Changes in version 2026-01-09                      

Bug fix: fixed the wrong logic in AlignmentCount.rx2idx() that caused
incorrect alignment counting in PMI distance calculation.

                     Changes in version 2026-01-06                      

Fixed several bugs and improved performance.

Bug fixes:

  - In alignment.cpp, fixed a bug that caused incorrect alignment
    results. All of the aligned sequences were accumulated into the last
    sequence.
  - Fixed all possible issues on double types comparison.
  - Fixed memory leak caused by RcppThread::ProgressBar not being
    destructed properly.
  - In some corner cases, when nwords==0, all distance functions would
    return negative distances. Now they return NA.
  - In dist_wjd.cpp, fixed a bug that caused incorrect WJD distance.
    wjd_form would never return 0.0 in the multi-category case.
  - In dist_wjd.cpp, added checks for vector lengths of
    multi_form_weights and multi_form_cats.
  - In dist_wjd.cpp, added checks for multi_form_weights sum being
    greater than 0.
  - In cost_table.cpp, added checks for symbols existing in both row and
    column names of the cost matrix.

Performance improvements:

  - In alignment.cpp, rewrited the DFS algorithm. Avoid insert to the
    front of a vector, which is slow.
  - In dist_pmi.cpp, rewrited the alignment counting logic with a new
    structure AlignmentCounter. Now we use a dense vector to store
    counts instead of a hash map, and a vector<string> for
    string-to-index searching. This is faster when the number of unique
    symbols is small, which is usually the case.

                     Changes in version 2026-01-04                      

Add quite parameters to all distance functions to control printing
messages and progress bars.

                     Changes in version 2025-12-26                      

Several improvements have been made:

  - long2squareform fills diagonal with 0 now; this can be specified
    with default_diag parameter.
  - CostTable is reconstructed to support both a normal and a fast
    implementation. In the fast case, get_cost will not lookup the cost
    table but directly return values to fasten classic edit distance
    computation.
  - pw_edit_dist now:
      - checks missing symbols in cost matrix by default; this can be
        disabled with check_missing_cost = FALSE.
      - builds fast cost table when cost matrix is not provided; the
        fast table costs can be specified with default_sub_cost and
        default_ins_del_cost parameters.
  - report more information in pw_pmi_dist.

Added WJD distance supporting hierarchical categorical data with
multiple forms.

                     Changes in version 2025-12-22                      

  - Reconstructed the whole C++ codes for edit distance calculation.
  - Added PMI distance supporting.

                        Changes in version 1.0.0                        

  - Initial CRAN submission.