diff --git a/CHANGELOG.md b/CHANGELOG.md index 2967eece..55cf8e3a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,32 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ## [Unreleased] -[Unreleased]: https://github.com/althonos/pyhmmer/compare/v0.1.0-a2...HEAD +[Unreleased]: https://github.com/althonos/pyhmmer/compare/v0.1.0-a3...HEAD + + +## [v0.1.0-a3] - 2020-11-19 +[v0.1.0-a3]: https://github.com/althonos/pyhmmer/compare/v0.1.0-a2...v0.1.0-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. ## [v0.1.0-a2] - 2020-11-12 diff --git a/pyhmmer/__init__.py b/pyhmmer/__init__.py index 4c0ab154..997bc706 100644 --- a/pyhmmer/__init__.py +++ b/pyhmmer/__init__.py @@ -24,7 +24,7 @@ __author__ = "Martin Larralde " __license__ = "MIT" -__version__ = "0.1.0-a2" +__version__ = "0.1.0-a3" __all__ = [errors.__name__, easel.__name__, plan7.__name__, hmmsearch.__name__] if __doc__ is not None: __doc__ += """See Also: