feat: add standard derives to all public types

[TheLostLambda]

Implement Rust API Guidelines C-COMMON-TRAITS and C-SERDE

In working with Rust bio, I needed to fork the project in order to serialize some public types like Orf. Missing derive implementations is a common problem I seem to encounter when working with many crates, so I took the afternoon to add every recommended trait (#[derive(Default, Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]) to every pub struct and pub enum in the crate using a script, then I sat down to sort out the compiler issues.

If derives failed because a private rust-bio type didn't implement a certain trait, then derives for those traits were added to private types until they compiled. For derives failing because types outside of rust-bio don't implement a trait, those derives were removed until the code compiled.

After adding all of those derives, I also cleaned up a few clippy lints in the second commit. Adding some of those Copy derives meant a lot of calls to Clone could be removed!

Sorry this looks like a massive change! Should be relatively trivial to review though, since it should only be adding derives and not touching anything more complex.

[TheLostLambda]

Oh, and sorry for that messy looking commit history! I assume you'll squash things, but a lot of those commits were me re-syncing my fork with your master branch before starting this work. Only the last two commits should actually contain any changes!

[coveralls]

Coverage decreased (-0.01%) to 88.38% when pulling e087b05 on TheLostLambda:main into f73cab7 on rust-bio:master.

[TheLostLambda]

As far as I can tell, @coveralls might just be confused by the changing of formatting from adding the derives! I don't see any other way coverage has changed!

[natir]

Hello @TheLostLambda,

Thank for this pull request and for discover of Rust API Guidelines.

Except some not required change in benchmark, this pull request seems good. I run a benchmark to check if change have an impact on computation time, moreover so noise in benchmark, it's seems this pull request didn't have any impact on runtime.

@TheLostLambda the lost of 0.01% of code coverage isn't realy important.

Before merge you could probably rebase your commit on top of rust-bio change ? @rust-bio/mergers I think this pull request is ready to merge.

[natir]

It's good for me

[TheLostLambda]

Could I poke @johanneskoester about getting this merged? I'd also be quite keen in joining the mergers team in the future! There is a lot of work with this library in my future and it would be great if could get a bit more involved in its maintenance!

Thanks a ton and sorry for pestering!

[johanneskoester]

Awesome @TheLostLambda! Thanks a lot!

1. Yes, at any time, feel free to contact me via mail or discord. Github notifications are a problem for me, because I get far too many via Bioconda and Snakemake.
2. And yes, I am now immediately including you into the mergers team. Welcome!

[johanneskoester]

You have an invite!