Pyhmmer

Latest version: v0.10.12

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0.10.6

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`.

0.10.5

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](https://github.com/althonos/pyhmmer/pull/59), by [arajkovic](https://github.com/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.

0.10.4

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.

0.10.3

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`.

0.10.2

Fixed
- Invalid buffer write in `DigitalSequenceBlock.translate` ([50](https://github.com/althonos/pyhmmer/issues/50)).

0.10.1

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.

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