To Do in Documentation

[MitraDarja]

• [x] A short sentence to describe what Configuration does on the Alignment overview in API references (modules)
• [x] Write detailed landing page for alignment
• [x] Write detailed landing page. for band in alignment (seqan/seqan3#1956)
• [x] banded section in Alignment configuration
• [x] Write detailed landing page. for matrix in alignment. (https://github.com/seqan/seqan3/issues/1957)
• [x] Document EditDistanceTrait in Alignment.
• [x] Function table in Alignment Matrix overview is too wide.
• [x] Table in Alphabet Overview for Different concepts is too wide. (Plus, there are some weird boxes in column Aux)
• [x] Link to customisation point manual in alphabet_size, in assign_char_to, assign_rank_to, char_is_valid_for, to_char, to_rank
• [x] weird spacing in is_char_adaptation_v, is_uint_adaptation_v
• [x] fix table private attributes in argument parser, is too wide
• [x] Related functions in validator of argument parser looks incomplete
• [x] Detailed description in validator_concept looks incomplete (https://github.com/seqan/seqan3/issues/1961)
• [x] Table Variables in core algorithm too wide
• [x] Write detailed landing page concept in core (https://github.com/seqan/seqan3/issues/1958)
• [x] Table Type definition in simd too wide
• [x] Write detailed description in simd (https://github.com/seqan/seqan3/issues/1959) Will be done once SIMD becomes non detail code
• [x] Write detailed description alignment file in IO
• [x] read_groups in alignment file in IO, barcode table is not correctly shown , same problem in ref_id_info
• [x] Type deduction guides table in alignment file in IO too wide
• [x] give overview of formats, once they are all implemented in alignment file input in IO
• [x] TODO linear in the size of the written alignments? in emplace_back()(push_back in IO
• [x] Write detailed description for sequence files in IO
• [x] Missing link to quality submodule in format_fastaq
• [x] table which files take which fields in seqan3::fields
• [x] Rewrite landing page. for kmer-indices in FM-Index (https://github.com/seqan/seqan3/issues/1960)
• [x] Update concepts and documentation of configuration_t everywhere once it has been refactored by rrahn.
• [x] (between a factor of X and Y depending on the configuration). in FM Indicies

Death links:

• ~std::view::single in Alignment Pairwise.~
• [ ] views::take in align_pairwise_range_input in Alignment Pairwise.
• [ ] seqan3::alphabet_size is never linked correctly in snippets
• ~std::Equality_comparable in mask in Alphabet~
• ~std::contrib::latch in Core Parallel`~
• [ ] seqan3::d/rna*_vector in operator""_d/rna*() in Nucleotide
• [ ] seqan3::detail::format_ctd in argument parser because format is not existing yet
• seqan3::print_list_item in argument parser (there is one for each format, not sure which one to pick for a link)
• [ ] seqan3::print_line in argument parser (there is one for each format, not sure which one to pick for a link)
• [ ] cereal::BinaryInputArchive, cereal::PortableBinaryInputArchive, cereal::JSONInputArchive, and cereal::XMLInputArchive
• [ ] the ranges concepts in every view documentation. e.g. std::ranges::forward_range
• [ ] std::optional<int32_t> (template parameter inhibits linking somehow)
• [ ] std::ignore
• [ ] concat_capacity() to concat_size() in Container
• [ ] seqan3::detail::configuration (is not detail)
• [ ] seqan3::detail::transfer_template_args_onto
• [ ] seqan3::detail::transfer_template_vargs_onto
• ~seqan3::detail::transformation_trait_or_t~
• [ ] seqan3::detail::is_value_specialisation_of
• [ ] seqan3::detail::buffer_queue and seqan3::buffer_queue

[marehr]

This is a code snippet. You will see many code snippets in our documentation. Most of them are compilable as-is, but some are only valid in their context, e.g. they depend on other code snippets given before/after the current one or other statements implied by the text. You can copy'n'paste freely from these examples, this implies no copyright-obligations (however distributing SeqAn3 or an application using it does, see "Copyright and Citing").

Make a link to Copyright and Citing.

[h-2]

http://docs.seqan.de/seqan/3-master-user/todo.html

[h-2]

What is the state here? Lot's of it got fixed for the release, did someone keep track?

[smehringer]

I checked off the ones I did :white_check_mark:

[smehringer]

@jwinkler Since Mitra is not working on Seqan currently, could check the documentation? :)

[joergi-w]

Yes, sure!

[eseiler]

@MitraDarja Can you check which points are still relevant? Quick scan would suggest concat_capacity() to concat_size() in Container but the rest seems rather resolved?

[smehringer]

This is done with #3064