Pyhmmer

Added
- `Bitfield.zeros` and `Bitfield.ones` classmethods for constructing an empty bitfield of known size.
- `Bitfield.copy` method to copy a bitfield object.
- `SequenceBlock` and `OptimizedProfileBlock` classes to store Python objects next to a contiguous array of pointers for iterating with the GIL released.
- `SequenceFile.read_block` method to read a whole sequence block from a file.
- `HMM.sample` class method to generate a HMM at random given a `Randomness` source.
- `hmmscan` function to scan a profile database with sequence queries.
- `deepcopy` implementations to `HMM`, `Profile` and `OptimizedProfile` classes of `plan7`.
- `rewind` method to `HMMFile`, `HMMPressedFile` and `SequenceFile` to reset a file back to its initial position.
- `name` attribute to `HMMFile`, `HMMPressedFile`, `MSAFile` and `SequenceFile` to expose the path of a file (when it was created from path).
- `local` property to `Profile` and `OptimizedProfile`, indicating whether a profile is in local or global mode.
- `multihit` property to `Profile` and `OptimizedProfile`, indicating whether a profile is in unihit or multihit mode, with a setter taking care of the reconfiguration.
- `Domain.included` and `Domain.reported` settable properties to report the inclusion and reporting status of a single domain.
- `TopHits.included` and `TopHits.reported` sized iterator to iterate only on included and reported hits.
- `Domains.included` and `Domains.reported` sized iterator to iterate only on included and reported domains.

Changed
- `Bitfield`, `Vector` and `Matrix` can now be created from an iterable.
- `Pipeline` search methods now expect a `DigitalSequenceBlock` or a `SequenceFile` for the target sequence database.
- `Pipeline` scan methods now expect an `OptimizedProfileBlock` or a `HMMPressedFile` for the target profile database.
- `TraceAligner` now expect a `DigitalSequenceBlock` for the sequences to align to the HMM.
- `Profile.configure` now uses a default value of 400 for the `L` argument.
- `hmmsearch`, `nhmmer` and `phmmer` support being given a single query instead of requiring an iterable.
- `HMMPressedFile` can now be created, closed and used as a context manager directly without having to manage the source `HMMFile`.
- Renamed `Profile.optimized` method to `Profile.to_optimized`.
- Replaced `Randomness.is_fast` method with the `Randomness.fast` property.
- Rewrite handling of `Hit` flags using settable properties (`Hit.included`, `Hit.reported`, `Hit.new`, `Hit.dropped`, `Hit.duplicate`) instead of methods.

Fixed
- Memory leak in the `LongTargetsPipeline` search loop.
- PyPy behaviour change of `readinto` methods now expecting `unsigned char*` instead of `char*` memoryview.
- `NULL`-pointer dereference in `Pipeline.search_hmm` when given a query without name.
- `LongTargetsPipeline` not recording the query name and accession.
- Memory leak caused by using a non-default prior scheme when constructing a `Builder`.

Removed
- `PipelineSearchTargets`, replaced in functionality with `easel.DigitalSequenceBlock`.
- `is_local` and `is_multihit` methods of `Profile` and `OptimizedProfile`, replaced with equivalent properties.
- `Hit.manually_drop` and `Hit.manually_include` methods, replaced with the different `Hit` properties.

Fixed
- Error not being raised on alphabet detection failure in `SequenceFile` or `MSAFile`.
- Add check in `DigitalSequence` constructor to make sure encoded characters are in valid range ([25](https://github.com/althonos/pyhmmer/issues/25)).

Added
- `SequenceFile.guess_alphabet` and `MSAFile.guess_alphabet` to guess the alphabet from an open file.
- `Alphabet.encode` and `Alphabet.decode` to convert raw sequences between digital and text format.

Changed
- `hmmsearch`, `phmmer` and `nhmmer` functions will reduce the requested number of threads to the number of queries, if it can be detected using `operator.length_hint`.

Added
- Documentation for loading all HMMs from an `HMMFile` object at once ([23](https://github.com/althonos/pyhmmer/issues/23)).
- List of projects depending on PyHMMER to the `Examples` page of the documentation.

Added
- `pickle` protocol support for `TopHits` objects, using the HMMER network serialization.
- `TopHits.write` method to write hits to a file in tabular format.
- `query_name` and `query_accession` properties to `TopHits` objects to access the name and accession of the query that produced the hits.

Fixed
- Extraction of filename from file-like objects in the `HMMFile` constructor.
- Use `os.cpu_count` instead of `multiprocessing.cpu_count` where applicable to preserve OS scheduling.
- Wrong return type in docstring of `HMM.insert_emissions`.
- `TopHits.searched_nodes` returning the searched number of residues instead of the searched number of model nodes.
- Unsound decoding of pickled `MatrixF` or `VectorF` when data comes from a source of different endianness.

Changed
- Rewrite `pyhmmer.hmmer` threading code using `Deque` instead of `collections.Queue` to store the queries and results.
- Reduce memory consumption of `pyhmmer.hmmer` by reducing the number of semaphores and event flags used concurrently.
- Make `pyhmmer.hmmer` main threads block on query insertion rather than result retrieval to make sure worker threads are never idling.

Added
- `pyhmmer.daemon` module with an client implementation to communicate to a `hmmpgmd` server.
- `Pipeline.arguments` methods to get a list of CLI arguments from the parameters used to initialize the `Pipeline`.
- Setters for `name`, `accession` and `description` properties of `plan7.Hit`.
- Constructor for individual `plan7.Trace` objects outside a `plan7.Traces` list.
- `plan7.Trace.from_sequence` constructor to create a faux trace from a single sequence.
- `manually_include` and `manually_drop` methods to `plan7.Hit` for manually selecting the inclusion status of a `Hit` in a `TopHits` instance.
- `compare_ranking` method to `plan7.TopHits` for comparing the order of the hits compared to a previous run on the same targets stored in an `easel.KeyHash` object.
- `Pipeline.iterate_seq` and `Pipeline.iterate_hmm` to run iterative queries like JackHMMER.
- `repr` implementations for `easel.MSAFile`, `easel.SequenceFile` and `easel.HMMFile` showing the path or file object they were created from.
- `repr` implementation for `easel.Randomness` showing the seed and the RNG algorithm in use.
- `str` implementation for `plan7.Alignment` using HMMER original code to display a domain alignment like in search/scan results.

Changed
- `plan7.Trace.posterior_probabilities` property may now be `None` in case no memory is allocated for the posteriors in the `P7_TRACE` struct.
- `TopHits.to_msa` can now add additional sequences passed as arguments to the alignment.
- `plan7.HMMPressedFile` now raises an exception on attempts to create a new instance manually.
- `ignore_gaps` argument of `easel.SequenceFile` is now deprecated.
- `repr` implementations for `easel` types now use the fully qualified class name.

Fixed
- `easel.SequenceFile.readinto` docstring not rendering properly in documentation.
- Type annotations of `hits_included` and `hits_reported` of `plan7.TopHits` marking these properties as `bool` instead of `int`.
- Setters of `name`, `accession`, `description` and `author` properties of `easel.MSA` crashing when given `None` values.
- Exception value raised from Easel code not being properly extracted.
- Plain strings being used in example for `easel.TextSequence` and `easel.TextMSA` constructors where byte strings are expected ([20](https://github.com/althonos/pyhmmer/pull/20)).

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__`.