v0.11.0

Added

• Missing type annotations to specific options of LongTargetsPipeline.
• __len__ implementation for HMMPressedFile using the entries in the SSI index.
• Setters for residue-wise annotation properties in HMM.
• Support for process-based parallelism in pyhmmer.hmmer in addition to thread-based.
• Read-only buffer protocol implementation for TextSequence and DigitalSequence classes.

Changed

• Drop support for Python 3.6.
• Use CMake and scikit-build-core to build the package instead of setuptools.
• Use TypedDict API to mark allowed keyword arguments in pyhmmer.hmmer functions.
• Reorganize detection and handling of alphabets for arbitrary queries in pyhmmer.hmmer.
• Allow passing a SequenceFile to most pyhmmer.hmmer functions.
• Use faster PyUnicode_FromStringAndSize function to decode strings of known lengths in several plan7 classes.
• Make SequenceFile and MSAFile generic on the individual sequence and MSA types.
• Reorganize pyhmmer.hmmer into different submodules.

Fixed

• Type annotations not using typing-extensions for Python3.8 to 3.10.
• Logic error causing out-of-bounds memory access in TopHits.__getstate__.
• Avoid creating a new Pipeline object when running single-threaded searches in pyhmmer.hmmer.
• Detect the appropriate SequenceFile type based on the digital flag value (#72).

Removed

• Deprecated properties of TopHits (query_name, query_length, query_accession).