Commit 90f3e3c0 authored by Martin Larralde's avatar Martin Larralde
Browse files

Release v0.5.0

parent 01dd0716
Pipeline #30776 passed with stage
in 4 minutes and 8 seconds
......@@ -6,7 +6,28 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
## [Unreleased]
[Unreleased]: https://github.com/althonos/pyhmmer/compare/v0.4.11...HEAD
[Unreleased]: https://github.com/althonos/pyhmmer/compare/v0.5.0...HEAD
## [v0.5.0] - 2022-03-14
[Unreleased]: https://github.com/althonos/pyhmmer/compare/v0.4.11...v0.5.0
### Added
- `plan7.PipelineSearchTargets` to reduce the overhead when searching the same sequences several times with different. query profiles.
- `TopHits.copy` method to duplicate a `TopHits` instance.
- `TopHits.merge` method to merge hits obtained with the same query on different targets.
- Buffer protocol implementation for `pyhmmer.easel.Bitfield`.
### Changed
- Renamed `TopHits.included` and `TopHits.reported` properties to `TopHits.hits_included` and `TopHits.hits_included`.
- `MSAFile` and `SequenceFile` are now directly in digital mode if they are instantiated with `digital=True`.
- `SequenceFile.parse` can now return a sequence in digital mode.
- Reorganized tests to make then runnable from a site install.
### Fixed
- Usage of `memcpy` in contexts where it may have had undefined behaviour.
- `VectorF.__eq__` crashing when comparing two empty objects.
- `SequenceFile` and `MSAFile` not closing file handles when raising an error in `__init__`.
## [v0.4.11] - 2021-12-15
......
MIT License
Copyright (c) 2020-2021 Martin Larralde <martin.larralde@embl.de>
Copyright (c) 2020-2022 Martin Larralde <martin.larralde@embl.de>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
......
......@@ -5,7 +5,7 @@ include COPYING
include pyproject.toml
recursive-include include *.pxd
recursive-include pyhmmer *.h *.pxd *.pxi *.py *.pyi *.pyx py.typed
prune tests
recursive-include pyhmmer/tests *
recursive-include vendor *
recursive-exclude vendor/hmmer *.ai
......
......@@ -150,7 +150,7 @@ and the version 33.1 of the [Pfam](https://pfam.xfam.org/) HMM library containin
18,259 domains. Commands were run 4 times on a warm SSD. *Plain lines show
the times for pressed HMMs, and dashed-lines the times for HMMs in text format.*
![Benchmarks](https://raw.github.com/althonos/pyhmmer/master/benches/v0.4.5/plot.svg)
![Benchmarks](https://raw.github.com/althonos/pyhmmer/master/benches/v0.5.0/plot.svg)
Raw numbers can be found in the [`benches` folder](https://github.com/althonos/pyhmmer/blob/master/benches/).
They suggest that `phmmer` should be run with the number of *logical* cores,
......
......@@ -25,7 +25,7 @@ from .hmmer import hmmalign, hmmsearch, hmmpress, nhmmer, phmmer
__author__ = "Martin Larralde <martin.larralde@embl.de>"
__license__ = "MIT"
__version__ = "0.4.11"
__version__ = "0.5.0"
__all__ = [
errors.__name__,
easel.__name__,
......
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