RLS Version 0.6.0

Big change is adding GROOT support

Full Changelog:

- argNorm supports the GROOT v1.1.2 ARG annotation tool: https://github.com/will-rowe/groot
- GROOT support is via the `GrootNormalizer` (for use in python scripts) and the `groot` tool parameter with the `groot-db`, `groot-core-db`, `groot-argannot`, `groot-card`, and `groot-resfinder` `db` parameters in the CLI.

Other
-----

- `__version__` attribute added to the package (accessible as `argnorm.__version__` or `argnorm.lib.__version__`)
- Use atomic writing for outputs (https://github.com/untitaker/python-atomicwrites/tree/master)

funcscan integration
--------------------

- argNorm has been included as an nf-core module: https://nf-co.re/modules/argnorm/
- argNorm will also be available on the funcscan pipeline: nf-core/funcscan#410

DB harmonisation
----------------

- SARG db link was changed in `crude_db_harmonisation` to https://raw.githubusercontent.com/xinehc/args_oap/a3e5cff4a6c09f81e4834cfd9a31e6ce7d678d71/src/args_oap/db/sarg.fasta as old link (Galaxy instance, http://smile.hku.hk/SARGs) is down
- RGI outputs in `crude_db_harmonisation` are concatenated so frequencies of `perfect`, `strict`, and `loose` hits can be calculated from concatenated file

CHANGELOG.md

@@ -2,7 +2,7 @@
 
 ## Unreleased
 
-### New Features
+## 0.6.0 - 21 August 2024
 
 #### GROOT support
 - argNorm supports the GROOT v1.1.2 ARG annotation tool: https://github.com/will-rowe/groot

argnorm/argnorm_version.py

@@ -1 +1 @@
-__version__ = '0.6.0.dev0'
+__version__ = '0.6.0'

docs/whatsnew.md

@@ -2,24 +2,21 @@
 
 argNorm is under active development and outputs may change between versions. Particular versions of argNorm should, however, be reproducible as the databases are bundled with the tool.
 
-## 0.6.0 (Coming Soon!)
+## 0.6.0 - 21 August 2024
 
 ### User-facing changes
 
 #### GROOT support
-- argNorm supports the GROOT v1.1.2 ARG annotation tool: https://github.com/will-rowe/groot
-- GROOT support is via the `GrootNormalizer` (for use in python scripts) and the `groot` tool parameter with the `groot-db`, `groot-core-db`, `groot-argannot`, `groot-card`, and `groot-resfinder` `db` parameters in the CLI.
-
-#### Other
+- argNorm supports [GROOT v1.1.2](https://github.com/will-rowe/groot). Use the `groot` tool parameter with the `groot-db`, `groot-core-db`, `groot-argannot`, `groot-card`, and `groot-resfinder` `db` parameters on the command line. The `GrootNormalizer` is available for use in Python scripts.
 - `__version__` attribute added to the package (accessible as `argnorm.__version__` or `argnorm.lib.__version__`)
-- Use atomic writing for outputs (https://github.com/untitaker/python-atomicwrites/tree/master)
+- atomic writing is used for outputs (https://github.com/untitaker/python-atomicwrites/tree/master). When everything is alright, this should not make a difference, but it avoids certain categories of failures.
 
 ### funcscan integration
 - argNorm has been included as an nf-core module: https://nf-co.re/modules/argnorm/
 - argNorm will also be available on the funcscan pipeline: https://github.com/nf-core/funcscan/pull/410
 
 ### Internal changes
-- SARG db link was changed in `crude_db_harmonisation` to https://raw.githubusercontent.com/xinehc/args_oap/a3e5cff4a6c09f81e4834cfd9a31e6ce7d678d71/src/args_oap/db/sarg.fasta as old link (Galaxy instance, http://smile.hku.hk/SARGs) is down
+- SARG db link was updated as old link is down
 - RGI outputs in `crude_db_harmonisation` are concatenated so frequencies of `perfect`, `strict`, and `loose` hits can be calculated from concatenated file 
 
 ## 0.5.0 - 25 June 2024