[dependabot]

Updates the requirements on pyhmmer to permit the latest version.

Release notes

Sourced from pyhmmer's releases.

v0.12.3

Fixed

• Syntax error in plan7.pyi stubs (#105, by @​aretasg).

Changelog

Sourced from pyhmmer's changelog.

v0.12.3 - 2026-08-19

Fixed

• Syntax error in plan7.pyi stubs (#105, by @​aretasg).

v0.12.2 - 2026-08-13

Fixed

• Segmentation fault in HMM.__eq__ for HMMs missing a creation_time (#103).

v0.12.1 - 2026-05-12

Added

• Sequence.L property to get the length of a sequence consistently with HMM.M.
• Matrix.flatten method to get a Vector over the whole C-contiguous buffer of a Matrix.
• allocM property to Profile and OptimizedProfile to get the allocated capacity.
• HMM.emit_sequence, HMM.emit_alignment and Profile.emit_sequence to generate sequences from a model (#102).
• Missing type hints for gap_index, gap_symbol and type properties of Alphabet.

Removed

• Profile.transition_scores due to memory leak.

Fixed

• SequenceFile.__init__ crashing on opening SSI indices for gzip-compressed files.

v0.12.0 - 2026-01-21

Added

• Support for Windows AMD64 builds with MinGW (#92, see documentation).
• SequenceBlock.write method to write all sequences from a block to a file.
• SequenceBlock.total_length to compute the sum of lengths of sequences in a block.
• Subclasses DNA, RNA and AA of pyhmmer.easel.Alphabet to allow marking the alphabet type with type annotations.
• VectorI and MatrixI classes to pyhmmer.easel to store C int types (usually 32 bits).
• OptimizedProfile.ssv_filter method for NEON target in addition to SSE.
• msv_filter method to Profile and OptimizedProfile classes.
• Background.null1 to compute the null1 lod score for an arbitrary Sequence.
• HMMFile._file exposing the internal file-like object given to HMMFile constructor, if any (#89).
• SSIReader.primary_keys exposing a read-only sequence of primary keys inside a SSI file.
• SequenceFile.indexed and MSAFile.indexed to access data indexed with a SSI index (#85).

Changed

• Setup compilation in Stable ABI mode for Python 3.12 and later.
• Setup distribution to generate a CMake package file to facilitate usage with downstream scikit-build-core dependent packages.
• breaking: Make most textual attributes and properties str rather than bytes (#88).

... (truncated)

Commits

• 956c542 Release v0.12.3
• 00d2b9d Fix syntax error in HMM.emit_alignment stub in plan7.pyi (#105)
• 52ef907 Release v0.12.2
• 755fa1a Add fast path on pointer equality in HMM.__eq__
• 5c55ffe Drop testing for Python 3.8 in GitHub Actions
• 4d5f248 Add patch for p7_hmm_Compare segfaulting on missing HMM.creation_time (#103)
• 0dd3258 Fix broken download badges in README.md [ci skip]
• 20e886f Bump AUR deployment Action in package.yml [ci skip]
• 620d7e2 Release v0.12.1
• 9a40e5f Add missing properties to Alphabet type hints [ci skip]
• Additional commits viewable in compare view