - Turn vignette URL as hyperlinks and similar cosmetics.
  - State that we mirror the R/Python APIs and C++/C APIs across the
    package.
  - Update tskit C to 1.3.1
  - TODO

                     Changes in version 2026-02-22                      

Added (new features)

  - Added TableCollection R6 class alongside tc_load() or
    TableCollection$new(), as well as dump(), tree_sequence(), and
    print() methods.

  - Added TreeSequence$dump_tables() to copy tables into a
    TableCollection.

  - Added TableCollection and reticulate Python round-trip helpers:
    TableCollection$r_to_py() and tc_py_to_r().

  - Changed the R API to follow tskit Python API for loading: ts_load(),
    tc_load(), TreeSequence$new(), and TableCollection$new() now use
    skip_tables and skip_reference_sequence logical arguments instead of
    an integer options bitmask.

  - Removed user-facing options from TreeSequence$dump(),
    TreeSequence$dump_tables(), TableCollection$dump(), and
    TableCollection$tree_sequence() to match R API with the tskit Python
    API, while C++ API has the bitwise options like the tskit C API.

  - The bitwise options passed to C++ are now validated.

Changed

  - We now specify C++20 standard to go around the CRAN Windows issue,
    see #63 for further details.

Maintenance

  - Used \dontrun{} with get_tskit_py() calls in examples to further
    reduce R CMD check time on CRAN.

  - Reduced bundled example tree-sequence sizes in
    inst/examples/test.trees and inst/examples/test2.trees to speed up
    examples and checks.

  - Delete temporary files in examples and tests after use.

  - Renamed unexported functions from RcppTskit:::ts_load_ptr() to
    RcppTskit:::ts_ptr_load() style.

                     Changes in version 2026-01-26                      

This is the first release.

Added (new features)

  - Initial version of RcppTskit using the tskit C API (1.3.0).

  - TreeSequence R6 class so R code looks Pythonic.

  - ts_load() or TreeSequence$new() to load a tree sequence from file
    into R.

  - Methods to summarise a tree sequence and its contents ts$print(),
    ts$num_nodes(), etc.

  - Method to save a tree sequence to a file ts$dump().

  - Method to push tree sequence between R and reticulate Python
    ts$r_to_py() and ts_py_to_r().

  - Most methods have an underlying (unexported) C++ function that works
    with a pointer to tree sequence object, for example,
    RcppTskit:::ts_ptr_load().

  - All implemented functionality is documented and demonstrated with a
    vignette.