refactor: Using submodules as features

[luiz10x]

Following the discussion in #342, this PR tries to get an initial MVP for (potentially) splitting into subcrates in the future.

The important change is in Cargo.toml: each submodule becomes a feature, and they are all enabled by default. In turn, all the dependencies are optional, and I mapped what deps are used for each submodule in the correspondent feature.

The main advantage of this approach is not making maintenance harder (it is still all one crate, with one version). It is a bit weird to have all the deps as optional, but I don't think that is too bad?

I also keep all new submodule features in the default feature set, so current users won't see a difference. In the future it might be worth adding docs/instructions to guide people in two directions:

• if you're using bio in an application, using the default bio = "0.x" dependency is fine; you might want to tune to reduce your build times, but it won't make it harder for new users to use rust-bio.
• for library writers disabling default features and using only what you need is recommended, because your choice of features has consequences for people using your library. In this case you might prefer to use bio = { version = "0.x", default-features = false, features = ["io"] }" if you only use the io features.

I also added extra CI checks for running tests for each feature/submodule individually, to guarantee they stay working (and minimally depend on each other).

Points for discussion

• the phylogeny feature was not tested in CI, and a docstring test was actually broken. I added a CI check, and since it is inside the io submodule I also made it activate the io feature if used.

Future work

• this opens the way to make serde into a feature too, but I didn't want to change the code too much
• newtype_derive and custom_derive are unmaintained (last releases are from many years ago), maybe find alternatives?

[coveralls]

Coverage remained the same at 88.675% when pulling 5491aab on luiz10x:lirber/features into 9e8a7ca on rust-bio:master.

[allan2]

I think splitting of the crates as discussed in #342 is a good idea.

However, I don't think it is helpful to turn submodules into a feature as a "middle step".
We should figure out how to split the crates properly, since the submodules as they are now may not be how we want the smaller crates to be organized.

Continuing discussion at #342

[johanneskoester]

Interesting idea @luiz10x! Please see my comment in the discussion issue.