0.7.1

Summary: fix some ranges by using our own tuple.

Added

• bio::meta::tuple which behaves like C++23's std::tuple.

Fixed

• bio::views::zip uses bio::meta::tuple and now also models std::ranges::output_range.
• bio::views::pairwise_combine uses bio::meta::tuple and now also models std::ranges::output_range.
• bio::ranges::dictionary uses bio::meta::tuple. Now bio::ranges::dictionary<> const works correctly.

API

• This release is not yet API-stable.
• This release is mostly backwards compatible with 0.7.0 (see changes above).

0.7.0

Summary: we now support LLVM/clang as a compiler; CIGARs have been much improved and there is a new container.

Added

• 🐉 Full support for Clang-16 as a compiler. This is a big milestone for 1.0.0!
• A new associative container: bio::ranges::dictionary. It has features of std::vector and std::unordered_map at the cost of extra size.
• New implementation for bio::alphabet::cigar. This is now 32bits in size (instead of 64bit) and ABI-compatible to BAM/htslib.
• bio::views::to_char, bio::views::char_to<> and bio::views::char_strictly_to<> now work for bio::alphabet::cigar (even though CIGARs are not full alphabets).

Fixed

• bio::views::to_char, bio::views::char_to<> and bio::views::char_strictly_to<> are now "no-op" views if no transformation needs to happen (e.g. when input and output alphabet would be char).
• When using find_package(biocpp COMPONENTS core io), the version strings were not set correctly.

Maintained

• bio::ranges::small_string now satisfies the std::ranges::view-concept for capacities <= 30.
• bio::views::interleave has been redefined in terms of bio::views::transform_by_pos (much less code); should also be a bit faster now.
• Clang-tidy is automatically run as part of the CI.
• Concepts are now properly supported and integrated into the documentation; doxygen-1.9.6 is recommended.

Renamed

• bio::alphabet::nucleotide_alphabet → bio::alphabet::nucleotide (same for aminoacid_alphabet, quality_alphabet and writable_quality_alphabet).

Removed

• bio::views::as_const has been removed, use C++23's std::views::as_const instead.
• bio::views::move has been removed, use C++23's std::views::as_rvalue instead.

API

• This release is not yet API-stable.
• This release is mostly backwards compatible with 0.6.0 (see changes above).

0.6.0

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).

0.5.0 – "less is more"

Features

• This release is a fork of SeqAn-3.0.2.
• The feature set is stripped to contain the important "core" aspects: Alphabets and Ranges, as well as metaprogramming support utilities.
• It has no dependencies.

Some notable changes for users coming from SeqAn3

• 🧹 Huge code cleanup and countless bug-fixes.
• ✂ Removal of all dependencies… and… most of the code :)
• 📦 Separate namespaces for each module.
• 🏷 Much simpler customisation points by using tag_invoke().
• 🖨 Replaced the debug_stream with {fmt}.
• 🛸 More Modern C++ goodness: use of the spaceship operator, consteval, …
• 📉 Compile-time down.
• 📈 Performance up (for a few things).

API stability

• This release is not yet API-stable.
• This release is not backwards compatible with any BioC++ or SeqAn version.