Commit 8ef2671d authored by Martin Larralde's avatar Martin Larralde
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Release v0.8.0

parent 7f771973
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......@@ -5,7 +5,29 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
## [Unreleased]
[Unreleased]: https://git.embl.de/grp-zeller/GECCO/compare/v0.7.0...master
[Unreleased]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.0...master
## [v0.8.0] - 2021-07-03
[v0.8.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.7.0...v0.8.0
### Changed
- Retrain internal model using new sequence embeddings and remove broken/duplicate BGCs from MIBiG 2.0.
- Bump minimum `pyhmmer` version to `v0.4.0` to improve exception handling.
- Bump minimum `pyrodigal` version to `v0.5.0` to fix sequence decoding on some platforms.
- Use p-values instead of e-values to filter domains obtained with HMMER.
- `gecco cv` and `gecco train` now seed the RNG with a user-defined seed before shuffling rows of training data.
### Fixed
- Extraction of BGC compositions for the type predictor while training.
- `ClusterCRF.trained` failing to open an external model.
### Added
- `Domain.pvalue` attribute to access the p-value of a domain annotation.
- Mandatory `pvalue` column to `FeatureTable` objects.
- Support for loading several feature tables in `gecco train` and `gecco cv`.
- Warnings to `ClusterCRF.fit` when selecting uninformative features.
- `--correction` flag to `gecco train` and `gecco cv`, allowing to give a multiple testing correction method when computing p-values with the Fisher Exact Tests.
### Removed
- Outdated `gecco embed` command.
- Unused `--truncate` flag from the `gecco train` CLI.
- Tigrfam domains, which is not improving performance on the new training data.
## [v0.7.0] - 2021-05-31
[v0.7.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.6.3...v0.7.0
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......@@ -10,4 +10,4 @@ See Also:
__author__ = "Martin Larralde"
__license__ = "GPLv3"
__version__ = "0.8.0-dev"
__version__ = "0.8.0"
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