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.

0.1.0-a5

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.

0.1.0-a4

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.

0.1.0-a3

Added

• TextSequence and DigitalSequence representing a Sequence in a given mode.
• E-value properties to Hit and Domain.
• TopHits now stores a reference to the pipeline it was obtained from.
• Pipeline.Z and Pipeline.domZ properties.
• Experimental pickling support to Alphabet.
• Experimental freelist to Sequence class to avoid allocation bottlenecks when iterating on a SequenceFile without recycling sequence buffers.

Changed

• Made Sequence an abstract base class.
• Additional Pipeline parameters can be passed as keyword arguments to pyhmmer.hmmsearch.
• SequenceFile.read can now be configured to skip reading the metadata or the content of a sequence.

Removed

• Redundant SequenceFile methods.

Fixed

• doctest loader crashing on Python 3.5.
• TopHits.threshold segfaulting when being called without prior Tophits.sort call
• Unknown format argument to SequenceFile constructor not raising the right error.

0.1.0-a2

Added

• Support for compilation on PowerPC big-endian platforms.
• Type annotations and stub files for Cython modules.

Changed

• distutils is now used to compile the package, instead of calling autotools and letting HMMER configure itself.
• Bitfield.count now allows passing an argument (for compatibility with collections.abc.Sequence).

0.1.0-a1

Initial alpha release (test deployment to PyPI).