Pyhmmer

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.

Fixed
- Linking issues on OSX caused by aggressive stripping of intermediate libraries.
- `plan7.Builder` RNG not reseeding between different HMMs.

Added
- `pyhmmer.plan7.HMM.checksum` property to get the 32-bit checksum of an HMM.

Added
- `pyhmmer.plan7.Builder` class to handle building a HMM from a sequence.
- `Pipeline.search_seq` to query a sequence against a sequence database.
- `psutil` dependency to detect the most efficient thread count for `hmmsearch` based on the number of *physical* CPUs.
- `pyhmmer.hmmer.phmmer` function to run a search of query sequences against a sequence database.

Changed
- `Pipeline.search` was renamed to `Pipeline.search_hmm` for disambiguation.
- `libeasel.random` sequences do not require the GIL anymore.
- Public API now have proper signature annotations.

Fixed
- Inaccurate exception messages in `Pipeline.search_hmm`.
- Unneeded RNG reallocation, replaced with re-initialisation where possible.
- `SequenceFile.__next__` not working after being set in digital mode.
- `sequences` argument of `hmmsearch` now only requires a `typing.Collection[DigitalSequence]` instead of a `typing.Collection[Sequence]` (not more `__getitem__` needed).

Removed
- `hits` argument to `Pipeline.search_hmm` to reduce risk of issues with `TopHits` reuse.
- Broken alignment coordinates on `Domain` classes.

Added
- `DigitalSequence.textize` to convert a digital sequence to a text sequence.
- `DigitalSequence.__init__` method allowing to create a digital sequence from any object implementing the buffer protocol.
- `Alignment.hmm_accession` property to retrieve the accession of the HMM in an alignment.