RLS Version 2.1.0

Main new feature is adding support for using output of strobealign-aemb.
Use of the `SemiBin` command (instead of `SemiBin2`) will continue to
work, but print a warning and set a delay to ask users to upgrade.

Full ChangeLog

- SemiBin: Support running SemiBin with strobealign-aemb (`--abundance`/`-a`)
- citation: Add citation subcommand
- SemiBin1: Introduce separate SemiBin1 command
- internal: Code simplification and refactor
- deprecation: Deprecate `--orf-finder=fraggenescan` option
- Update abundance normalization
- SemiBin: do not use more processes than can be taken advantage of (#155)

Author: luispedro

ChangeLog

@@ -1,11 +1,12 @@
 Unreleased
+	* SemiBin: Support running SemiBin with strobealign-aemb
+	(--abundance/-a)
 	* citation: Add citation subcommand
 	* SemiBin1: Introduce separate SemiBin1 command
 	* internal: Code simplification and refactor
 	* deprecation: Deprecate --orf-finder=fraggenescan option
 	* Update abundance normalization
 	* SemiBin: do not use more processes than can be taken advantage of (#155)
-	* Support running SemiBin with strobealign-aemb
 
 Version 2.0.2 Oct 31 2023 by BigDataBiology
 	* multi_easy_bin: Fix multi_easy_bin with --write-pre-recluster (#128)

SemiBin/main.py

@@ -295,7 +295,7 @@ def parse_args(args, is_semibin2):
                               dest='bams',
                               default=None,
                               )
-            p.add_argument('-a', '--abundance',
+            p.add_argument('-a', '--abundance', '--abundances',
                            required=False,
                            nargs='*',
                            help='Path to the abundance file from strobealign-aemb. This can only be used when samples used in binning above or equal 5.',

docs/whatsnew.md

@@ -1,5 +1,28 @@
 # What's New
 
+## Version 2.1.0
+
+*Released Mar 6, 2024*
+
+Main new feature is adding support for using output of strobealign-aemb.
+
+Use of the `SemiBin` command (instead of `SemiBin2`) will continue to work, but
+print a warning and set a delay to ask users to upgrade.
+
+### User-visible changes
+
+- Support running SemiBin with [strobealign-aemb](https://github.com/ksahlin/strobealign/releases/tag/v0.13.0) (`--abundance`/`-a`)
+- Add `citation` subcommand
+- Introduce separate `SemiBin1` command as use of `SemiBin` is now deprecated and will trigger a warning
+
+### Internal improvements
+- Code simplification and refactor
+- deprecation: Deprecate --orf-finder=fraggenescan option
+- Update abundance normalization
+
+### Bugfixes
+- SemiBin: do not use more processes than can be taken advantage of [#155](https://github.com/BigDataBiology/SemiBin/issues/155)
+
 ## Version 2.0.2
 
 *Released Oct 31, 2023*