Pyhmmer

Added
- `plan7.PipelineSearchTargets` to reduce the overhead when searching the same sequences several times with different. query profiles.
- `TopHits.copy` method to duplicate a `TopHits` instance.
- `TopHits.merge` method to merge hits obtained with the same query on different targets.
- Buffer protocol implementation for `pyhmmer.easel.Bitfield`.

Changed
- Renamed `TopHits.included` and `TopHits.reported` properties to `TopHits.hits_included` and `TopHits.hits_included`.
- `MSAFile` and `SequenceFile` are now directly in digital mode if they are instantiated with `digital=True`.
- `SequenceFile.parse` can now return a sequence in digital mode.
- Reorganized tests to make then runnable from a site install.

Fixed
- Usage of `memcpy` in contexts where it may have had undefined behaviour.
- `VectorF.__eq__` crashing when comparing two empty objects.
- `SequenceFile` and `MSAFile` not closing file handles when raising an error in `__init__`.

Added
- `plan7.HMMFile.read` method to read a single `plan7.HMM` from an `plan7.HMMFile` (instead of using `next`).
- `closed` property on `easel.SequenceFile`, `easel.MSAFile` and `plan7.HMMFile` to mark whether a file object is closed.
- `plan7.HMMFile.is_pressed` method to check whether a HMM file has associated pressed data.
- `plan7.HMMFile.optimized_profiles` methods to read the `plan7.OptimizedProfile` entries in an `plan7.HMMFile` is there are associated pressed data available.
- Getters for the `name`, `accession`, `description`, `consensus`, `consensus_structure`, `evalue_parameters` and `cutoffs` properties of a `plan7.OptimizedProfile`.
- `plan7.OptimizedProfile.__eq__` implementation to compare two optimized profiles.
- `__sizeof__` implementations for `plan7.OptimizedProfile` and `plan7.Profile` to get the allocated size of a profile.

Fixed
- Double-free caused by the Cython cycle breaking feature on several view types (`easel.Randomness`, `easel.Vector`, `easel.Matrix`, `plan7.Cutoffs`, `plan7.EvalueParameters`, `plan7.Offsets`, `plan7.Trace`)
- `plan7.Hit.description` using the pointer to the accession string erroneously, causing occasional NULL dereference.
- `plan7.OptimizedProfile.copy` performing a shallow copy instead of a deep copy as expected.

Changed
- `pyhmmer.hmmer` type annotations now explicit support for `plan7.Profile` or `plan7.OptimizedProfile` inputs where applicable.

Added
- `entropy` and `relative_entropy` methods to `easel.VectorF` to compute the Shannon entropy of a vector and the Kullback-Leibler divergence of two vectors.
- `mean_match_entropy`, `mean_match_information` and `mean_match_relative_entropy` methods to `plan7.HMM` to get information statistics of an HMM model.
- `match_occupancy` method to `plan7.HMM` to compute the occupancy for each match state as an `easel.VectorF`.

Fixed
- `plan7.Builder.build_msa` using the gap-open and gap-extend probabilities instead of the MSA itself to compute the transition probabilities for the new HMM.

Changed
- `plan7.Builder.build` will now only load the score system once and reuse it unless a different score system is requested between calls.

Added
- `plan7.ScoreData` class to store the substitution scores and maximal extensions for a long target search.
- `plan7.LongTargetsPipeline` to run searches on targets longer than 100,000 residues.
- `Alphabet` methods to check whether an `Alphabet` object is a DNA, RNA, nucleotide or protein alphabet.
- `window_length` and `window_beta` arguments to `plan7.Builder` to set the max length of nucleotide `HMM` created by builder objects.

Changed
- `pyhmmer.hmmer.nhmmer` now uses a `LongTargetsPipeline` instead of a `Pipeline` to search the target sequences.
- `pyhmmer.hmmer.nhmmer` now supports `HMM` queries in addition to `DigitalSequence` and `DigitalMSA` queries.
- `pyhmmer.hmmer.phmmer` now always assumes protein queries.
- `Z` and `domZ` attributes of `plan7.TopHits` objects is now read-only.

Fixed
- `nhmmer` now uses DNA as the default alphabet instead of amino acid alphabet like it did before ([12](https://github.com/althonos/pyhmmer/issues/12)).

Added
- Constructor arguments and properties to `plan7.Pipeline` to support bit score thresholds instead to filter top hits.
- Support for creating a `SequenceFile` and an `MSAFile` using a Python file-like object instead of only supporting filenames.
- Support for reading individual sequences from an MSA file with `SequenceFile`.
- `TextMSA.alignment` to access the actual alignment as a tuple of strings.
- Subtraction and division support for `easel.Vector` subclasses

Changed
- `plan7.Cutoffs` now support setting the bit score cutoffs, but requires both to be set or cleared at the same time.
- `easel.Vector` will always allocate some memory when created manually to avoid having a special empty case in every vector method.
- `pyhmmer.easel.AllocationError` now stores the size it failed to allocate, and the number of elements when allocating an array.

Fixed
- `TextSequence.digitize` will not raise a `ValueError` when the sequence contains invalid characters for the alphabet (previously was an `UnexpectedError`).

Added
- `TraceAligner`, `Trace` and `Traces` classes to `pyhmmer.plan7` to get tracebacks after aligning several sequences against an HMM.
- `pyhmmer.hmmalign` function with the same features as the `hmmalign` binary from HMMER3.
- Support for out-of-band pickling in `easel.Vector` and `easel.Matrix`.

Changed
- Allow creating an empty `Vector` or `Matrix` by calling their constructor without arguments.

Fixed
- Potential unreported exceptions in `plan7.OptimizedProfile.write` and several `plan7.SSIWriter` methods.