Pyhmmer

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`.

Added
- `HMM.validate` method to ensure a HMM holds HMMER structural constraints.
- `plan7.Transitions` enum with transition names for indexing `HMM.transition_probabilities`.

PyHMMER has been accepted for publication in [Bioinformatics](https://academic.oup.com/bioinformatics). Paper can be reached at [doi:10.1093/bioinformatics/btad214](https://doi.org/10.1093/bioinformatics/btad214).

Added
- `pyhmmer.hmmer.jackhmmer` function to run several JackHMMER iterative searches in parallel using multithreading ([35](https://github.com/althonos/pyhmmer/pull/35), by [zdk123](https://github.com/zdk123)).
- `HMM.to_profile` shortcut method to allocate and configure a new `Profile` object.

Fixed
- Type annotations of `Pipeline.iterate_seq` and `Pipeline.iterate_hmm`.
- Potential memory leak on exceptions raised by `HMMPressedFile.read`.
- `Offsets.profile` not recording offsets properly, causing `pyhmmer.hmmer.hmmpress` to produce invalid pressed files ([37](https://github.com/althonos/pyhmmer/issues/36)).

Changed
- `HMM.__init__` and `HMM.sample` now take the `Alphabet` as the first argument, for consistency with the rest of the API.
- `HMM` now require a `name` argument.

Removed
- Deprecated `ignore_gaps` argument in `SequenceFile.__init__`.
- Deprecated `Sequence.taxonomy_id` property.

Added
- *Recipes* page to the documentation with code example for loading multiple HMM files ([24](https://github.com/althonos/pyhmmer/issues/24), by [zdk123](https://github.com/zdk123)).

Fixed
- `TraceAligner` methods causing a segfault when passed an uninitialized HMM ([36](https://github.com/althonos/pyhmmer/issues/36)).

Changed
- `HMM` default constructor now always creates a valid HMM (with respects to probability arrays).
- `TraceAligner` now validates the input `HMM` before calling the HMMER code.
- Use stack allocation for all error buffers instead of creating empty `bytearray` objects where applicable.