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).

v0.10.15

Added

• query property TopHits referencing the original object used to create the TopHits #76.

Changed

• Require the query object to create a TopHits object.
• Make TopHits generic over its query property.
• Deprecate old query properties of TopHits (query_name, query_length, query_accession).

Removed

• Detection of SSE flush from setup.py (#71).

v0.10.14

Added

• Detection of SSE flush modes to setup.py for possible performance gains on x86 platforms.

Changed

• Migrate documentation to pydata-sphinx-theme.

Fixed

• Documentation examples not using permanent resource links.

v0.10.13

Changed

• Allow AlphabetMismatch error to allow for an unknown actual alphabet.
• Make HMMFile and HMMPressedFile raise AlphabetMismatch on files with mixed alphabets.

Fixed

• Avoid calling fclose with null pointers in Sequence.write and MSA.write.

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).