Release v0.10.0

Author: althonos

CHANGELOG.md

@@ -8,24 +8,14 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 [Unreleased]: https://github.com/zellerlab/GECCO/compare/v0.9.10...master
 
 
-## [v0.10.0-alpha.3] - 2025-08-13
-[v0.10.0-alpha.3]: https://github.com/zellerlab/GECCO/compare/v0.10.0-alpha.2...v0.10.0-alpha.3
+## [v0.10.0] - 2025-10-17
+[v0.10.0]: https://github.com/zellerlab/GECCO/compare/v0.9.10...v0.10.0
 
 ### Added
 - Support for changing the CLI argument defaults from a call to the `gecco.cli.main` function.
 
-
-## [v0.10.0-alpha.2] - 2025-08-13
-[v0.10.0-alpha.2]: https://github.com/zellerlab/GECCO/compare/v0.10.0-alpha.1...v0.10.0-alpha.2
-
-### Fixed
-- `gecco.cli` and `gecco.crf` submodules not being included in wheel distribution.
-
-
-## [v0.10.0-alpha.1] - 2025-08-13
-[v0.10.0-alpha.1]: https://github.com/zellerlab/GECCO/compare/v0.9.10...v0.10.0-alpha.1
-
 ### Changed
+- Allow training with sequences only containing negative samples (with a warning).
 - Add an error in `gecco convert` when given input is not a folder.
 - Update `numpy`, `polars`, `pyhmmer` and `psutil` to latest versions.
 - Replace `docopt` with `argparse` parser for CLI argument parsing.
@@ -34,6 +24,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - Allow changing the default `ClusterCRF` and `TypeClassifier` classes used in `gecco.cli`.
 
 ### Fixed
+- `gecco.cli` and `gecco.crf` submodules not being included in wheel distribution.
 - `gecco convert` issue when given a relative path.
 - Unused `tqdm` import in `gecco.crf` module.
 - Unused build dependencies from `setup.cfg` and `pyproject.toml`.

galaxy/gecco.xml

@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool id="gecco" name="GECCO" version="0.10.0-alpha.2" python_template_version="3.5">
+<tool id="gecco" name="GECCO" version="0.10.0" python_template_version="3.5">
     <description>is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs).</description>
     <creator>
         <organization name="Zeller Team" url="https://www.embl.org/groups/zeller/"/>
@@ -11,7 +11,7 @@
         <edam_operation>operation_0415</edam_operation>
     </edam_operations>
     <requirements>
-        <requirement type="package" version="0.10.0-alpha.2">gecco</requirement>
+        <requirement type="package" version="0.10.0">gecco</requirement>
     </requirements>
     <version_command>gecco --version</version_command>
     <command detect_errors="aggressive"><![CDATA[

gecco/__init__.py

@@ -10,4 +10,4 @@
 
 __author__ = "Martin Larralde"
 __license__ = "GPLv3"
-__version__ = "0.10.0-alpha.3"
+__version__ = "0.10.0"