Pyhmmer

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.

Fixed
- Wrong argument type in `IterativeSearch.iterate_hmm` method ([34](https://github.com/althonos/pyhmmer/pull/34), by [zdk123](https://github.com/zdk123)).

Added
- `easel.GeneticCode` class wrapping an `ESL_GENCODE` struct for configuring translation.
- `DigitalSequence.translate` method to translate a nucleotide sequence to a protein sequence. Metadata is copied from the source sequence to its translation ([31](https://github.com/althonos/pyhmmer/pull/31), by [valentynbez](https://github.com/valentynbez)).

Deprecated
- `Sequence.taxonomy_id` property, as it is not used by Easel and implementation is not consistent (see [EddyRivasLab/easel68](https://github.com/EddyRivasLab/easel/issues/68)).

Added
- Missing `__reduce__` method to `TopHits`.

Fixed
- Build detection of available platform functions in `setup.py`.