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.