Pyhmmer

Latest version: v0.10.12

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0.2.1

Added
- `pyhmmer.plan7.HMM.checksum` property to get the 32-bit checksum of an HMM.

0.2.0

Added
- `pyhmmer.plan7.Builder` class to handle building a HMM from a sequence.
- `Pipeline.search_seq` to query a sequence against a sequence database.
- `psutil` dependency to detect the most efficient thread count for `hmmsearch` based on the number of *physical* CPUs.
- `pyhmmer.hmmer.phmmer` function to run a search of query sequences against a sequence database.

Changed
- `Pipeline.search` was renamed to `Pipeline.search_hmm` for disambiguation.
- `libeasel.random` sequences do not require the GIL anymore.
- Public API now have proper signature annotations.

Fixed
- Inaccurate exception messages in `Pipeline.search_hmm`.
- Unneeded RNG reallocation, replaced with re-initialisation where possible.
- `SequenceFile.__next__` not working after being set in digital mode.
- `sequences` argument of `hmmsearch` now only requires a `typing.Collection[DigitalSequence]` instead of a `typing.Collection[Sequence]` (not more `__getitem__` needed).

Removed
- `hits` argument to `Pipeline.search_hmm` to reduce risk of issues with `TopHits` reuse.
- Broken alignment coordinates on `Domain` classes.

0.1.4

Added
- `DigitalSequence.textize` to convert a digital sequence to a text sequence.
- `DigitalSequence.__init__` method allowing to create a digital sequence from any object implementing the buffer protocol.
- `Alignment.hmm_accession` property to retrieve the accession of the HMM in an alignment.

0.1.3

Fixed
- Compilation issues in OSX-specific Cython code.

0.1.2

Fixed
- Required Cython files not being included in source distribution.

0.1.1

Fixed
- `HMMFile` calling `file.peek` without arguments, causing it to crash when passed some types, e.g. `gzip.GzipFile`.
- `HMMFile` failing to work with PyPy file objects because of a bug with their implementation of `readinto`.
- C/Python file object implementation using `strcpy` instead of `memcpy`, causing issues when null bytes were read.

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