v0.10.5

Added

• Alignment properties to get the original lengths of the sequence and HMM being stored.
• Hit.length property storing the length of the hit sequence (or HMM).
• TopHits.query_length storing the length of the hit HMM (or query).
• Alignment.posterior_probabilities property showing an encoded representation of posteriors (#59, by @arajkovic).
• Trace.score method to compute a trace score from a given profile and sequence.
• Alignment.__sizeof__ implementation leveraing p7_alidisplay_SizeOf.

Fixed

• Cutoffs proxy objects not recording their owner to prevent deallocation.
• Avoid GIL re-acquisition in GeneticCode.translate.
• Query metadata not being recorded in Hits obtained from daemon.Client.
• Empty MatrixU8 creation attempting zero-allocation.
• VectorU8.zeros allocating 4x more memory than required.
• Memory leak caused by string duplication in __getbuffer__ methods of Matrix and Vector types.

v0.10.4

Added

• residue_markups argument to TextSequence and DigitalSequence constructors.
• __reduce__ implementation to TextSequence, DigitalSequence, TextSequenceBlock and DigitalSequenceBlock.

Changed

• Handling of easel I/O methods to avoid implicit GIL acquisition for error checking.

Fixed

• Syntax errors in type annotation files.

v0.10.3

Added

• Out-of-band pickle serialization of Bitfield objects.
• Getters for float attributes and forward/backward parameters of OptimizedProfile.
• InvalidHMM error raised by HMM.validate.

Changed

• Mark HMM.zero method as noexcept.
• Increase size of buffer for the query queue in the hmmer dispatcher.

Fixed

• Unneeded semaphore in pyhmmer.hmmer message passing implementation.
• Broken assertion in Bitfield._from_raw_bytes.
• Relax tolerance of HMM validation in TraceAligner.align_traces.

v0.10.2

Fixed

• Invalid buffer write in DigitalSequenceBlock.translate (#50).

v0.10.1

Added

• HMM.set_consensus method to set the consensus for a method or compute it from the emission probabilities.

Fixed

• Platform detection for MacOS and Armv7 platforms in setup.py.
• pyhmmer.plan7.HMM constructor setting a consensus string forcefully.

v0.10.0

Added

• Support for compiling wheels for Aarch64 and NEON-enabled Arm platforms.

Changed

• Updated HMMER to v3.4.
• Updated Easel to v0.49.
• Use cibuildwheel to build wheel distributions.

Fixed

• Patch missing PyInterpreterState_GetID preventing the package from working on PyPy 3.9.

v0.9.0

Added

• TopHits.mode property showing from which pipeline mode (search or scan) the hits were obtained.

Changed

• Updated the code for Cython v3.0.

Fixed

• TopHits.merge not properly handling inclusion and reporting for domains (#46, #47, by @zdk123).

v0.8.2

Added

• Bracket-style repr implementation to HMM, Profile and OptimizedProfile showing model alphabet, length and name.
• MissingCutoffs and InvalidParameter exceptions inheriting ValueError.

Changed

• Replace pthread locks with PyThread API for synchronizing models in OptimizedProfileBlock.

Fixed

• Sequence length extraction in LongTargetsPipeline.search_hmm (#42).
• LongTargetsPipeline.search_msa not building a HMM with Builder.build_msa.

v0.8.1

Added

• HMM.validate method to ensure a HMM holds HMMER structural constraints.
• plan7.Transitions enum with transition names for indexing HMM.transition_probabilities.

v0.8.0

PyHMMER has been accepted for publication in Bioinformatics. Paper accessible here: doi:10.1093/bioinformatics/btad214.

Added

• pyhmmer.hmmer.jackhmmer function to run several JackHMMER iterative searches in parallel using multithreading (#35, by @zdk123).
• HMM.to_profile shortcut method to allocate and configure a new Profile object.

Fixed

• Type annotations of Pipeline.iterate_seq and Pipeline.iterate_hmm.
• Potential memory leak on exceptions raised by HMMPressedFile.read.
• Offsets.profile not recording offsets properly, causing pyhmmer.hmmer.hmmpress to produce invalid pressed files (#37).

Changed

• HMM.__init__ and HMM.sample now take the Alphabet as the first argument, for consistency with the rest of the API.
• HMM now require a name argument.

Removed

• Deprecated ignore_gaps argument in SequenceFile.__init__.
• Deprecated Sequence.taxonomy_id property.