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@h-2 h-2 released this 20 Oct 18:11
· 69 commits to main since this release
0.6.0
1623832

Summary: The alphabet module is almost API-stable. Several things in meta and ranges were cleaned up.

Added

  • bio::meta::one_of, bio::meta::decays_to and bio::meta::different_from concepts.
  • bio::meta::vtag, bio::meta::ttag and bio::meta::priority_tag.
  • bio::ranges::back_insertable and bio::ranges::back_insertable_with as light-weight "container" concepts.
  • bio::views::char_strictly_to and bio::views::validate_char_for; as well as bio::views::char_conversion_view_t.
  • bio::views::transform_by_pos, a more flexible version of std::views::transform.
  • bio::views::add_reverse_complement which turns a range of sequences into a range of sequences with their reverse complements interleaved as every second element.

Fixed

  • Some edge-cases with composite alphabets were fixed.
  • Many potential bugs and missed optimisations found by clang-tidy (and fixed).
  • bio::ranges::dynamic_bitset was not an output_range<bool> because of incomplete proxy types.

Maintained

  • bio::views::translate* have been redefined in terms of bio::views::transform_by_pos (much less code); bio::views::translate_single is now in include/bio/ranges/views/translate_single.hpp.
  • Cleaned up most of the concept mess in composite alphabets.
  • All alphabet literals (e.g. 'C'_dna4, "GATTACA"_dna4) are now strict and validated at compile-time. Character literals are consteval. This prevents bugs early on.

Renamed

  • bio::alphabet::alphabet_* to bio::alphabet::*, e.g. bio::alphabet::alphabet_variant to bio::alphabet::variant.
  • bio::alphabet::cpo:: to bio::alphabet::custom::; rename bio/alphabet/adaptation to bio/alphabet/custom and move customisation tags to that folder.
  • bio::ranges::views::to() has been renamed to bio::ranges::to() to be in line with C++23.

Removed

  • bio::alphabet::*_vector aliases were removed; just use std::vector<alphabet> instead.
  • bio::meta::* several unused traits were removed.
  • bio::ranges::pseudo_random_access_iterator and bio::ranges::pseudo_random_access_range have been removed (because they are not used).
  • bio::ranges::sequence concept has been removed (because it is not used).
  • bio::views::get has been removed. Use std::views::elements instead (same functionality).

API

  • This release is not yet API-stable.
  • This release is mostly backwards compatible with 0.5.0 (see changes above).
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