v0.10.12

Fixed

• HMM.__setstate__ not properly extracting the cutoff from pickle state for some HMMs (#67).

Changed

• Update and remove some test files to reduce size of distributed package data.

v0.10.11

Fixed

• Compilation of Easel and HMMER code not using SSE4.1 extensions.

v0.10.10

Fixed

• Implement write function for fopencookie with off_t instead of off64_t for compatibility.
• Fix handling of NULL buffers passed to read and write methods of fopencookie.

v0.10.9

Fixed

• Reallocation issue causing segmentation faults in nhmmer with more than 64 sequences (#62).

v0.10.8

Added

• Getter to access the strand of a Domain produced by a LongTargetsPipeline.

Changed

• Display model and cutoff names in MissingCutoffs error message, if any.
• Allow LongTargetsPipeline to be configured with window length and beta parameters.
• Make nhmmer use the window length and beta from the options when creating a Builder.

Fixed

• nhmmer not computing E-values for non-default window lengths (moshi4/pybarrnap#2).
• SequenceFile and MSAFile crashing with a segmentation fault when given the path to a folder rather than a file.

v0.10.7

Added

• Pre-compiled wheels for PyPy 3.10.

Fixed

• Invalid pointer cast in __getbuffer__ method of Matrix and Vector objects.
• Remaining tests failing to run on missing importlib-resources.
• pyhmmer.hmmer dispatchers possibly dead-locking on background thread errors (#60).

v0.10.6

Added

• armv7 and aarch64 to the PKGBUILD architectures.

Changed

• SSIReader and SSIWriter constructors now accept path-like objects.
• Skip tests dependending on importlib.resources.files when it is not available on the host machine.

Fixed

• Memory leak caused by alphabet allocation in Pipeline._scan_loop_file.

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.