althonos/pyhmmer: v0.7.0

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