Pyhmmer

Added
- Out-of-band pickle serialization of `Bitfield` objects.
- Getters for `float` attributes and forward/backward parameters of `OptimizedProfile`.
- `InvalidHMM` error raised by `HMM.validate`.

Changed
- Mark `HMM.zero` method as `noexcept`.
- Increase size of buffer for the query queue in the `hmmer` dispatcher.

Fixed
- Unneeded semaphore in `pyhmmer.hmmer` message passing implementation.
- Broken assertion in `Bitfield._from_raw_bytes`.
- Relax tolerance of HMM validation in `TraceAligner.align_traces`.

Fixed
- Invalid buffer write in `DigitalSequenceBlock.translate` ([50](https://github.com/althonos/pyhmmer/issues/50)).

Added
- `HMM.set_consensus` method to set the consensus for a method or compute it from the emission probabilities.

Fixed
- Platform detection for MacOS and Armv7 platforms in `setup.py`.
- `pyhmmer.plan7.HMM` constructor setting a consensus string forcefully.

Added
- Support for compiling wheels for Aarch64 and NEON-enabled Arm platforms.

Changed
- Updated HMMER to [`v3.4`](https://github.com/EddyRivasLab/hmmer/releases/tag/hmmer-3.4).
- Updated Easel to [`v0.49`](https://github.com/EddyRivasLab/easel/releases/tag/easel-0.49).
- Use [`cibuildwheel`](https://github.com/pypa/cibuildwheel) to build wheel distributions.

Fixed
- Patch missing `PyInterpreterState_GetID` preventing the package from working on PyPy 3.9.

Added
- `TopHits.mode` property showing from which pipeline mode (*search* or *scan*) the hits were obtained.

Changed
- Updated the code for Cython `v3.0`.

Fixed
- `TopHits.merge` not properly handling inclusion and reporting for domains ([46](https://github.com/althonos/pyhmmer/issues/46), [#47](https://github.com/althonos/pyhmmer/pull/47), by [zdk123](https://github.com/zdk123)).

Added
- Bracket-style `repr` implementation to `HMM`, `Profile` and `OptimizedProfile` showing model alphabet, length and name.
- `MissingCutoffs` and `InvalidParameter` exceptions inheriting `ValueError`.

Changed
- Replace `pthread` locks with `PyThread` API for synchronizing models in `OptimizedProfileBlock`.

Fixed
- Sequence length extraction in `LongTargetsPipeline.search_hmm` ([42](https://github.com/althonos/pyhmmer/issues/42)).
- `LongTargetsPipeline.search_msa` not building a HMM with `Builder.build_msa`.