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.
0.1.0
Initial beta release.
Fixed - `TextSequence` uses the sequence argument it's given on instantiation. - Segmentation fault in `Sequence.__eq__` caused by implicit type conversion. - Segmentation fault on `SequenceFile.read` failure. - Missing type annotations for the `pyhmmer.easel` module.
0.1.0a5
Added - `Sequence.__len__` magic method so that `len(seq)` returns the number of letters in `seq`. - Python file-handle support when opening an `pyhmmer.plan7.HMMFile`. - Context manager protocol to `pyhmmer.easel.SSIWriter`. - Type annotations for `pyhmmer.easel.SSIWriter`. - `add_alias` to `pyhmmer.easel.SSIWriter`. - `write` method to `pyhmmer.plan7.OptimizedProfile` to write an optimized profile in binary format. - `offsets` property to interact with the disk offsets of a `pyhmmer.plan7.OptimizedProfile` instance. - `pyhmmer.hmmer.hmmpress` emulating the `hmmpress` binary from HMMER. - `M` property to `pyhmmer.plan7.HMM` exposing the number of nodes in the model.
Changed - Bumped vendored Easel to `v0.48`. - Bumped vendored HMMER to `v3.3.2`. - `pyhmmer.plan7.HMMFile` will raise an `EOFError` when given an empty file. - Renamed `length` property to `L` in `pyhmmer.plan7.Background`.
Fixed - Segmentation fault when `close` method of `pyhmmer.easel.SSIWriter` was called more than once. - `close` method of `pyhmmer.easel.SSIWriter` not writing the index contents.
0.1.0a4
Added - `MSA`, `TextMSA` and `DigitalMSA` classes representing a multiple sequence alignment to `pyhmmer.easel`. - Methods and protocol to copy a `Sequence` and a `MSA`. - `pyhmmer.plan7.OptimizedProfile` wrapping a platform-specific optimized profile. - `SSIReader` and `SSIWriter` classes interacting with sequence/subsequence indices to `pyhmmer.easel`. - Exception handler using Python exceptions to report Easel errors.
Changed - `pyhmmer.hmmsearch` returns an iterator of `TopHits`, with one instance per `HMM` in the input. - `pyhmmer.hmmsearch` properly raises errors happenning in the background threads without deadlock. - `pyhmmer.plan7.Pipeline` recycles memory between `Pipeline.search` calls.
Fixed - Missing type annotations for the `pyhmmer.errors` module.
Removed - Unneeded or private methods from `pyhmmer.plan7`.