Pyhmmer

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](https://github.com/althonos/pyhmmer/issues/72)).

Removed
- Deprecated properties of `TopHits` (`query_name`, `query_length`, `query_accession`).

Added
- `query` property `TopHits` referencing the original object used to create the `TopHits` [76](https://github.com/althonos/pyhmmer/issues/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](https://github.com/althonos/pyhmmer/issues/71)).

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.

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`.

Fixed
- `HMM.__setstate__` not properly extracting the cutoff from `pickle` state for some HMMs ([67](https://github.com/althonos/pyhmmer/issues/67)).

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

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