Replace align_cfg::gap with align_cfg::gap_cost_affine

[wvdtoorn]

Fixes seqan/product_backlog#176.

Replaces seqan3::align_cfg::gap by seqan3::align_cfg::gap_cost_affine.
Deprecates seqan3::gap_scheme,seqan3::gap_open_score and seqan3::gap_score.

[simonsasse]

Some tiny things and a suggestion why travis does not build.
Otherwise 👍

[codecov]

Codecov Report

Merging #2037 into release-3.0.2 will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@              Coverage Diff               @@
##           release-3.0.2    #2037   +/-   ##
==============================================
  Coverage          97.82%   97.83%           
==============================================
  Files                264      264           
  Lines               9947     9926   -21     
==============================================
- Hits                9731     9711   -20     
+ Misses               216      215    -1     

Impacted Files	Coverage Δ
...wise/detail/policy_affine_gap_recursion_banded.hpp	100.00% <ø> (ø)
...qan3/alignment/configuration/align_config_edit.hpp	100.00% <100.00%> (ø)
...ent/configuration/align_config_gap_cost_affine.hpp	100.00% <100.00%> (ø)
...qan3/alignment/pairwise/alignment_configurator.hpp	100.00% <100.00%> (ø)
...nt/pairwise/detail/policy_affine_gap_recursion.hpp	100.00% <100.00%> (ø)
...n3/alignment/pairwise/policy/affine_gap_policy.hpp	100.00% <100.00%> (ø)
...ignment/pairwise/policy/simd_affine_gap_policy.hpp	100.00% <100.00%> (ø)

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[simonsasse]

Sorry that I commented before being done with the review. Here are some more tiny things 🧐😊

[simonsasse]

Looks good, thanks 👍

[marehr]

Thank you :) My first pass-through. I asked the others if we really want to make the affine.extension_score member a strong type.

[marehr]

Reminder for myself: I thought open_score/extension_score is an integer type and not a strong type.

[marehr]

Thank you!

This is basically an approval, can you rebase and then reassign me?

There is one open discussion in the core team, whether

    // Accessing the members of the gap scheme
    int open = affine_cfg.open_score.get(); // open == -1
    int extension = affine_cfg.extension_score.get(); // extension == -10

or

    // Accessing the members of the gap scheme
    int open = affine_cfg.open_score; // open == -1
    int extension = affine_cfg.extension_score; // extension == -10

So that the members of the config element is a strong_type or the bare type.

[marehr]

The members of affine_cfg shouldn't be strong types.

    // Accessing the members of the gap scheme
    int open = affine_cfg.open_score; // open == -1
    int extension = affine_cfg.extension_score; // extension == -10

We decided on this, see seqan/product_backlog#202

@wvandertoorn Is this enough for you and do you know what this means and can you make the changes? If not I can explain it to you :)

[marehr]

Thank you so much :) (Sorry for the delay 😿)

[marehr]

👍 nice catch