Update CI to build for Python 3.13 and linux-aarch64

[apcamargo]

This PR:

• Updates the CI to include builds for Python 3.9, 3.10, 3.13, and linux-aarch64.
• Updates the code for compatibility with PyO3 0.24, incorporating support for free-threaded Python by using locks in FastxReader.
• Exposes PyFastxReader as FastxReader in the Python module.
• Adds a stub file to enable IDE type hinting and docstring display upon hovering.

[audy]

@apcamargo thanks for taking this on! Do you have any insights on the overhead impact of the mutex? Maybe it's worth benchmarking this against other approaches (I'm not sure if Atomics is suitable here, but it might be worth looking into).

Also, do you know if free-threading support is required for building a 3.13 wheel? If not, it might be best to split this into two PRs.

[apcamargo]

It seems that starting from PyO3 0.23.0 we will have to take free-threading into account. I think it's best to not postpone, since we will have to update PyO3 anyway.

I'll do some benchmarking and get back to you!

[apcamargo]

@audy I gave it a try, but I couldn't figure out how to use atomics here. I also ran a quick benchmark reading a large FASTA file, comparing this branch to master, and the performance difference was negligible.

For reference, here is the error I get when trying to compile without changing anything in the function:

error[E0277]: `(dyn FastxReader + 'static)` cannot be shared between threads safely
   --> src/python.rs:58:12
    |
58  | pub struct PyFastxReader {
    |            ^^^^^^^^^^^^^ `(dyn FastxReader + 'static)` cannot be shared between threads safely
    |
    = help: the trait `std::marker::Sync` is not implemented for `(dyn FastxReader + 'static)`

[audy]

Ran a simple benchmark of the Python bindings and also saw no significant impact on performance.

This is good to go @apcamargo. Do you mind resolving the merge conflict? Then, I will release a new version to PyPI.

Thanks :)

[apcamargo]

Thanks, @audy!

Before pushing a new release to PyPI, I wanted to make some additional changes. These changes were originally intended for a separate pull request, but I forgot to create a branch before committing 😅

Could you review and confirm if you’re ok with these changes?

• Expose PyFastxReader as FastxReader in the Python module.
• Add a stub file to enable IDE type hinting and docstring display upon hovering.

Before:

After:

[audy]

@apcamargo yes, those would be excellent additions

[apcamargo]

Ok then. Those are already committed, só I think we can merge :)

[audy]

Awesome. Thanks @apcamargo