Release v0.9.1

CHANGELOG.md

@@ -5,7 +5,14 @@ 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/v0.9.1-alpha4...master
+[Unreleased]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.1...master
+
+## [v0.9.1] - 2022-04-05
+[v0.9.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.1-alpha4...v0.9.1
+
+### Changed
+- Make the `genes.tsv` and `features.tsv` table contain all genes even when they come from a contig too short to be processed by the CRF sliding window.
+- Replaced the `--force-clusters-tsv` flag with a `--force-tsv` flag to force writing TSV tables even when no genes or clusters were found in `gecco run` or `gecco annotate`.
 
 ## [v0.9.1-alpha4] - 2022-03-31
 [v0.9.1-alpha4]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.1-alpha3...v0.9.1-alpha4
@@ -15,7 +22,7 @@ Retrain internal model with:
 $ python -m gecco -vv train --c1 0.4 --c2 0 --select 0.25 --window-size 20 \
          -f mibig-2.0.proG2.Pfam-v35.0.features.tsv \
          -c mibig-2.0.proG2.clusters.tsv \
-         -g GECCO-data/data/embeddings/mibig-2.0.proG2.genes.gff \
+         -g GECCO-data/data/embeddings/mibig-2.0.proG2.genes.tsv \
          -o models/v0.9.1-alpha4
 ```
 

gecco/__init__.py

@@ -10,4 +10,4 @@
 
 __author__ = "Martin Larralde"
 __license__ = "GPLv3"
-__version__ = "0.9.1-alpha4"
+__version__ = "0.9.1"