Pyhmmer

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`.

Added
- `Pipeline.scan_seq` method to query a database of profiles with one or more sequences.
- `transition_probabilities`, `match_emissions`, `insert_emissions` properties to the `HMM` class, providing access to the numerical parameters of the HMM.
- `consensus_structure` and `consensus_accessibility` properties to the `HMM` class to get consensus lines from the source alignment if the HMM was created from a MSA.
- `nseq` and `nseq_effective` properties to the `HMM` class to get the number of training sequences and effective sequences used to build the HMM.

Changed
- `HMM.checksum` is now `None` if the `p7H_CHKSUM` flag is not set.
- `Builder` methods will now record `sys.argv` when creating a HMM.

Fixed
- `HMM.write(..., binary=False)` crashing on HMMs without a consensus line. ([5](https://github.com/althonos/pyhmmer/issues/5)). Fixed upstream in ([EddyRivasLab/HMMER#236](https://github.com/EddyRivasLab/hmmer/pull/236)).
- `Pipeline.reset` mishandling the `Z` and `domZ` values if those were detected from the number of targets.
- `pyhmmer.hmmer` functions will not block until all results have been collected anymore when run in multithreaded mode.

Added
- `easel.MSAFile` to read from a file containing
- `accession`, `author`, `name` and `description` properties to `easel.MSA` objects.
- `plan7.Builder.build_msa` to build a pHMM from a sequence alignment.
- Additional methods to `easel.KeyHash`, allowing to use it as a `dict`/`set` hybrid.
- `Sequence.write` and `MSA.write` methods to format a sequence or an alignment to a file handle.
- `plan7.TopHits.to_msa` method to convert all the top hits of a query against a database into a multiple sequence alignment.
- `easel.MSA.sequences` attribute to access individual sequences of an alignment using the `collections.abc.Sequence` interface.
- `easel.DigitalMSA.textize` method to convert a multiple sequence alignment in digital mode to its text-mode counterpart.
- Read-only `name`, `accession` and `description` properties to `plan7.Profile` showing attributes inherited from the HMM it was configured with.
- `plan7.HMM.consensus` property, allowing to access the consensus sequence of a pHMM.
- `plan7.HMM` equality implementation, using zero tolerance.
- `plan7.Pipeline.search_msa` to query a MSA against a sequence database.
- `easel.Sequence.reverse_complement` method allowing to reverse-complement inplace or to build a copy.
- `errors.AlphabetMismatch` exception for use in cases where an alphabet is expected but not matched by the input.
- `hmmer.nhmmer` function with the same behaviour as `hmmer.phmmer`, except it expects inputs with a DNA alphabet.

Fixed
- `plan7.Builder.copy` not copying some parameters correctly, causing `pyhmmer.hmmer.phmmer` to give inconsistent results in multithreaded mode.
- `easel.Bitfield` not properly handling index overflows.
- Documentation not rendering for the `__init__` method of all classes.

Changed
- `plan7.Builder` gap-open and gap-extend probabilities are now set on instantiation and depend on the alphabet type.
- Constructors for `easel.TextMSA` and `easel.DigitalMSA`, which can now be given an iterable of `easel.Sequence` objects to store in the alignment.

Removed
- Unimplemented `easel.SequenceFile.fetch` and `easel.SequenceFile.fetchinto` methods.