Pyhmmer

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.

Added
- `pickle` protocol for `easel.Alphabet`, `easel.Bitfield`, `easel.KeyHash`, `easel.Vector`, `easel.Matrix` and `plan7.HMM`.
- `taxonomy_id` and `residue_markups` properties to `easel.Sequence`.
- `sum_score` property to `plan7.Hit`.
- `plan7.EvalueParameters` class to expose the e-value parameters of a `plan7.HMM` or a `plan7.Profile`.
- Equality checks and slicing for `easel.Matrix` and `easel.Vector`.
- Support for creating and manipulating zero-sized `easel` matrices and vectors.
- `plan7.Cutoffs` class to expose the Pfam score cutoffs of a `plan7.HMM` or a `plan7.Profile`.
- Keyword arguments to configure E-value thresholds when creating a `plan7.Pipeline` object.
- Support for using model-specific thresholding options in `plan7.Pipeline`.

Changed
- Use the *replace* error handler when decoding error messages to skip potential decoding issues when already building an exception.
- Improve `pyhmmer.hmmer` to ensure background threads exit on a `KeyboardInterrupt`.
- `easel.VectorU8.__eq__` accepts any object implementing the buffer protocol.
- `plan7.HMM.creation_time` now takes and returns a `datetime.datetime` object, assuming the field is only ever set with `asctime`.
- Refactor `easel.Vector` and `easel.Matrix` and mark exposed memory as C-contiguous.

Fixed
- `easel.Alphabet` not reporting potential allocation errors.
- Potential buffer overflow in `easel.Matrix` and `easel.Vector` when calling `__init__` more than once.