Pyhmmer

Added
- `OptimizedProfile.convert` method to configure an optimized profile from a `Profile` without reallocating a new `P7_OPROFILE` struct.

Changed
- Rewrite the `plan7.Pipeline` search loop to avoid reacquiring the GIL between reference sequences.
- Require the reference sequences to be stored in a collection (instead of an iterable) when passing them to the `search_hmm`, `search_msa` and `search_seq` methods of `plan7.Pipeline`.
- Avoid reallocating a new `OptimizedProfile` every time a new HMM is passed to `Pipeline.search_hmm`.
- Relax the GIL while sorting and thresholding `TopHits` in `Pipeline` search methods.

Added
- `ignore_gaps` parameter to `pyhmmer.plan7.SequenceFile`, allowing to skip the gap characters when reading a sequence from an ungapped format.
- `__sizeof__` implementation for some
- Dedicated check for sequence length before running the platform-specific code in `pyhmmer.plan7.Pipeline`.

Fixed
- Score system not being set in `pyhmmer.plan7.Builder.build_msa`.
- Alphabet not being checked after the first sequence in `Pipeline` search and scan methods.

Fixed
- File object wrappers not reporting exceptions raised when seeking on OSX/BSD platforms.

Added
- `pyhmmer.easel.Randomness` class exposing a deterministic random number generator.
- `pyhmmer.plan7.Builder.randomness` and `pyhmmer.plan7.Pipeline.randomness` attributes exposing the internal random number generator used by each object.
- `pyhmmer.plan7.Hit.best_domain` property mapping to the highest scoring domain of a hit.
- `pyhmmer.plan7.OptimizedProfile.rbv` property exposing match scores.
- `pyhmmer.plan7.Domain.pvalue` and `pyhmmer.plan7.Hit.pvalue` reporting the p-value for a domain or hit bitscore.

Fixed
- Dimensions of the `pyhmmer.plan7.OptimizedProfile.sbv` matrix not being properly set.

Fixed
- Main buffer not being freed in `MatrixF.__dealloc__` and `MatrixU8.__dealloc__` when created without owner.

Added
- Additional configuration values for `pyhmmer.plan7.Pipeline` as both constructor arguments and mutable properties.
- `consensus`, `consensus_structure` and `offsets` properties to `pyhmmer.plan7.Profile` objects.

Changed
- Make `OptimizedProfile.ssv_filter` check the alphabet of the given sequence.

Added
- Linear algebra primitives to expose 1D (`Vector`) and 2D (`Matrix`) contiguous buffers containing numerical values to `pyhmmer.easel`.
- Documentation for the `Z` and `domZ` parameters of the `pyhmmer.plan7.Pipeline` constructor.
- `pyhmmer.errors.AlphabetMismatch` exception deriving from `ValueError` to specifically report mismatching Easel alphabets where applicable.
- `scale` and `normalize` methods to `pyhmmer.plan7.HMM` objects.
- Property to access `pyhmmer.plan7.Background` residue frequencies as a `VectorF` object.
- Property to access `pyhmmer.plan7.HMM` mean residue composition as a `VectorF` object.
- Property to access `pyhmmer.plan7.HMM` probabilities and emissions as `MatrixF` objects.
- `ssv_filter` methods to `pyhmmer.plan7.OptimizedProfile` to get the SSV filter score of the profile for a given sequence.
- Several additional properties to access the `pyhmmer.plan7.OptimizedProfile` internals.

Removed
- Unused `report_e` parameter of `pyhmmer.plan7.Pipeline` constructor.
- `pyhmmer.plan7.TopHits.clear` method which could lead to segfault if it was called while a `Hit` is being held.

Changed
- Multithreaded loop in `pyhmmer.hmmer` to reduce memory consumption while still yielding hits in order.
- `pyhmmer.easel.DigitalSequence.sequence` property is now a `VectorU8`.

Fixed
- Type annotations in `pyhmmer.hmmer`.
- Potential double free in `pyhmmer.plan7.HMM.command_line` property setter.
- Minor floating-point precision issues in `pyhmmer.plan7.Builder` constructor.
- Segfault in `TextMSA.digitize` caused by `esl_msa_Copy` not digitizing on-the-fly like `esl_sq_Copy`.
- Exceptions not being raised in some methods of `pyhmmer.plan7.Profile` and `pyhmmer.plan7.TopHits`.