Fix some doxygen warnings #127
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Replace `\defgroup alphabet` with `\defgroup alphabet Alphabet` ```terminal perl -i -p -e 's/(^.+\\defgroup )(\w)(\w+)($)/\1\2\3 \U\2\E\3\4/g;' **/*.hpp ```
/seqan3/include/seqan3/alphabet/aminoacid/all.hpp:35: warning: the name `all.hpp' supplied as the second argument in the \file statement matches the following input files: /seqan3/include/seqan3/alphabet/adaptation/all.hpp /seqan3/include/seqan3/alphabet/all.hpp /seqan3/include/seqan3/alphabet/aminoacid/all.hpp /seqan3/include/seqan3/alphabet/composition/all.hpp /seqan3/include/seqan3/alphabet/gap/all.hpp /seqan3/include/seqan3/alphabet/nucleotide/all.hpp /seqan3/include/seqan3/alphabet/quality/all.hpp /seqan3/include/seqan3/alphabet/structure/all.hpp Remove optional argument behind \file ```terminal perl -i -p -e 's/(^.+\\file)(.+)($)/\1\3/g;' **/*.hpp ```
…between _
warning: unable to resolve link to `operator""_dna5' for \link command
```terminal
perl -i -p -e 's/(operator) ("") (_\w+)/\1\2\3/g;' **/*.hpp
```
…assumed class-members /seqan3/include/seqan3/alphabet/nucleotide/all.hpp:252: warning: explicit link request to 'A' could not be resolved /seqan3/include/seqan3/alphabet/nucleotide/all.hpp:252: warning: explicit link request to 'C' could not be resolved /seqan3/include/seqan3/alphabet/nucleotide/all.hpp:252: warning: explicit link request to 'G' could not be resolved /seqan3/include/seqan3/alphabet/nucleotide/all.hpp:252: warning: explicit link request to 'T' could not be resolved /seqan3/include/seqan3/alphabet/nucleotide/all.hpp:252: warning: explicit link request to 'U' could not be resolved /seqan3/include/seqan3/alphabet/nucleotide/all.hpp:252: warning: explicit link request to 'UNKNOWN' could not be resolved /seqan3/include/seqan3/alphabet/nucleotide/all.hpp:334: warning: explicit link request to 'T' could not be resolved /seqan3/include/seqan3/alphabet/nucleotide/all.hpp:334: warning: explicit link request to 'U' could not be resolved
This is now auto-linkable:
```c++
template <typename semi_alphabet_type>
using underlying_rank_t = typenam underlying_rank<semi_alphabet_type>::type;
```
This example is still not able to auto-link:
```c++
template <typename alphabet_type>
//!\cond
requires requires (alphabet_type alph) {alphabet_size<alphabet_type>::value; }
//!\endcond
constexpr auto alphabet_size_v = alphabet_size<alphabet_type>::value;
```
Fixes warnings:
/seqan3/include/seqan3/alphabet/concept_pre.hpp:167: warning: explicit link request to 'type' could not be resolved
/seqan3/include/seqan3/alphabet/concept_pre.hpp:79: warning: explicit link request to 'type' could not be resolved
/seqan3/include/seqan3/alphabet/concept_pre.hpp:80: warning: unable to resolve link to `seqan3::underlying_rank_t<>' for \link command
/seqan3/include/seqan3/alphabet/gap/gap.hpp:100: warning: argument 'c' of command @param is not found in the argument list of seqan3::gap::assign_char(char_type const)
/seqan3/include/seqan3/range/container/concatenated_sequences.hpp:227: warning: argument 'count' of command @param is not found in the argument list of seqan3::concatenated_sequences< inner_type, data_delimiters_type >::concatenated_sequences(rng_of_rng_type &&rng_of_rng) /seqan3/include/seqan3/range/container/concatenated_sequences.hpp:227: warning: argument 'value' of command @param is not found in the argument list of seqan3::concatenated_sequences< inner_type, data_delimiters_type >::concatenated_sequences(rng_of_rng_type &&rng_of_rng) /seqan3/include/seqan3/range/container/concatenated_sequences.hpp:345: warning: argument 'count' of command @param is not found in the argument list of seqan3::concatenated_sequences< inner_type, data_delimiters_type >::assign(rng_of_rng_type &&rng_of_rng) /seqan3/include/seqan3/range/container/concatenated_sequences.hpp:345: warning: argument 'value' of command @param is not found in the argument list of seqan3::concatenated_sequences< inner_type, data_delimiters_type >::assign(rng_of_rng_type &&rng_of_rng)
/include/seqan3/range/view/trim.hpp:117: warning: Found ';' while parsing initializer list! (doxygen could be confused by a macro call without semicolon)
Member
Author
|
Remaining open issues:
This is ready to be merged from my pow. |
Member
Author
|
!rebuild |
4 tasks
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Fix doxygen warnings that are not due to being undocumented.