[FEATURE] Add sharg-parser submodule and replace the seqan3::argument_parser.

[smehringer]

Blocked by ~#2952~ #2970

This PR does a lot.

• [x] it adds the sharg parser as submodule
• [x] it fixes a test in format_parse_validator_test where enum foo needs an enumeration_names overload in order to work with validators and the argument parser. This was not enforced by the validator itself, but is enforced in sharg. Since you don't use validators without the argument_parser this can be considered a fix not an API break.
  • [ ] A note in the changelog should still be added I guess
• [x] It replaces the help page tests in format_parse_validator_test by comparing the output with filter views instead of accessing the private member console_layout to set the terminal width, s.t. the output is comparable. The sharg::detail::help+format would otherwise need to befriend the seqan3 test accessor but this would add a dependency on seqan3.
• [x] It deletes all detail files since they are not for the user and are not needed in seqan3
• [x] It replaces all public seqan3 API by sharg API via using namespace sharg; declaration. The following exceptions had to be made:
  • [x] The argument_parser class will have differences to the sharg parser and thus must inherit from it.
  • [x] The input and output validators had I/O specific functionality that was removed in sharg and added again here to avoid breaking code for now. We can discuss if we want to deprecate them completely.
• [x] The enumeration_names CPO can be satisfied by overloading seqan3::custom::argument_parsing. This must be done with the explicit, complete namespace instead of opening the namespace seqan3::custom{ ... }.
  • [ ] Adjust snippet or tutorial

Once everything compiles I will make separate commits for reviews

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Codecov Report

Merging #2954 (bbeac7e) into master (d9294eb) will increase coverage by 0.38%. The diff coverage is 100.00%.

:exclamation: Current head bbeac7e differs from pull request most recent head e4a3969. Consider uploading reports for the commit e4a3969 to get more accurate results

@@            Coverage Diff             @@
##           master    #2954      +/-   ##
==========================================
+ Coverage   98.21%   98.59%   +0.38%     
==========================================
  Files         274      258      -16     
  Lines       12216    10336    -1880     
==========================================
- Hits        11998    10191    -1807     
+ Misses        218      145      -73     

Impacted Files	Coverage Δ
include/seqan3/argument_parser/argument_parser.hpp	100.00% <100.00%> (+2.51%)	:arrow_up:
include/seqan3/argument_parser/validators.hpp	100.00% <100.00%> (ø)
include/seqan3/core/debug_stream/variant.hpp	80.00% <0.00%> (-5.72%)	:arrow_down:
...clude/seqan3/search/detail/search_configurator.hpp	93.33% <0.00%> (-3.64%)	:arrow_down:
...an3/alignment/scoring/aminoacid_scoring_scheme.hpp	89.47% <0.00%> (-2.84%)	:arrow_down:
include/seqan3/utility/views/single_pass_input.hpp	97.22% <0.00%> (-2.78%)	:arrow_down:
include/seqan3/io/detail/in_file_iterator.hpp	94.28% <0.00%> (-2.69%)	:arrow_down:
include/seqan3/io/views/detail/take_until_view.hpp	96.55% <0.00%> (-1.67%)	:arrow_down:
include/seqan3/io/detail/misc_output.hpp	94.44% <0.00%> (-0.30%)	:arrow_down:
include/seqan3/io/sam_file/detail/cigar.hpp	97.82% <0.00%> (-0.22%)	:arrow_down:
... and 220 more

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[eseiler]

We have to do either of both:

namespace seqan3::custom
{
// Specialise the seqan3::custom::argument_parsing data structure to enable parsing of std::errc.
template <>
struct sharg::custom::argument_parsing<std::errc>
{
    // ...
};

} // namespace seqan3::custom

namespace sharg::custom
{
// Specialise the sharg::custom::argument_parsing data structure to enable parsing of std::errc.
template <>
struct argument_parsing<std::errc>
{
    // ...
};

} // namespace sharg::custom

[smehringer]

// Specialise the seqan3::custom::argument_parsing data structure to enable parsing of std::errc.
template <>
struct seqan3::custom::argument_parsing<std::errc>
{
    // ...
};

works and should be promoted

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Name	Status	Preview	Updated
seqan3	❌ Failed (Inspect)		Jun 3, 2022 at 10:33AM (UTC)

[SGSSGene]

We will include sharg as a submodule, but not integrate it into seqan3 namespace