0.4.6

Added

• pickle protocol for easel.Alphabet, easel.Bitfield, easel.KeyHash, easel.Vector, easel.Matrix and plan7.HMM.
• taxonomy_id and residue_markups properties to easel.Sequence.
• sum_score property to plan7.Hit.
• plan7.EvalueParameters class to expose the e-value parameters of a plan7.HMM or a plan7.Profile.
• Equality checks and slicing for easel.Matrix and easel.Vector.
• Support for creating and manipulating zero-sized easel matrices and vectors.
• plan7.Cutoffs class to expose the Pfam score cutoffs of a plan7.HMM or a plan7.Profile.
• Keyword arguments to configure E-value thresholds when creating a plan7.Pipeline object.
• Support for using model-specific thresholding options in plan7.Pipeline.

Changed

• Use the replace error handler when decoding error messages to skip potential decoding issues when already building an exception.
• Improve pyhmmer.hmmer to ensure background threads exit on a KeyboardInterrupt.
• easel.VectorU8.__eq__ accepts any object implementing the buffer protocol.
• plan7.HMM.creation_time now takes and returns a datetime.datetime object, assuming the field is only ever set with asctime.
• Refactor easel.Vector and easel.Matrix and mark exposed memory as C-contiguous.

Fixed

• easel.Alphabet not reporting potential allocation errors.
• Potential buffer overflow in easel.Matrix and easel.Vector when calling __init__ more than once.